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Posts Tagged ‘TCA cycle’


H2S-mediated protein sulfhydration in stress reveals metabolic reprogramming

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

 

Quantitative H2S-mediated protein sulfhydration reveals metabolic reprogramming during the Integrated Stress Response

” data-author-inst=”CaseWesternReserveUniversityUnitedStates”>Bo-JhihGuan, 

Ilya Bederman
Department of Pediatrics, Case Western Reserve University, Cleveland, United States
No competing interests declared

” data-author-inst=”CaseWesternReserveUniversityUnitedStates”>IlyaBederman, 

Mithu Majumder
Department of Pharmacology, Case Western Reserve University, Cleveland, United States
No competing interests declared

” data-author-inst=”CaseWesternReserveUniversityUnitedStates”>MithuMajumder, et al.
eLife 2015;10.7554/eLife.10067    

http://elifesciences.org/content/early/2015/11/23/eLife.10067http://dx.doi.org/10.7554/eLife.10067

The sulfhydration of cysteine residues in proteins is an important mechanism involved in diverse biological processes. We have developed a proteomics approach to quantitatively profile the changes of sulfhydrated cysteines in biological systems. Bioinformatics analysis revealed that sulfhydrated cysteines are part of a wide range of biological functions. In pancreatic β cells exposed to endoplasmic reticulum (ER) stress, elevated H2S promotes the sulfhydration of enzymes in energy metabolism and stimulates glycolytic flux. We propose that transcriptional and translational reprogramming by the Integrated Stress Response (ISR) in pancreatic β cells is coupled to metabolic alternations triggered by sulfhydration of key enzymes in intermediary metabolism.
Posttranslational modification is a fundamental mechanism in the regulation of structure and function of proteins. The covalent modification of specific amino acid residues influences diverse biological processes and cell physiology across species. Reactive cysteine residues in proteins have high nucleophilicity and low pKa values and serve as a major target for oxidative modifications, which can vary depending on the subcellular environment, including the type and intensity of intracellular or environmental cues. Oxidative environments cause different post-translational cysteine modifications, including disulfide bond formation (-S-S-), sulfenylation (-S-OH), nitrosylation (-S-NO), glutathionylation (-S-SG), and sulfhydration (-S-SH) (also called persulfidation) (Finkel, 2012; Mishanina et al., 2015). In the latter, an oxidized cysteine residue included glutathionylated, 60 sulfenylated and nitrosylated on a protein reacts with the sulfide anion to form a cysteine persulfide. The reversible nature of this modification provides a mechanism to fine tune biological processes in different cellular redox states. Sulfhydration coordinates with other post-translational protein modifications such as phosphorylation and nitrosylation to regulate cellular functions (Altaany et al., 2014; Sen et al., 2012). Despite great progress in bioinformatics and advanced mass spectroscopic techniques (MS), identification of different cysteine-based protein modifications has been slow compared to other post-translational modifications. In the case of sulfhydration, a small number of proteins have been identified, among them the glycolytic enzyme glyceraldehyde phosphate dehydrogenase, GAPDH (Mustafa et al., 2009). Sulfhydrated GAPDH at Cys150 exhibits an increase in its catalytic activity, in contrast to the inhibitory effects of nitrosylation or glutathionylation of the same cysteine residue (Mustafa et al., 2009; Paul and Snyder, 2012). The biological significance of the Cys150 modification by H2S is not well-studied, but H2S could serve as a biological switch for protein function acting via oxidative modification of specific cysteine residues in response to redox homeostasis (Paul and Snyder, 2012). Understanding the physiological significance of protein sulfhydration requires the development of genome-wide innovative experimental approaches. Current methodologies based on the modified biotin switch technique do not allow detection of a broad spectrum of sulfhydrated proteins (Finkel, 2012). Guided by a previously reported strategy (Sen et al., 2012), we developed an experimental approach that allowed us to quantitatively evaluate the sulfhydrated proteome and the physiological consequences of H2S synthesis during chronic ER stress. The new methodology allows a quantitative, close-up view of the integrated cellular response to environmental and intracellular cues, and is pertinent to our understanding of human disease development.
The ER is an organelle involved in synthesis of proteins followed by various modifications. Disruption of this process results in the accumulation of misfolded proteins, causing ER stress (Tabas and Ron, 2011; Walter and Ron, 2011), which is associated with development of many diseases ranging from metabolic dysfunction to neurodegeneration (Hetz, 2012). ER stress induces transcriptional, translational, and metabolic reprogramming, all of which are interconnected through the transcription factor Atf4. Atf4 increases expression of genes promoting adaptation to stress via their protein products. One such gene is the H2S-producing enzyme, γ-cystathionase (CTH), previously shown to be involved in the signaling pathway that negatively regulates the activity of the protein tyrosine phosphatase 1B (PTP1B) via sulfhydration (Krishnan et al., 2011). We therefore hypothesized that low or even modest levels of reactive oxygen species (ROS) during ER stress may reprogram cellular metabolism via H2S-mediated protein sulfhydration (Figure 1A).
In summary, sulfhydration of specific cysteines in proteins is a key function of H2S (Kabil and Banerjee, 2010; Paul and Snyder, 2012; Szabo et al., 2013). Thus, the development of tools that can quantitatively measure genome-wide protein sulfhydration in physiological or pathological conditions is of central importance. However, a significant challenge in studies of the biological significance of protein sulfhydration is the lack of an approach to selectively detect sulfhydrated cysteines from other modifications (disulfide bonds, glutathionylated thiols and sulfienic acids) in complex biological samples. In this study, we introduced the BTA approach that allowed the quantitative assessment of changes in the sulfhydration of specific cysteines in the proteome and in individual proteins. BTA is superior to other reported methodologies that aimed to profile cysteine modifications, such as the most commonly used, a modified biotin switch technique (BST). BST was originally designed to study protein nitrosylation and postulated to differentiate free thiols and persulfides (Mustafa et al., 2009). A key advantage of BTA over the existing methodologies, is that the experimental approach has steps to avoid false-positive and negative results, as target proteins for sulfhydration. BST is commonly generating such false targets for cysteine modifications (Forrester et al., 2009; Sen et al., 2012). Using mutiple validations, our data support the specificity and reliability of the BTA assay for analysis of protein sulfhydration both in vitro and in vivo. With this approach, we found that ATF4 is the master regulator of protein sulfhydration in pancreatic β cells during ER stress, by means of its function as a transcription factor. A large number of protein targets have been discovered to undergo sulfhydration in β cells by the BTA approach. Almost 1,000 sulfhydrated cysteine- containing peptides were present in the cells under the chronic ER stress condition of treatment with Tg for 18 h. Combined with the isotopic-labeling strategy, almost 820 peptides on more than 500 proteins were quantified in the 405 cells overexpressing ATF4. These data show the potential of the BTA method for further systematic studies of biological events. To our knowledge, the current dataset encompasses most known sulfhydrated cysteine residues in proteins in any organism. Our bioinformatics analyses revealed sulfhydrated cysteine residues located on a variety of structure-function domains, suggesting the possibility of regulatory mechanism(s) mediated by protein sulfhydration. Structure and sequence analysis revealed consensus motifs that favor sulfhydration; an arginine residue and alpha-helix dipoles are both contributing to stabilize sulfhydrated cysteine thiolates in the local environment.
Pathway analyses showed that H2S-mediated sulfhydration of cysteine residues is that part of the ISR with the highest enrichment in proteins involved in energy metabolism. The metabolic flux revealed that H2S promotes aerobic glycolysis associated with decreased oxidative phosphorylation in mitochondria during ER stress in β cells. The TCA cycle revolves by the action of the respiratory chain that requires oxygen to operate. In response to ER stress, mitochondrial function and cellular respiration are down-regulated to limit oxygen demand and to sustain mitochondria. When ATP production from the TCA cycle becomes limited and glycolytic flux increases, there is a risk of accumulation of lactate from pyruvate. One way to escape accumulation of lactate is the mitochondrial conversion of pyruvate to oxalacetic acid (OAA) by pyruvate carboxylase. This latter enzyme was found to be sulfhydrated, consistent with the notion that sulfhydration is linked to metabolic reprogramming towards glycolysis.
The switch of energy production from mitochondria to glycolysis is known as a signature of hypoxic conditions. This metabolic switch has also been observed in many cancer cells characterized as the Warburg effect, which contributes to tumor growth. The Warburg effect provides advantages to cancer cell survival via the rapid ATP production through glycolysis, as well as the increased conversion of glucose into anabolic biomolecules (amino acid, nucleic acid and lipid biosynthesis) and reducing power (NADPH) for regeneration of antioxidants. This metabolic response of tumor cells contributes to tumor growth and metastasis (Vander Heiden et al., 2009). By analogy, the aerobic glycolysis trigged by increased H2S production could give β cells the capability to acquire ATP and nutrients to adapt their cellular metabolism towards maintaining ATP levels in the ER (Vishnu et al., 2014), increasing synthesis of glycerolphospholipids, glycoproteins and protein (Krokowski et al., 2013b), all important components of the ISR. Similar to hypoxic conditions, a phenotype associated with most tumors, the decreased mitochondria function in β cells during ER stress, can also be viewed as an adaptive response by limiting mitochondria ROS and mitochondria-mediated apoptosis. We therefore view that the H2S-mediated increase in glycolysis is an adaptive mechanism for survival of β cells to chronic ER stress, along with the improved ER function and insulin production and folding, both critical factors controlling hyperglycemia in diabetes. Future work should determine which are the key proteins targeted by H2S and thus contributing to metabolic reprogramming of β cells, and if and how insulin synthesis and secretion is affected by sulfhydration of these proteins during ER stress.
Abnormal H2S metabolism has been reported to occur in various diseases, mostly through the deregulation of gene expression encoding for H2S-generating enzymes (Wallace and Wang, 2015). An increase of their levels by stimulants is expected to have similar effects on sulfhydration of proteins like the ATF4- induced CTH under conditions of ER stress. It is the levels of H2S under oxidative conditions that influence cellular functions. In the present study, ER stress in β cells induced elevated Cth levels, whereas CBS was unaffected. The deregulated oxidative modification at cysteine residues by H2S may be a major contributing factor to disease development. In this case, it would provide a rationale for the design of therapeutic agents that would modulate the activity of the involved enzymes.
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Refined Warburg hypothesis -2.1.2

Writer and Curator: Larry H. Bernstein, MD, FCAP

Refined Warburg Hypothesis -2.1.2

The Warburg discoveries from 1922 on, and the influence on metabolic studies for the next 50 years was immense, and then the revelations of the genetic code took precedence.  Throughout this period, however, the brilliant work of Briton Chance, a giant of biochemistry at the University of Pennsylvania, opened new avenues of exploration that led to a recent resurgence in this vital need for answers in cancer research. The next two series of presentations will open up this resurgence of fundamental metabolic research in cancer and even neurodegenerative diseases.

2.1.2.1 Cancer Cell Metabolism. Warburg and Beyond

Hsu PP, Sabatini DM
Cell, Sep 5, 2008; 134:703-707
http://dx.doi.org:/10.016/j.cell.2008.08.021

Described decades ago, the Warburg effect of aerobic glycolysis is a key metabolic hallmark of cancer, yet its significance remains unclear. In this Essay, we re-examine the Warburg effect and establish a framework for understanding its contribution to the altered metabolism of cancer cells.

It is hard to begin a discussion of cancer cell metabolism without first mentioning Otto Warburg. A pioneer in the study of respiration, Warburg made a striking discovery in the 1920s. He found that, even in the presence of ample oxygen, cancer cells prefer to metabolize glucose by glycolysis, a seeming paradox as glycolysis, when compared to oxidative phosphorylation, is a less efficient pathway for producing ATP (Warburg, 1956). The Warburg effect has since been demonstrated in different types of tumors and the concomitant increase in glucose uptake has been exploited clinically for the detection of tumors by fluorodeoxyglucose positron emission tomography (FDG-PET). Although aerobic glycolysis has now been generally accepted as a metabolic hallmark of cancer, its causal relationship with cancer progression is still unclear. In this Essay, we discuss the possible drivers, advantages, and potential liabilities of the altered metabolism of cancer cells (Figure 1). Although our emphasis on the Warburg effect reflects the focus of the field, we would also like to encourage a broader approach to the study of cancer metabolism that takes into account the contributions of all interconnected small molecule pathways of the cell.

Figure 1. The Altered Metabolism of Cancer Cells

Drivers (A and B). The metabolic derangements in cancer cells may arise either from the selection of cells that have adapted to the tumor microenvironment or from aberrant signaling due to oncogene activation. The tumor microenvironment is spatially and temporally heterogeneous, containing regions of low oxygen and low pH (purple). Moreover, many canonical cancer-associated signaling pathways induce metabolic reprogramming. Target genes activated by hypoxia inducible factor (HIF) decrease the dependence of the cell on oxygen, whereas Ras, Myc, and Akt can also upregulate glucose consumption and glycolysis. Loss of p53 may also recapitulate the features of the Warburg effect, that is, the uncoupling of glycolysis from oxygen levels. Advantages (C–E). The altered metabolism of cancer cells is likely to imbue them with several proliferative and survival advantages, such as enabling cancer cells to execute the biosynthesis of macromolecules (C), to avoid apoptosis (D), and to engage in local metabolite-based paracrine and autocrine signaling (E). Potential Liabilities (F and G). This altered metabolism, however, may also confer several vulnerabilities on cancer cells. For example, an upregulated metabolism may result in the build up of toxic metabolites, including lactate and noncanonical nucleotides, which must be disposed of (F). Moreover, cancer cells may also exhibit a high energetic demand, for which they must either increase flux through normal ATP-generating processes, or else rely on an increased diversity of fuel sources (G).

The Tumor Microenvironment Selects for Altered Metabolism

One compelling idea to explain the Warburg effect is that the altered metabolism of cancer cells confers a selective advantage for survival and proliferation in the unique tumor microenvironment. As the early tumor expands, it outgrows the diffusion limits of its local blood supply, leading to hypoxia and stabilization of the hypoxia-inducible transcription factor, HIF. HIF initiates a transcriptional program that provides multiple solutions to hypoxic stress (reviewed in Kaelin and Ratcliffe, 2008). Because a decreased dependence on aerobic respiration becomes advantageous, cell metabolism is shifted toward glycolysis by the increased expression of glycolytic enzymes, glucose transporters, and inhibitors of mitochondrial metabolism. In addition, HIF stimulates angiogenesis (the formation of new blood vessels) by upregulating several factors, including most prominently vascular endothelial growth factor (VEGF).

The oxygen levels within a tumor vary both spatially and temporally, and the resulting rounds of fluctuating oxygen levels potentially select for tumors that constitutively upregulate glycolysis. Interestingly, with the possible exception of tumors that have lost the von Hippel-Lindau protein (VHL), which normally mediates degradation of HIF, HIF is still coupled to oxygen levels, as evident from the heterogeneity of HIF expression within the tumor microenvironment (Wiesener et al., 2001; Zhong et al., 1999). Therefore, the Warburg effect—that is, an uncoupling of glycolysis from oxygen levels—cannot be explained solely by upregulation of HIF.

Recent work has demonstrated that the key components of the Warburg effect—increased glucose consumption, decreased oxidative phosphorylation, and accompanying lactate production—are also distinguishing features of oncogene activation. The signaling molecule Ras, a powerful oncogene when mutated, promotes glycolysis (reviewed in Dang and Semenza, 1999; Samanathan et al., 2005). Akt kinase, a well-characterized downstream effector of insulin signaling, reprises its role in glucose uptake and utilization in the cancer setting (reviewed in Manning and Cantley, 2007), whereas the Myc transcription factor upregulates the expression of various metabolic genes (reviewed in Gordan et al., 2007). The most parsimonious route to tumorigenesis may be activation of key oncogenic nodes that execute a proliferative program, of which metabolism may be one important arm. Moreover, regulation of metabolism is not exclusive to oncogenes. Loss of the tumor suppressor protein p53 prevents expression of the gene encoding SCO2 (the synthesis of cytochrome c oxidase protein), which interferes with the function of the mitochondrial respiratory chain (Matoba et al., 2006). A second p53 effector, TIGAR (TP53-induced glycolysis and apoptosis regulator), inhibits glycolysis by decreasing levels of fructose-2,6-bisphosphate, a potent stimulator of glycolysis and inhibitor of gluconeogenesis (Bensaad et al., 2006). Other work also suggests that p53-mediated regulation of glucose metabolism may be dependent on the transcription factor NF-κB (Kawauchi et al., 2008).
It has been shown that inhibition of lactate dehydrogenase A (LDH-A) prevents the Warburg effect and forces cancer cells to revert to oxidative phosphorylation in order to reoxidize NADH and produce ATP (Fantin et al., 2006; Shim et al., 1997). While the cells are respiratory competent, they exhibit attenuated tumor growth, suggesting that aerobic glycolysis might be essential for cancer progression. In a primary fibroblast cell culture model of stepwise malignant transformation through overexpression of telomerase, large and small T antigen, and the H-Ras oncogene, increasing tumorigenicity correlates with sensitivity to glycolytic inhibition. This finding suggests that the Warburg effect might be inherent to the molecular events of transformation (Ramanathan et al., 2005). However, the introduction of similar defined factors into human mesenchymal stem cells (MSCs) revealed that transformation can be associated with increased dependence on oxidative phosphorylation (Funes et al., 2007). Interestingly, when introduced in vivo these transformed MSCs do upregulate glycolytic genes, an effect that is reversed when the cells are explanted and cultured under normoxic conditions. These contrasting models suggest that the Warburg effect may be context dependent, in some cases driven by genetic changes and in others by the demands of the microenvironment. Regardless of whether the tumor microenvironment or oncogene activation plays a more important role in driving the development of a distinct cancer metabolism, it is likely that the resulting alterations confer adaptive, proliferative, and survival advantages on the cancer cell.

Altered Metabolism Provides Substrates for Biosynthetic Pathways

Although studies in cancer metabolism have largely been energy-centric, rapidly dividing cells have diverse requirements. Proliferating cells require not only ATP but also nucleotides, fatty acids, membrane lipids, and proteins, and a reprogrammed metabolism may serve to support synthesis of macromolecules. Recent studies have shown that several steps in lipid synthesis are required for and may even actively promote tumorigenesis. Inhibition of ATP citrate lyase, the distal enzyme that converts mitochondrial-derived citrate into cytosolic acetyl coenzyme A, the precursor for many lipid species, prevents cancer cell proliferation and tumor growth (Hatzivassiliou et al., 2005). Fatty acid synthase, expressed at low levels in normal tissues, is upregulated in cancer and may also be required for tumorigenesis (reviewed in Menendez and Lupu, 2007). Furthermore, cancer cells may also enhance their biosynthetic capabilities by expressing a tumor-specific form of pyruvate kinase (PK), M2-PK. Pyruvate kinase catalyzes the third irreversible reaction of glycolysis, the conversion of phosphoenolpyruvate (PEP) to pyruvate. Surprisingly, the M2-PK of cancer cells is thought to be less active in the conversion of PEP to pyruvate and thus less efficient at ATP production (reviewed in Mazurek et al., 2005). A major advantage to the cancer cell, however, is that the glycolytic intermediates upstream of PEP might be shunted into synthetic processes.

Biosynthesis, in addition to causing an inherent increase in ATP demand in order to execute synthetic reactions, should also cause a decrease in ATP supply as various glycolytic and Krebs cycle intermediates are diverted. Lipid synthesis, for example, requires the cooperation of glycolysis, the Krebs cycle, and the pentose phosphate shunt. As pyruvate must enter the mitochondria in this case, it avoids conversion to lactate and therefore cannot contribute to glycolysis-derived ATP. Moreover, whereas increased biosynthesis may explain the glucose hunger of cancer cells, it cannot explain the increase in lactic acid production originally described by Warburg, suggesting that lactate must also result from the metabolism of non-glucose substrates. Recently, it has been demonstrated that glutamine may be metabolized by the citric acid cycle in cancer cells and converted into lactate, producing NADPH for lipid biosynthesis and oxaloacetate for replenishment of Krebs cycle intermediates (DeBerardinis et al., 2007).

Metabolic Pathways Regulate Apoptosis

In addition to involvement in proliferation, altered metabolism may promote another cancer-essential function: the avoidance of apoptosis. Loss of the p53 target TIGAR sensitizes cancer cells to apoptosis, most likely by causing an increase in reactive oxygen species (Bensaad et al., 2006). On the other hand, overexpression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) prevents caspase-independent cell death, presumably by stimulating glycolysis, increasing cellular ATP levels, and promoting autophagy (Colell et al., 2007). Whether or not GAPDH plays a physiological role in the regulation of cell death remains to be determined. Intriguingly, Bonnet et al. (2007) have reported that treating cancer cells with dichloroacetate (DCA), a small molecule inhibitor of pyruvate dehydrogenase kinase, has striking effects on their survival and on xenograft tumor growth.

DCA, a currently approved treatment for congenital lactic acidosis, activates oxidative phosphorylation and promotes apoptosis by two mechanisms. First, increased flux through the electron transport chain causes depolarization of the mitochondrial membrane potential (which the authors found to be hyperpolarized specifically in cancer cells) and release of the apoptotic effector cytochrome c. Second, an increase in reactive oxygen species generated by oxidative phosphorylation upregulates the voltage-gated K+ channel, leading to potassium ion efflux and caspase activation. Their work suggests that cancer cells may shift their metabolism to glycolysis in order to prevent cell death and that forcing cancer cells to respire aerobically can counteract this adaptation.

Cancer Cells May Signal Locally in the Tumor Microenvironment

Cancer cells may rewire metabolic pathways to exploit the tumor microenvironment and to support cancer-specific signaling. Without access to the central circulation, it is possible that metabolites can be concentrated locally and reach suprasystemic levels, allowing cancer cells to engage in metabolite-mediated autocrine and paracrine signaling that does not occur in normal tissues. So called androgen-independent prostate cancers may only be independent from exogenous, adrenal-synthesized androgens. Androgen-independent prostate cancer cells still express the androgen receptor and may be capable of autonomously synthesizing their own androgens (Stanbrough et al., 2006).

Metabolism as an Upstream Modulator of Signaling Pathways

Not only is metabolism downstream of oncogenic pathways, but an altered upstream metabolism may affect the activity of signaling pathways that normally sense the state of the cell. Individuals with inherited mutations in succinate dehydrogenase and fumarate hydratase develop highly angiogenic tumors, not unlike those exhibiting loss of the VHL tumor suppressor protein that acts upstream of HIF (reviewed in Kaelin and Ratcliffe, 2008). The mechanism of tumorigenesis in these cancer syndromes is still contentious. However, it has been proposed that loss of succinate dehydrogenase and fumarate hydratase causes an accumulation of succinate or fumarate, respectively, leading to inhibition of the prolyl hydroxylases that mark HIF for VHL-mediated degradation (Isaacs et al., 2005; Pollard et al., 2005; Selak et al., 2005). In this rare case, succinate dehydrogenase and fumarate hydratase are acting as bona fide tumor suppressors.

There are many complex questions to be answered: Is it possible that cancer cells exhibit “metabolite addiction”? Are there unique cancer-specific metabolic pathways, or combinations of pathways, utilized by the cancer cell but not by normal cells? Are different stages of metabolic adaptations required for the cancer cell to progress from the primary tumor stage to invasion to metastasis? How malleable is cancer metabolism?

2.1.2.2 Cancer metabolism. The Warburg effect today

Ferreira LMR
Exp Molec Pathol 2010; 89:372-383.
http://dx.doi.org/10.1016/j.yexmp.2010.08.006

One of the first studies on the energy metabolism of a tumor was carried out, in 1922, in the laboratory of Otto Warburg. He established that cancer cells exhibited a specific metabolic pattern, characterized by a shift from respiration to fermentation, which has been later named the Warburg effect. Considerable work has been done since then, deepening our understanding of the process, with consequences for diagnosis and therapy. This review presents facts and perspectives on the Warburg effect for the 21st century.

Research highlights

► Warburg first established a tumor metabolic pattern in the 1920s. ► Tumors’ increased glucose uptake has been studied since then. ► Cancer bioenergetics’ study provides insights in all its hallmarks. ► New cancer diagnostic and therapeutic techniques focus on cancer metabolism.

Introduction
Contestation to Warburg’s ideas
Glucose’s uptake and intracellular fates
Lactate production and induced acidosis
Hypoxia
Impairment of mitochondrial function
Tumour microenvironment
Proliferating versus cancer cells
More on cancer bioenergetics – integration of metabolism
Perspectives

2.1.2.3 New aspects of the Warburg effect in cancer cell biology

Bensinger SJ, Cristofk HR
Sem Cell Dev Biol 2012; 23:352-361
http://dx.doi.org:/10.1016/j.semcdb.2012.02.003

Altered cellular metabolism is a defining feature of cancer [1]. The best studied metabolic phenotype of cancer is aerobic glycolysis–also known as the Warburg effect–characterized by increased metabolism of glucose to lactate in the presence of sufficient oxygen. Interest in the Warburg effect has escalated in recent years due to the proven utility of FDG-PET for imaging tumors in cancer patients and growing evidence that mutations in oncogenes and tumor suppressor genes directly impact metabolism. The goals of this review are to provide an organized snapshot of the current understanding of regulatory mechanisms important for Warburg effect and its role in tumor biology. Since several reviews have covered aspects of this topic in recent years, we focus on newest contributions to the field and reference other reviews where appropriate.

Highlights

► This review discusses regulatory mechanisms that contribute to the Warburg effect in cancer. ► We list cancers for which FDG-PET has established applications as well as those cancers for which FDG-PET has not been established. ► PKM2 is highlighted as an important integrator of diverse cellular stimuli to modulate metabolic flux and cancer cell proliferation. ► We discuss how cancer metabolism can directly influence gene expression programs. ► Contribution of aerobic glycolysis to the cancer microenvironment and chemotherapeutic resistance/susceptibility is also discussed.

Regulation of the Warburg effect

PKM2 integrates diverse signals to modulate metabolic flux and cell proliferation

PKM2 integrates diverse signals to modulate metabolic flux and cell proliferation

Fig. 1. PKM2 integrates diverse signals to modulate metabolic flux and cell proliferation

Metabolism can directly influence gene expression programs

Metabolism can directly influence gene expression programs

Fig. 2. Metabolism can directly influence gene expression programs. A schematic representation of how metabolism can intrinsically influence epigenetics resulting in durable and heritable gene expression programs in progeny.

2.1.2.4 Choosing between glycolysis and oxidative phosphorylation. A tumor’s dilemma

Jose C, Ballance N, Rossignal R
Biochim Biophys Acta 201; 1807(6): 552-561.
http://dx.doi.org/10.1016/j.bbabio.2010.10.012

A considerable amount of knowledge has been produced during the last five years on the bioenergetics of cancer cells, leading to a better understanding of the regulation of energy metabolism during oncogenesis, or in adverse conditions of energy substrate intermittent deprivation. The general enhancement of the glycolytic machinery in various cancer cell lines is well described and recent analyses give a better view of the changes in mitochondrial oxidative phosphorylation during oncogenesis. While some studies demonstrate a reduction of oxidative phosphorylation (OXPHOS) capacity in different types of cancer cells, other investigations revealed contradictory modifications with the upregulation of OXPHOS components and a larger dependency of cancer cells on oxidative energy substrates for anabolism and energy production. This apparent conflictual picture is explained by differences in tumor size, hypoxia, and the sequence of oncogenes activated. The role of p53, C-MYC, Oct and RAS on the control of mitochondrial respiration and glutamine utilization has been explained recently on artificial models of tumorigenesis. Likewise, the generation of induced pluripotent stem cells from oncogene activation also showed the role of C-MYC and Oct in the regulation of mitochondrial biogenesis and ROS generation. In this review article we put emphasis on the description of various bioenergetic types of tumors, from exclusively glycolytic to mainly OXPHOS, and the modulation of both the metabolic apparatus and the modalities of energy substrate utilization according to tumor stage, serial oncogene activation and associated or not fluctuating microenvironmental substrate conditions. We conclude on the importance of a dynamic view of tumor bioenergetics.

Research Highlights

►The bioenergetics of cancer cells differs from normals. ►Warburg hypothesis is not verified in tumors using mitochondria to synthesize ATP. ►Different oncogenes can either switch on or switch off OXPHOS. ►Bioenergetic profiling is a prerequisite to metabolic therapy. ►Aerobic glycolysis and OXPHOS cooperate during cancer progression.

  1. Cancer cell variable bioenergetics

Cancer cells exhibit profound genetic, bioenergetic and histological differences as compared to their non-transformed counterpart. All these modifications are associated with unlimited cell growth, inhibition of apoptosis and intense anabolism. Transformation from a normal cell to a malignant cancer cell is a multi-step pathogenic process which includes a permanent interaction between cancer gene activation (oncogenes and/or tumor-suppressor genes), metabolic reprogramming and tumor-induced changes in microenvironment. As for the individual genetic mapping of human tumors, their metabolic characterization (metabolic–bioenergetic profiling) has evidenced a cancer cell-type bioenergetic signature which depends on the history of the tumor, as composed by the sequence of oncogenes activated and the confrontation to intermittent changes in oxygen, glucose and amino-acid delivery.

In the last decade, bioenergetic studies have highlighted the variability among cancer types and even inside a cancer type as regards to the mechanisms and the substrates preferentially used for deriving the vital energy. The more popular metabolic remodeling described in tumor cells is an increase in glucose uptake, the enhancement of glycolytic capacity and a high lactate production, along with the absence of respiration despite the presence of high oxygen concentration (Warburg effect) [1]. To explain this abnormal bioenergetic phenotype pioneering hypotheses proposed the impairment of mitochondrial function in rapidly growing cancer cells [2].

Although the increased consumption of glucose by tumor cells was confirmed in vivo by positron emission tomography (PET) using the glucose analog 2-(18F)-fluoro-2-deoxy-d-glucose (FDG), the actual utilization of glycolysis and oxidative phosphorylation (OXPHOS) cannot be evaluated with this technique. Nowadays, Warburg’s “aerobic-glycolysis” hypothesis has been challenged by a growing number of studies showing that mitochondria in tumor cells are not inactive per se but operate at low capacity [3] or, in striking contrast, supply most of the ATP to the cancer cells [4]. Intense glycolysis is effectively not observed in all tumor types. Indeed not all cancer cells grow fast and intense anabolism is not mandatory for all cancer cells. Rapidly growing tumor cells rely more on glycolysis than slowly growing tumor cells. This is why a treatment with bromopyruvate, for example is very efficient only on rapidly growing cells and barely useful to decrease the growth rate of tumor cells when their normal proliferation is slow. Already in 1979, Reitzer and colleagues published an article entitled “Evidence that glutamine, not sugar, is the major energy source for cultured Hela cells”, which demonstrated that oxidative phosphorylation was used preferentially to produce ATP in cervical carcinoma cells [5]. Griguer et al. also identified several glioma cell lines that were highly dependent on mitochondrial OXPHOS pathway to produce ATP [6]. Furthermore, a subclass of glioma cells which utilize glycolysis preferentially (i.e., glycolytic gliomas) can also switch from aerobic glycolysis to OXPHOS under limiting glucose conditions  [7] and [8], as observed in cervical cancer cells, breast carcinoma cells, hepatoma cells and pancreatic cancer cells [9][10] and [11]. This flexibility shows the interplay between glycolysis and OXPHOS to adapt the mechanisms of energy production to microenvironmental changes as well as differences in tumor energy needs or biosynthetic activity. Herst and Berridge also demonstrated that a variety of human and mouse leukemic and tumor cell lines (HL60, HeLa, 143B, and U937) utilize mitochondrial respiration to support their growth [12]. Recently, the measurement of OXPHOS contribution to the cellular ATP supply revealed that mitochondria generate 79% of the cellular ATP in HeLa cells, and that upon hypoxia this contribution is reduced to 30% [4]. Again, metabolic flexibility is used to survive under hypoxia. All these studies demonstrate that mitochondria are efficient to synthesize ATP in a large variety of cancer cells, as reviewed by Moreno-Sanchez [13]. Despite the observed reduction of the mitochondrial content in tumors [3][14][15][16][17][18] and [19], cancer cells maintain a significant level of OXPHOS capacity to rapidly switch from glycolysis to OXPHOS during carcinogenesis. This switch is also observed at the level of glutamine oxidation which can occur through two modes, “OXPHOS-linked” or “anoxic”, allowing to derive energy from glutamine or serine regardless of hypoxia or respiratory chain reduced activity [20].
While glutamine, glycine, alanine, glutamate, and proline are typically oxidized in normal and tumor mitochondria, alternative substrate oxidations may also contribute to ATP supply by OXPHOS. Those include for instance the oxidation of fatty-acids, ketone bodies, short-chain carboxylic acids, propionate, acetate and butyrate (as recently reviewed in [21]).

  1. Varying degree of mitochondrial utilization during tumorigenesis

In vivo metabolomic analyses suggest the existence of a continuum of bioenergetic remodeling in rat tumors according to tumor size and its rate of growth [22]. Peter Vaupel’s group showed that small tumors were characterized by a low conversion of glucose to lactate whereas the conversion of glutamine to lactate was high. In medium sized tumors the flow of glucose to lactate as well as oxygen utilization was increased whereas glutamine and serine consumption were reduced. At this stage tumor cells started with glutamate and alanine production. Large tumors were characterized by a low oxygen and glucose supply but a high glucose and oxygen utilization rate. The conversion of glucose to glycine, alanine, glutamate, glutamine, and proline reached high values and the amino acids were released [22]. Certainly, in the inner layers constituting solid tumors, substrate and oxygen limitation is frequently observed. Experimental studies tried to reproduce these conditions in vitro and revealed that nutrients and oxygen limitation does not affect OXPHOS and cellular ATP levels in human cervix tumor [23]. Furthermore, the growth of HeLa cells, HepG2 cells and HTB126 (breast cancer) in aglycemia and/or hypoxia even triggered a compensatory increase in OXPHOS capacity, as discussed above. Yet, the impact of hypoxia might be variable depending on cell type and both the extent and the duration of oxygen limitation.
In two models of sequential oncogenesis, the successive activation of specific oncogenes in non-cancer cells evidenced the need for active OXPHOS to pursue tumorigenesis. Funes et al. showed that the transformation of human mesenchymal stem cells increases their dependency on OXPHOS for energy production [24], while Ferbeyre et al. showed that cells expressing oncogenic RAS display an increase in mitochondrial mass, mitochondrial DNA, and mitochondrial production of reactive oxygen species (ROS) prior to the senescent cell cycle arrest [25]. Such observations suggest that waves of gene regulation could suppress and then restore OXPHOS in cancer cells during tumorigenesis [20]. Therefore, the definition of cancer by Hanahan and Weinberg [26] restricted to six hallmarks (1—self-sufficiency in growth signals, 2—insensitivity to growth-inhibitory (antigrowth) signals, 3—evasion of programmed cell death (apoptosis), 4—limitless replicative potential, 5—sustained angiogenesis, and 6—tissue invasion and metastases) should also include metabolic reprogramming, as the seventh hallmark of cancer. This amendment was already proposed by Tennant et al. in 2009 [27]. In 2006, the review Science published a debate on the controversial views of Warburg theory [28], in support of a more realistic description of cancer cell’s variable bioenergetic profile. The pros think that high glycolysis is an obligatory feature of human tumors, while the cons propose that high glycolysis is not exclusive and that tumors can use OXPHOS to derive energy. A unifying theory closer to reality might consider that OXPHOS and glycolysis cooperate to sustain energy needs along tumorigenesis [20]. The concept of oxidative tumors, against Warburg’s proposal, was introduced by Guppy and colleagues, based on the observation that breast cancer cells can generate 80% of their ATP by the mitochondrion [29]. The comparison of different cancer cell lines and excised tumors revealed a variety of cancer cell’s bioenergetic signatures which raised the question of the mechanisms underlying tumor cell metabolic reprogramming, and the relative contribution of oncogenesis and microenvironment in this process. It is now widely accepted that rapidly growing cancer cells within solid tumors suffer from a lack of oxygen and nutrients as tumor grows. In such situation of compromised energy substrate delivery, cancer cell’s metabolic reprogramming is further used to sustain anabolism (Fig. 1), through the deviation of glycolysis, Krebs cycle truncation and OXPHOS redirection toward lipid and protein synthesis, as needed to support uncontrolled tumor growth and survival [30] and [31]. Again, these features are not exclusive to all tumors, as Krebs cycle truncation was only observed in some cancer cells, while other studies indicated that tumor cells can maintain a complete Krebs cycle [13] in parallel with an active citrate efflux. Likewise, generalizations should be avoided to prevent over-interpretations.
Fig. 1. Energy metabolism at the crossroad between catabolism and anabolism.

Energy metabolism at the crossroad between catabolism and anabolism.

Energy metabolism at the crossroad between catabolism and anabolism.

The oncogene C-MYC participate to these changes via the stimulation of glutamine utilization through the coordinate expression of genes necessary for cells to engage in glutamine catabolism [30]. According to Newsholme EA and Board M [32] both glycolysis and glutaminolysis not only serve for ATP production, but also provide precious metabolic intermediates such as glucose-6-phosphate, ammonia and aspartate required for the synthesis of purine and pyrimidine nucleotides (Fig. 1). In this manner, the observed apparent excess in the rates of glycolysis and glutaminolysis as compared to the requirement for energy production could be explained by the need for biosynthetic processes. Yet, one should not reduce the shift from glycolysis to OXPHOS utilization to the sole activation of glutaminolysis, as several other energy substrates can be used by tumor mitochondria to generate ATP [21]. The contribution of these different fuels to ATP synthesis remains poorly investigated in human tumors.

  1. The metabolism of pre-cancer cells and its ongoing modulation by carcinogenesis

At the beginning of cancer, there might have been a cancer stem cell hit by an oncogenic event, such as alterations in mitogen signaling to extracellular growth factor receptors (EGFR), oncogenic activation of these receptors, or oncogenic alterations of downstream targets in the pathways that leads to cell proliferation (RAS–Raf–ERK and PI3K–AKT, both leading to m-TOR activation stimulating cell growth). Alterations of checkpoint genes controlling the cell cycle progression like Rb also participate in cell proliferation (Fig. 2) and this re-entry in the cell cycle implies three major needs to fill in: 1) supplying enough energy to grow and 2) synthesize building blocks de novo and 3) keep vital oxygen and nutrients available. However, the bioenergetic status of the pre-cancer cell could determine in part the evolution of carcinogenesis, as shown on mouse embryonic stem cells. In this study, Schieke et al. showed that mitochondrial energy metabolism modulates both the differentiation and tumor formation capacity of mouse embryonic stem cells [37]. The idea that cancer derives from a single cell, known as the cancer stem cell hypothesis, was introduced by observations performed on leukemia which appeared to be organized as origination from a primitive hematopoietic cell [38]. Nowadays cancer stem cells were discovered for all types of tumors [39][40][41] and [42], but little is known of their bioenergetic properties and their metabolic adaptation to the microenvironment. This question is crucial as regards the understanding of what determines the wide variety of cancer cell’s metabolic profile.

Impact of different oncogenes on tumor progression and energy metabolism remodeling.

Impact of different oncogenes on tumor progression and energy metabolism remodeling.

Fig. 2. Impact of different oncogenes on tumor progression and energy metabolism remodeling.

The analysis of the metabolic changes that occur during the transformation of adult mesenchymal stem cells revealed that these cells did not switch to aerobic glycolysis, but their dependency on OXPHOS was even increased [24]. Hence, mitochondrial energy metabolism could be critical for tumorigenesis, in contrast with Warburg’s hypothesis. As discussed above, the oncogene C-MYC also stimulates OXPHOS [30]. Furthermore, it was recently demonstrated that cells chronically treated with oligomycin repress OXPHOS and produce larger tumors with higher malignancy [19]. Likewise, alteration of OXPHOS by mutations in mtDNA increases tumorigenicity in different types of cancer cells [43][44] and [45].

Recently, it was proposed that mitochondrial energy metabolism is required to generate reactive oxygen species used for the carcinogenetic process induced by the K-RAS mutation [46]. This could explain the large number of mitochondrial DNA mutations found in several tumors. The analysis of mitochondria in human embryonic cells which derive energy exclusively from anaerobic glycolysis have demonstrated an immature mitochondrial network characterized by few organelles with poorly developed cristae and peri-nuclear distribution [47] and [48]. The generation of human induced pluripotent stem cell by the introduction of different oncogenes as C-MYC and Oct4 reproduced this reduction of mitochondrial OXPHOS capacity[49] and [50]. This indicates again the impact of oncogenes on the control of OXPHOS and might explain the existence of pre-cancer stem cells with different bioenergetic backgrounds, as modeled by variable sequences of oncogene activation. Accordingly, the inhibition of mitochondrial respiratory chain has been recently found associated with enhancement of hESC pluripotency [51].

Based on the experimental evidence discussed above, one can argue that 1) glycolysis is indeed a feature of several tumors and associates with faster growth in high glucose environment, but 2) active OXPHOS is also an important feature of (other) tumors taken at a particular stage of carcinogenesis which might be more advantageous than a “glycolysis-only” type of metabolism in conditions of intermittent shortage in glucose delivery. The metabolic apparatus of cancer cells is not fixed during carcinogenesis and might depend both on the nature of the oncogenes activated and the microenvironment. It was indeed shown that cancer cells with predominant glycolytic metabolism present a higher malignancy when submitted to carcinogenetic induction and analysed under fixed experimental conditions of high glucose [19]. Yet, if one grows these cells in a glucose-deprived medium they shift their metabolism toward predominant OXPHOS, as shown in HeLa cells and other cell types [9]. Therefore, one might conclude that glycolytic cells have a higher propensity to generate aggressive tumors when glucose availability is high. However, these cells can become OXPHOS during tumor progression [24] and [52]. All these observations indicate again the importance of maintaining an active OXPHOS metabolism to permit evolution of both embryogenesis and carcinogenesis, which emphasizes the importance of targeting mitochondria to alter this malignant process.

  1. Oncogenes and the modulation of energy metabolism

Several oncogenes and associated proteins such as HIF-1α, RAS, C-MYC, SRC, and p53 can influence energy substrate utilization by affecting cellular targets, leading to metabolic changes that favor cancer cell survival, independently of the control of cell proliferation. These oncogenes stimulate the enhancement of aerobic glycolysis, and an increasing number of studies demonstrate that at least some of them can also target directly the OXPHOS machinery, as discussed in this article (Fig. 2). For instance, C-MYC can concurrently drive aerobic glycolysis and/or OXPHOS according to the tumor cell microenvironment, via the expression of glycolytic genes or the activation of mitochondrial oxidation of glutamine [53]. The oncogene RAS has been shown to increase OXPHOS activity in early transformed cells [24][52] and [54] and p53 modulates OXPHOS capacity via the regulation of cytochrome c oxidase assembly [55]. Hence, carcinogenic p53 deficiency results in a decreased level of COX2 and triggers a shift toward anaerobic metabolism. In this case, lactate synthesis is increased, but cellular ATP levels remain stable [56]. The p53-inducible isoform of phosphofructokinase, termed TP53-induced glycolysis and apoptotic regulator, TIGAR, a predominant phosphatase activity isoform of PFK-2, has also been identified as an important regulator of energy metabolism in tumors [57].

  1. Tumor specific isoforms (or mutated forms) of energy genes

Tumors are generally characterized by a modification of the glycolytic system where the level of some glycolytic enzymes is increased, some fetal-like isozymes with different kinetic and regulatory properties are produced, and the reverse and back-reactions of the glycolysis are strongly reduced [60]. The GAPDH marker of the glycolytic pathway is also increased in breast, gastric, lung, kidney and colon tumors [18], and the expression of glucose transporter GLUT1 is elevated in most cancer cells. The group of Cuezva J.M. developed the concept of cancer bioenergetic signature and of bioenergetic index to describe the metabolic profile of cancer cells and tumors [18], [61], [64], [65]. This signature describes the changes in the expression level of proteins involved in glycolysis and OXPHOS, while the BEC index gives a ratio of OXPHOS protein content to glycolytic protein content, in good correlation with cancer prognostic[61]. Recently, this group showed that the beta-subunit of the mitochondrial F1F0-ATP synthase is downregulated in a large number of tumors, thus contributing to the Warburg effect [64] and [65]. It was also shown that IF1 expression levels were increased in hepatocellular carcinomas, possibly to prevent the hydrolysis of glytolytic ATP [66]. Numerous changes occur at the level of OXPHOS and mitochondrial biogenesis in human tumors, as we reviewed previously [67]. Yet the actual impact of these changes in OXPHOS protein expression level or catalytic activities remains to be evaluated on the overall fluxes of respiration and ATP synthesis. Indeed, the metabolic control analysis and its extension indicate that it is often required to inhibit activity beyond a threshold of 70–85% to affect the metabolic fluxes [68] and [69]. Another important feature of cancer cells is the higher level of hexokinase II bound to mitochondrial membrane (50% in tumor cells). A study performed on human gliomas (brain) estimated the mitochondrial bound HK fraction (mHK) at 69% of total, as compared to 9% for normal brain [70]. This is consistent with the 5-fold amplification of the type II HK gene observed by Rempel et al. in the rapidly growing rat AS-30D hepatoma cell line, relative to normal hepatocytes [71]. HKII subcellular fractionation in cancer cells was described in several studies [72][73] and [74]. The group led by Pete Pedersen explained that mHK contributes to (i) the high glycolytic capacity by utilizing mitochondrially regenerated ATP rather than cytosolic ATP (nucleotide channelling) and (ii) the lowering of OXPHOS capacity by limiting Pi and ADP delivery to the organelle [75] and [76].

All these observations are consistent with the increased rate of FDG uptake observed by PET in living tumors which could result from both an increase in glucose transport, and/or an increase in hexokinase activity. However, FDG is not a complete substrate for glycolysis (it is only transformed into FDG-6P by hexokinase before to be eliminated) and cannot be used to evidence a general increase in the glycolytic flux. Moreover, FDG-PET scan also gives false positive and false negative results, indicating that some tumors do not depend on, or do not have, an increased glycolytic capacity. The fast glycolytic system described above is further accommodated in cancer cells by an increase in the lactate dehydrogenase isoform A (LDH-A) expression level. This isoform presents a higher Vmax useful to prevent the inhibition of high glycolysis by its end product (pyruvate) accumulation. Recently, Fantin et al. showed that inhibition of LDH-A in tumors diminishes tumorigenicity and was associated with the stimulation of mitochondrial respiration [79]. The preferential expression of the glycolytic pyruvate kinase isoenzyme M2 (PKM2) in tumor cells, determines whether glucose is converted to lactate for regeneration of energy (active tetrameric form, Warburg effect) or used for the synthesis of cell building blocks (nearly inactive dimeric form) [80]. In the last five years, mutations in proteins of the respiratory system (SDH, FH) and of the TCA cycle (IDH1,2) leading to the accumulation of metabolite and the subsequent activation of HIF-1α were reported in a variety of human tumors [81], [82] and [83].

  1. Tumor microenvironment modulates cancer cell’s bioenergetics

It was extensively described how hypoxia activates HIF-1α which stimulates in turn the expression of several glycolytic enzymes such as HK2, PFK, PGM, enolase, PK, LDH-A, MCT4 and glucose transporters Glut 1 and Glut 3. It was also shown that HIF-1α can reduce OXPHOS capacity by inhibiting mitochondrial biogenesis [14] and [15], PDH activity [87] and respiratory chain activity [88]. The low efficiency and uneven distribution of the vascular system surrounding solid tumors can lead to abrupt changes in oxygen (intermittent hypoxia) but also energy substrate delivery. .. The removal of glucose, or the inhibition of glycolysis by iodoacetate led to a switch toward glutamine utilization without delay followed by a rapid decrease in acid release. This illustrates once again how tumors and human cancer cell lines can utilize alternative energy pathway such as glutaminolysis to deal with glucose limitation, provided the presence of oxygen. It was also observed that in situations of glucose limitation, tumor derived-cells can adapt to survive by using exclusively an oxidative energy substrate [9] and [10]. This is typically associated with an enhancement of the OXPHOS system. … In summary, cancer cells can survive by using exclusively OXPHOS for ATP production, by altering significantly mitochondrial composition and form to facilitate optimal use of the available substrate (Fig. 3). Yet, glucose is needed to feed the pentose phosphate pathway and generate ribose essential for nucleotide biosynthesis. This raises the question of how cancer cells can survive in the growth medium which do not contain glucose (so-called “galactose medium” with dialysed serum [9]). In the OXPHOS mode, pyruvate, glutamate and aspartate can be derived from glutamine, as glutaminolysis can replenish Krebs cycle metabolic pool and support the synthesis of alanine and NADPH [31]. Glutamine is a major source for oxaloacetate (OAA) essential for citrate synthesis. Moreover, the conversion of glutamine to pyruvate is associated with the reduction of NADP+ to NADPH by malic enzyme. Such NADPH is a required electron donor for reductive steps in lipid synthesis, nucleotide metabolism and GSH reduction. In glioblastoma cells the malic enzyme flux was estimated to be high enough to supply all of the reductive power needed for lipid synthesis [31].

Fig. 3. Interplay between energy metabolism, oncogenes and tumor microenvironment during tumorigenesis (the “metabolic wave model”).

Interplay between energy metabolism, oncogenes and tumor microenvironment

Interplay between energy metabolism, oncogenes and tumor microenvironment

While the mechanisms leading to the enhancement of glycolytic capacity in tumors are well documented, less is known about the parallel OXPHOS changes. Both phenomena could result from a selection of pre-malignant cells forced to survive under hypoxia and limited glucose delivery, followed by an adaptation to intermittent hypoxia, pseudo-hypoxia, substrate limitation and acidic environment. This hypothesis was first proposed by Gatenby and Gillies to explain the high glycolytic phenotype of tumors [91], [92] and [93], but several lines of evidence suggest that it could also be used to explain the mitochondrial modifications observed in cancer cells.

  1. Aerobic glycolysis and mitochondria cooperate during cancer progression

Metabolic flexibility considers the possibility for a given cell to alternate between glycolysis and OXPHOS in response to physiological needs. Louis Pasteur found that in most mammalian cells the rate of glycolysis decreases significantly in the presence of oxygen (Pasteur effect). Moreover, energy metabolism of normal cell can vary widely according to the tissue of origin, as we showed with the comparison of five rat tissues[94]. During stem cell differentiation, cell proliferation induces a switch from OXPHOS to aerobic glycolysis which might generate ATP more rapidly, as demonstrated in HepG2 cells [95] or in non-cancer cells[96] and [97]. Thus, normal cellular energy metabolism can adapt widely according to the activity of the cell and its surrounding microenvironment (energy substrate availability and diversity). Support for this view came from numerous studies showing that in vitro growth conditions can alter energy metabolism contributing to a dependency on glycolysis for ATP production [98].

Yet, Zu and Guppy analysed numerous studies and showed that aerobic glycolysis is not inherent to cancer but more a consequence of hypoxia[99].

Table 1. Impact of different oncogenes on energy metabolism

Impact of different oncogenes on energy metabolism.

Impact of different oncogenes on energy metabolism.

2.1.2.5 Mitohormesis

Yun J, Finkel T
Cell Metab May 2014; 19(5):757–766
http://dx.doi.org/10.1016/j.cmet.2014.01.011

For many years, mitochondria were viewed as semiautonomous organelles, required only for cellular energetics. This view has been largely supplanted by the concept that mitochondria are fully integrated into the cell and that mitochondrial stresses rapidly activate cytosolic signaling pathways that ultimately alter nuclear gene expression. Remarkably, this coordinated response to mild mitochondrial stress appears to leave the cell less susceptible to subsequent perturbations. This response, termed mitohormesis, is being rapidly dissected in many model organisms. A fuller understanding of mitohormesis promises to provide insight into our susceptibility for disease and potentially provide a unifying hypothesis for why we age.

Figure 1. The Basis of Mitohormesis. Any of a number of endogenous or exogenous stresses can perturb mitochondrial function. These perturbations are relayed to the cytosol through, at present, poorly understood mechanisms that may involve mitochondrial ROS as well as other mediators. These cytoplasmic signaling pathways and subsequent nuclear transcriptional changes induce various long-lasting cytoprotective pathways. This augmented stress resistance allows for protection from a wide array of subsequent stresses.

Figure 2. Potential Parallels between the Mitochondrial Unfolded Protein Response and Quorum Sensing in Gram-Positive Bacteria. In the C. elegans UPRmt response, mitochondrial proteins (indicated by blue swirls) are degraded by matrix proteases, and the oligopeptides that are generated are then exported through the ABC transporter family member HAF-1. Once in the cytosol, these peptides can influence the subcellular localization of the transcription factor ATFS-1. Nuclear ATFS-1 is capable of orchestrating a broad transcriptional response to mitochondrial stress. As such, this pathway establishes a method for mitochondrial and nuclear genomes to communicate. In some gram-positive bacteria, intracellularly generated peptides can be similarly exported through an ABC transporter protein. These peptides can be detected in the environment by a membrane-bound histidine kinases (HK) sensor. The activation of the HK sensor leads to phosphorylation of a response regulator (RR) protein that, in turn, can alter gene expression. This program allows communication between dispersed gram-positive bacteria and thus coordinated behavior of widely dispersed bacterial genomes.

Figure 3. The Complexity of Mitochondrial Stresses and Responses. A wide array of extrinsic and intrinsic mitochondrial perturbations can elicit cellular responses. As detailed in the text, genetic or pharmacological disruption of electron transport, incorrect folding of mitochondrial proteins, stalled mitochondrial ribosomes, alterations in signaling pathways, or exposure to toxins all appear to elicit specific cytoprotective programs within the cell. These adaptive responses include increased mitochondrial number (biogenesis), alterations in metabolism, increased antioxidant defenses, and augmented protein chaperone expression. The cumulative effect of these adaptive mechanisms might be an extension of lifespan and a decreased incidence of age-related pathologies.

2.1.2.6 Mitochondrial function and energy metabolism in cancer cells. Past overview and future perspectives

Mayevsky A
Mitochondrion. 2009 Jun; 9(3):165-79
http://dx.doi.org:/10.1016/j.mito.2009.01.009

The involvements of energy metabolism aspects of mitochondrial dysfunction in cancer development, proliferation and possible therapy, have been investigated since Otto Warburg published his hypothesis. The main published material on cancer cell energy metabolism is overviewed and a new unique in vivo experimental approach that may have significant impact in this important field is suggested. The monitoring system provides real time data, reflecting mitochondrial NADH redox state and microcirculation function. This approach of in vivo monitoring of tissue viability could be used to test the efficacy and side effects of new anticancer drugs in animal models. Also, the same technology may enable differentiation between normal and tumor tissues in experimental animals and maybe also in patients.

 Energy metabolism in mammalian cells

Fig. 1. Schematic representation of cellular energy metabolism and its relationship to microcirculatory blood flow and hemoglobin oxygenation.

Fig. 2. Schematic representation of the central role of the mitochondrion in the various processes involved in the pathology of cancer cells and tumors. Six issues marked as 1–6 are discussed in details in the text.

In vivo monitoring of tissue energy metabolism in mammalian cells

Fig. 3. Schematic presentation of the six parameters that could be monitored for the evaluation of tissue energy metabolism (see text for details).

Optical spectroscopy of tissue energy metabolism in vivo

Multiparametric monitoring system

Fig. 4. (A) Schematic representation of the Time Sharing Fluorometer Reflectometer (TSFR) combined with the laser Doppler flowmeter (D) for blood flow monitoring. The time sharing system includes a wheel that rotates at a speed of3000 rpm wit height filters: four for the measurements of mitochondrial NADH(366 nm and 450 nm)and four for oxy-hemoglobin measurements (585 nm and 577 nm) as seen in (C). The source of light is a mercury lamp. The probe includes optical fibers for NADH excitation (Ex) and emission (Em), laser Doppler excitation (LD in), laser Doppler emission (LD out) as seen in part E The absorption spectrum of Oxy- and Deoxy- Hemoglobin indicating the two wave length used (C).

Fig. 7. Comparison between mitochondrial metabolic states in vitro and the typical tissue metabolic states in vivo evaluated by NADH redox state, tissue blood flow and hemoglobin oxygenation as could be measured by the suggested monitoring system.

(very important)

2.1.2.7 Metabolic Reprogramming. Cancer Hallmark Even Warburg Did Not Anticipate

Ward PS, Thompson CB.
Cancer Cell 2012; 21(3):297-308
http://dx.doi.org/10.1016/j.ccr.2012.02.014

Cancer metabolism has long been equated with aerobic glycolysis, seen by early biochemists as primitive and inefficient. Despite these early beliefs, the metabolic signatures of cancer cells are not passive responses to damaged mitochondria but result from oncogene-directed metabolic reprogramming required to support anabolic growth. Recent evidence suggests that metabolites themselves can be oncogenic by altering cell signaling and blocking cellular differentiation. No longer can cancer-associated alterations in metabolism be viewed as an indirect response to cell proliferation and survival signals. We contend that altered metabolism has attained the status of a core hallmark of cancer.

The propensity for proliferating cells to secrete a significant fraction of glucose carbon through fermentation was first elucidated in yeast. Otto Warburg extended these observations to mammalian cells, finding that proliferating ascites tumor cells converted the majority of their glucose carbon to lactate, even in oxygen-rich conditions. Warburg hypothesized that this altered metabolism was specific to cancer cells, and that it arose from mitochondrial defects that inhibited their ability to effectively oxidize glucose carbon to CO2. An extension of this hypothesis was that dysfunctional mitochondria caused cancer (Koppenol et al., 2011). Warburg’s seminal finding has been observed in a wide variety of cancers. These observations have been exploited clinically using 18F-deoxyglucose positron emission tomography (FDG-PET). However, in contrast to Warburg’s original hypothesis, damaged mitochondria are not at the root of the aerobic glycolysis exhibited by most tumor cells. Most tumor mitochondria are not defective in their ability to carry out oxidative phosphorylation. Instead, in proliferating cells mitochondrial metabolism is reprogrammed to meet the challenges of macromolecular synthesis. This possibility was never considered by Warburg and his contemporaries.

Advances in cancer metabolism research over the last decade have enhanced our understanding of how aerobic glycolysis and other metabolic alterations observed in cancer cells support the anabolic requirements associated with cell growth and proliferation. It has become clear that anabolic metabolism is under complex regulatory control directed by growth factor signal transduction in non-transformed cells. Yet despite these advances, the repeated refrain from traditional biochemists is that altered metabolism is merely an indirect phenomenon in cancer, a secondary effect that pales in importance to the activation of primary proliferation and survival signals (Hanahan and Weinberg, 2011). Most proto-oncogenes and tumor suppressor genes encode components of signal transduction pathways. Their roles in carcinogenesis have traditionally been attributed to their ability to regulate the cell cycle and sustain proliferative signaling while also helping cells evade growth suppression and/or cell death (Hanahan and Weinberg, 2011). But evidence for an alternative concept, that the primary functions of activated oncogenes and inactivated tumor suppressors are to reprogram cellular metabolism, has continued to build over the past several years. Evidence is also developing for the proposal that proto-oncogenes and tumor suppressors primarily evolved to regulate metabolism.

We begin this review by discussing how proliferative cell metabolism differs from quiescent cell metabolism on the basis of active metabolic reprogramming by oncogenes and tumor suppressors. Much of this reprogramming depends on utilizing mitochondria as functional biosynthetic organelles. We then further develop the idea that altered metabolism is a primary feature selected for during tumorigenesis. Recent advances have demonstrated that altered metabolism in cancer extends beyond adaptations to meet the increased anabolic requirements of a growing and dividing cell. Changes in cancer cell metabolism can also influence cellular differentiation status, and in some cases these changes arise from oncogenic alterations in metabolic enzymes themselves.

Metabolism in quiescent vs. proliferating cells nihms-360138-f0001

Metabolism in quiescent vs. proliferating cells: both use mitochondria.
(A) In the absence of instructional growth factor signaling, cells in multicellular organisms lack the ability to take up sufficient nutrients to maintain themselves. Neglected cells will undergo autophagy and catabolize amino acids and lipids through the TCA cycle, assuming sufficient oxygen is available. This oxidative metabolism maximizes ATP production. (B) Cells that receive instructional growth factor signaling are directed to increase their uptake of nutrients, most notably glucose and glutamine. The increased nutrient uptake can then support the anabolic requirements of cell growth: mainly lipid, protein, and nucleotide synthesis (biomass). Excess carbon is secreted as lactate. Proliferating cells may also use strategies to decrease their ATP production while increasing their ATP consumption. These strategies maintain the ADP:ATP ratio necessary to maintain glycolytic flux. Green arrows represent metabolic pathways, while black arrows represent signaling.

Metabolism is a direct, not indirect, response to growth factor signaling nihms-360138-f0002

Metabolism is a direct, not indirect, response to growth factor signaling nihms-360138-f0002

Metabolism is a direct, not indirect, response to growth factor signaling.
(A) The traditional demand-based model of how metabolism is altered in proliferating cells. In response to growth factor signaling, increased transcription and translation consume free energy and decrease the ADP:ATP ratio. This leads to enhanced flux of glucose carbon through glycolysis and the TCA cycle for the purpose of producing more ATP. (B) Supply-based model of how metabolism changes in proliferating cells. Growth factor signaling directly reprograms nutrient uptake and metabolism. Increased nutrient flux through glycolysis and the mitochondria in response to growth factor signaling is used for biomass production. Metabolism also impacts transcription and translation through mechanisms independent of ATP availability.

Alterations in classic oncogenes directly reprogram cell metabolism to increase nutrient uptake and biosynthesis. PI3K/Akt signaling downstream of receptor tyrosine kinase (RTK) activation increases glucose uptake through the transporter GLUT1, and increases flux through glycolysis. Branches of glycolytic metabolism contribute to nucleotide and amino acid synthesis. Akt also activates ATP-citrate lyase (ACL), promoting the conversion of mitochondria-derived citrate to acetyl-CoA for lipid synthesis. Mitochondrial citrate can be synthesized when glucose-derived acetyl-CoA, generated by pyruvate dehydrogenase (PDH), condenses with glutamine-derived oxaloacetate (OAA) via the activity of citrate synthase (CS). mTORC1 promotes protein synthesis and mitochondrial metabolism. Myc increases glutamine uptake and the conversion of glutamine into a mitochondrial carbon source by promoting the expression of the enzyme glutaminase (GLS). Myc also promotes mitochondrial biogenesis. In addition, Myc promotes nucleotide and amino acid synthesis, both through direct transcriptional regulation and through increasing the synthesis of mitochondrial metabolite precursors.

Pyruvate kinase M2 (PKM2) expression in proliferating cells is regulated by signaling and mitochondrial metabolism to facilitate macromolecular synthesis. PKM2 is a less active isoform of the terminal glycolytic enzyme pyruvate kinase. It is also uniquely inhibited downstream of tyrosine kinase signaling. The decreased enzymatic activity of PKM2 in the cytoplasm promotes the accumulation of upstream glycolytic intermediates and their shunting into anabolic pathways. These pathways include the serine synthetic pathway that contributes to nucleotide and amino acid production. When mitochondrial metabolism is excessive, reactive oxygen species (ROS) from the mitochondria can feedback to inhibit PKM2 activity. Acetylation of PKM2, dependent on acetyl-CoA availability, may also promote PKM2 degradation and further contribute to increased flux through anabolic synthesis pathways branching off glycolysis.

IDH1 and IDH2 mutants convert glutamine carbon to the oncometabolite 2-hydroxyglutarate to dysregulate epigenetics and cell differentiation. (A) α-ketoglutarate, produced in part by wild-type isocitrate dehydrogenase (IDH), can enter the nucleus and be used as a substrate for dioxygenase enzymes that modify epigenetic marks. These enzymes include the TET2 DNA hydroxylase enzyme which converts 5-methylcytosine to 5-hydroxymethylcytosine, typically at CpG dinucleotides. 5-hydroxymethylcytosine may be an intermediate in either active or passive DNA demethylation. α-ketoglutarate is also a substrate for JmjC domain histone demethylase enzymes that demethylate lysine residues on histone tails. (B) The common feature of cancer-associated mutations in cytosolic IDH1 and mitochondrial IDH2 is the acquisition of a neomorphic enzymatic activity. This activity converts glutamine-derived α-ketoglutarate to the oncometabolite 2HG. 2HG can competitively inhibit α-ketoglutarate-dependent enzymes like TET2 and the JmjC histone demethylases, thereby impairing normal epigenetic regulation. This results in altered histone methylation marks, in some cases DNA hypermethylation at CpG islands, and dysregulated cellular differentiation.

Hypoxia and HIF-1 activation promote an alternative pathway for citrate synthesis through reductive metabolism of glutamine. (A) In proliferating cells under normoxic conditions, citrate is synthesized from both glucose and glutamine. Glucose carbon provides acetyl-CoA through the activity of PDH. Glutamine carbon provides oxaloacetate through oxidative mitochondrial metabolism dependent on NAD+. Glucose-derived acetyl-CoA and glutamine-derived oxaloacetate condense to form citrate via the activity of citrate synthase (CS). Citrate can be exported to the cytosol for lipid synthesis. (B) In cells proliferating in hypoxia and/or with HIF-1 activation, glucose is diverted away from mitochondrial acetyl-CoA and citrate production. Citrate can be maintained through an alternative pathway of reductive carboxylation, which we propose to rely on reverse flux of glutamine-derived α-ketoglutarate through IDH2. This reverse flux in the mitochondria would promote electron export from the mitochondria when the activity of the electron transport chain is inhibited because of the lack of oxygen as an electron acceptor. Mitochondrial reverse flux can be accomplished by NADH conversion to NADPH by mitochondrial transhydrogenase and the resulting NADPH use in α-ketoglutarate carboxylation. When citrate/isocitrate is exported to the cytosol, some may be metabolized in the oxidative direction by IDH1 and contribute to a shuttle that produces cytosolic NADPH.

A major paradox remaining with PKM2 is that cells expressing PKM2 produce more glucose-derived pyruvate than PKM1-expressing cells, despite having a form of the pyruvate kinase enzyme that is less active and more sensitive to inhibition. One way to get around the PKM2 bottleneck and maintain/enhance pyruvate production may be through an proposed alternative glycolytic pathway, involving an enzymatic activity not yet purified, that dephosphorylates PEP to pyruvate without the generation of ATP (Vander Heiden et al., 2010). Another answer to this paradox may emanate from the serine synthetic pathway. The decreased enzymatic activity of PKM2 can promote the accumulation of the 3-phosphoglycerate glycolytic intermediate that serves as the entry point for the serine synthetic pathway branch off glycolysis. The little studied enzyme serine dehydratase can then directly convert serine to pyruvate. A third explanation may lie in the oscillatory activity of PKM2 from the inactive dimer to active tetramer form. Regulatory inputs into PKM2 like tyrosine phosphorylation and ROS destabilize the tetrameric form of PKM2 (Anastasiou et al., 2011; Christofk et al., 2008b; Hitosugi et al., 2009), but other inputs present in glycolytic cancer cells like fructose-1,6-bisphosphate and serine can continually allosterically activate and/or promote reformation of the PKM2 tetramer (Ashizawa et al., 1991; Eigenbrodt et al., 1983). Thus, PKM2 may be continually switching from inactive to active forms in cells, resulting in an apparent upregulation of flux through anabolic glycolytic branching pathways while also maintaining reasonable net flux of glucose carbon through PEP to pyruvate. With such an oscillatory system, small changes in the levels of any of the above-mentioned PKM2 regulatory inputs can cause exquisite, rapid, adjustments to glycolytic flux. This would be predicted to be advantageous for proliferating cells in the setting of variable extracellular nutrient availability. The capability for oscillatory regulation of PKM2 could also provide an explanation for why tumor cells do not select for altered glycolytic metabolism upstream of PKM2 through deletions and/or loss of function mutations of other glycolytic enzymes.

IDH1 mutations at R132 are not simply loss-of-function for isocitrate and α-ketoglutarate interconversion, but also acquire a novel reductive activity to convert α-ketoglutarate to 2-hydroxyglutarate (2HG), a rare metabolite found at only trace amounts in mammalian cells under normal conditions (Dang et al., 2009). However, it still remained unclear if 2HG was truly a pathogenic “oncometabolite” resulting from IDH1 mutation, or if it was just the byproduct of a loss of function mutation. Whether 2HG production or the loss of IDH1 normal function played a more important role in tumorigenesis remained uncertain.

A potential answer to whether 2HG production was relevant to tumorigenesis arrived with the study of mutations in IDH2, the mitochondrial homolog of IDH1. Up to this point a small fraction of gliomas lacking IDH1 mutations were known to harbor mutations at IDH2 R172, the analogous residue to IDH1 R132 (Yan et al., 2009). However, given the rarity of these IDH2 mutations, they had not been characterized for 2HG production. The discovery of IDH2 R172 mutations in AML as well as glioma samples prompted the study of whether these mutations also conferred the reductive enzymatic activity to produce 2HG. Enzymatic assays and measurement of 2HG levels in primary AML samples confirmed that these IDH2 R172 mutations result in 2HG elevation (Gross et al., 2010; Ward et al., 2010).

It was then investigated if the measurement of 2HG levels in primary tumor samples with unknown IDH mutation status could serve as a metabolite screening test for both cytosolic IDH1 and mitochondrial IDH2 mutations. AML samples with low to undetectable 2HG were subsequently sequenced and determined to be IDH1 and IDH2 wild-type, and several samples with elevated 2HG were found to have neomorphic mutations at either IDH1 R132 or IDH2 R172 (Gross et al., 2010). However, some 2HG-elevated AML samples lacked IDH1 R132 or IDH2 R172 mutations. When more comprehensive sequencing of IDH1 and IDH2 was performed, it was found that the common feature of this remaining subset of 2HG-elevated AMLs was another mutation in IDH2, occurring at R140 (Ward et al., 2010). This discovery provided additional evidence that 2HG production was the primary feature being selected for in tumors.

In addition to intensifying efforts to find the cellular targets of 2HG, the discovery of the 2HG-producing IDH1 and IDH2 mutations suggested that 2HG measurement might have clinical utility in diagnosis and disease monitoring. While much work is still needed in this area, serum 2HG levels have successfully correlated with IDH1 R132 mutations in AML, and recent data have suggested that 1H magnetic resonance spectroscopy can be applied for 2HG detection in vivo for glioma (Andronesi et al., 2012; Choi et al., 2012; Gross et al., 2010; Pope et al., 2012). These methods may have advantages over relying on invasive solid tumor biopsies or isolating leukemic blast cells to obtain material for sequencing of IDH1 and IDH2. Screening tumors and body fluids by 2HG status also has potentially increased applicability given the recent report that additional IDH mutations can produce 2HG (Ward et al., 2011). These additional alleles may account for the recently described subset of 2HG-elevated chondrosarcoma samples that lacked the most common IDH1 or IDH2 mutations but were not examined for other IDH alterations (Amary et al., 2011). Metabolite screening approaches can also distinguish neomorphic IDH mutations from SNPs and sequencing artifacts with no effect on IDH enzyme activity, as well as from an apparently rare subset of loss-of-function, non 2HG-producing IDH mutations that may play a secondary tumorigenic role in altering cellular redox (Ward et al., 2011).

Will we find other novel oncometabolites like 2HG? We should consider basing the search for new oncometabolites on those metabolites already known to cause disease in pediatric inborn errors of metabolism (IEMs). 2HG exemplifies how advances in research on IEMs can inform research on cancer metabolism, and vice versa. Methods developed by those studying 2HG aciduria were used to demonstrate that R(-)-2HG (also known as D-2HG) is the exclusive 2HG stereoisomer produced by IDH1 and IDH2 mutants (Dang et al., 2009; Ward et al., 2010). Likewise, following the discovery of 2HG-producing IDH2 R140 mutations in leukemia, researchers looked for and successfully found germline IDH2 R140 mutations in D-2HG aciduria. IDH2 R140 mutations now account for nearly half of all cases of this devastating disease (Kranendijk et al., 2010). While interest has surrounded 2HG due to its apparent novelty as a metabolite not found in normal non-diseased cells, there are situations where 2HG appears in the absence of metabolic enzyme mutations. For example, in human cells proliferating in hypoxia, α-ketoglutarate can accumulate and be metabolized through an enhanced reductive activity of wild-type IDH2 in the mitochondria, leading to 2HG accumulation in the absence of IDH mutation (Wise et al., 2011). The ability of 2HG to alter epigenetics may reflect its evolutionary ancient status as a signal for elevated glutamine/glutamate metabolism and/or oxygen deficiency.

With this broadened view of what constitutes an oncometabolite, one could argue that the discoveries of two other oncometabolites, succinate and fumarate, preceded that of 2HG. Loss of function mutations in the TCA cycle enzymes succinate dehydrogenase (SDH) and fumarate hydratase (FH) have been known for several years to occur in pheochromocytoma, paraganglioma, leiomoyoma, and renal carcinoma. It was initially hypothesized that these mutations contribute to cancer through mitochondrial damage producing elevated ROS (Eng et al., 2003). However, potential tumorigenic effects were soon linked to the elevated levels of succinate and fumarate arising from loss of SDH and FH function, respectively. Succinate was initially found to impair PHD2, the α-ketoglutarate-dependent enzyme regulating HIF stability, through product inhibition (Selak et al., 2005). Subsequent work confirmed that fumarate could inhibit PHD2 (Isaacs et al., 2005), and that succinate could also inhibit the related enzyme PHD3 (Lee et al., 2005). These observations linked the elevated HIF levels observed in SDH and FH deficient tumors to the activity of the succinate and fumarate metabolites. Recent work has suggested that fumarate may have other important roles that predominate in FH deficiency. For example, fumarate can modify cysteine residues to inhibit a negative regulator of the Nrf2 transcription factor. This post-translational modification leads to the upregulation of antioxidant response genes (Adam et al., 2011; Ooi et al., 2011).

There are still many unanswered questions regarding the biology of SDH and FH deficient tumors. In light of the emerging epigenetic effects of 2HG, it is intriguing that succinate has been shown to alter histone demethylase activity in yeast (Smith et al., 2007). Perhaps elevated succinate and fumarate resulting from SDH and FH mutations can promote tumorigenesis in part through epigenetic modulation.

Despite rapid technological advances in studying cell metabolism, we remain unable to reliably distinguish cytosolic metabolites from those in the mitochondria and other compartments. Current fractionation methods often lead to metabolite leakage. Even within one subcellular compartment, there may be distinct pools of metabolites resulting from channeling between metabolic enzymes. A related challenge lies in the quantitative measurement of metabolic flux; i.e., measuring the movement of carbon, nitrogen, and other atoms through metabolic pathways rather than simply measuring the steady-state levels of individual metabolites. While critical fluxes have been quantified in cultured cancer cells and methods for these analyses continue to improve (DeBerardinis et al., 2007; Mancuso et al., 2004; Yuan et al., 2008), many obstacles remain such as cellular compartmentalization and the reliance of most cell culture on complex, incompletely defined media.

Over the past decade, the study of metabolism has returned to its rightful place at the forefront of cancer research. Although Warburg was wrong about mitochondria, he was prescient in his focus on metabolism. Data now support the concepts that altered metabolism results from active reprogramming by altered oncogenes and tumor suppressors, and that metabolic adaptations can be clonally selected during tumorigenesis. Altered metabolism should now be considered a core hallmark of cancer. There is much work to be done.

2.1.2.8 A Role for the Mitochondrial Pyruvate Carrier as a Repressor of the Warburg Effect and Colon Cancer Cell Growth

Schell JC, Olson KA, …, Xie J, Egnatchik RA, Earl EG, DeBerardinis RJ, Rutter J.
Mol Cell. 2014 Nov 6; 56(3):400-13
http://dx.doi.org:/10.1016/j.molcel.2014.09.026

Cancer cells are typically subject to profound metabolic alterations, including the Warburg effect wherein cancer cells oxidize a decreased fraction of the pyruvate generated from glycolysis. We show herein that the mitochondrial pyruvate carrier (MPC), composed of the products of the MPC1 and MPC2 genes, modulates fractional pyruvate oxidation. MPC1 is deleted or underexpressed in multiple cancers and correlates with poor prognosis. Cancer cells re-expressing MPC1 and MPC2 display increased mitochondrial pyruvate oxidation, with no changes in cell growth in adherent culture. MPC re-expression exerted profound effects in anchorage-independent growth conditions, however, including impaired colony formation in soft agar, spheroid formation, and xenograft growth. We also observed a decrease in markers of stemness and traced the growth effects of MPC expression to the stem cell compartment. We propose that reduced MPC activity is an important aspect of cancer metabolism, perhaps through altering the maintenance and fate of stem cells.

Figure 2. Re-Expressed MPC1 and MPC2 Form a Mitochondrial Complex (A and B) (A) Western blot and (B) qRT-PCR analysis of the indicated colon cancer cell lines with retroviral expression of MPC1 (or MPC1-R97W) and/or MPC2. (C) Western blots of human heart tissue, hematologic cancer cells, and colon cancer cell lines with and without MPC1 and MPC2 re-expression. (D) Fluorescence microscopy of MPC1-GFP and MPC2-GFP overlaid with Mitotracker Red in HCT15 cells. Scale bar: 10 mm. (E) Blue-native PAGE analysis of mitochondria from control and MPC1/2-expressing cells. (F) Western blots of metabolic and mitochondrial proteins across four colon cancer cell lines with or without MPC1/2 expression

Figure 3. MPC Re-Expression Alters Mitochondrial Pyruvate Metabolism (A) OCR at baseline and maximal respiration in HCT15 (n = 7) and HT29 (n = 13) with pyruvate as the sole carbon source (mean ± SEM). (B and C) Schematic and citrate mass isotopomer quantification in cells cultured with D-[U-13C]glucose and unlabeled glutamine for 6 hr (mean ± SD, n = 2). (D) Glucose uptake and lactate secretion normalized to protein concentration (mean ± SD, n = 3). (E–G) (E) Western blots of PDH, phospho-PDH, and PDK1; (F) PDH activity assay and (G) CS activity assay with or without MPC1 and MPC2 expression (mean ± SD, n = 4). (H and I) Effects of MPC1/2 re-expression on mitochondrial membrane potential and ROS production (mean ± SD, n = 3). *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001.

Figure 4. MPC Re-Expression Alters Growth under Low-Attachment Conditions (A) Cell number of control and MPC1/2 re-expressing cell lines in adherent culture (mean ± SD, n = 7). (B) Cell viability determined by trypan blue exclusion and Annexin V/PI staining (mean ± SD, n = 3). (C–F) (C) EdU incorporation of MPC re-expressing cell lines at 3 hr post EdU pulse. Growth in 3D culture evaluated by (D) soft agar colony formation (mean ± SD, n = 12, see also Table S1) and by ([E] and [F]) spheroid formation ± MPC inhibitor UK5099 (mean ± SEM, n = 12). *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001.

Figure 7. MPC Re-Expression Alters the Cancer Initiating Cell Population (A) Western blot quantification of ALDHA and Lin28A from control or MPC re-expressing HT29 xenografts (mean ± SEM, n = 10). (B and C) Percentage of ALDHhi (n = 3) and CD44hi (n = 5) cells as determined by flow cytometry (mean ± SEM). (D) Western blot analysis of stem cell markers in control and MPC re-expressing cell lines. (E) Relative MPC1 and MPC2 mRNA levels in ALDH sorted HCT15 cells (n = 4,mean ± SEM). 2D growth of (F) whole-population HCT15 cells and (G) ALDH sorted cells. Area determined by ImageJ after crystal violet staining (mean ± SD, n = 6). (H and I) (H) Adherent and (I) spheroid growth of main population (MP) versus side population (SP) HCT15 cells. (mean ± SD, n = 6). *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001

Our demonstration that the MPC is lost or underexpressed in many cancers might provide clarifying context for earlier attempts to exploit metabolic regulation for cancer therapeutics. The PDH kinase inhibitor dichloroacetate, which impairs PDH phosphorylation and increases pyruvate oxidation, has been explored extensively as a cancer therapy (Bonnet et al., 2007; Olszewski et al., 2010). It has met with mixed results, however, and has typically failed to dramatically decrease tumor burden as a monotherapy (Garon et al., 2014;
Sanchez-Arago et al., 2010; Shahrzadetal.,2010). Is one possible reason for these failures that the MPC has been lost or inactivated, thereby limiting the metabolic effects of PDH activity? The inclusion of the MPC adds additional complexity to targeting cancer metabolism for therapy but has the potential to explain why treatments may be more effective in some studies than in others (Fulda et al., 2010; Hamanaka and Chandel, 2012; Tennant et al., 2010; Vander Heiden, 2011). The redundant measures to limit pyruvate oxidation make it easy to understand why expression of the MPC leads to relatively modest metabolic changes in cells grown in adherent culture conditions. While subtle, we observed a number of changes in metabolic parameters, all of which are consistent with enhanced mitochondrial pyruvate entry and oxidation. There are at least two possible explanations for the discrepancy that we observed between the impact on adherent and nonadherent cell proliferation. One hypothesis is that the stress of nutrient deprivation and detachment combines with these subtle metabolic effects to impair survival and proliferation.

2.1.2.9  ECM1 promotes the Warburg effect through EGF-mediated activation of PKM2

Lee KM, Nam K, Oh S, Lim J, Lee T, Shin I.
Cell Signal. 2015 Feb; 27(2):228-35
http://dx.doi.org:/10.1016/j.cellsig.2014.11.004

The Warburg effect is an oncogenic metabolic switch that allows cancer cells to take up more glucose than normal cells and favors anaerobic glycolysis. Extracellular matrix protein 1 (ECM1) is a secreted glycoprotein that is overexpressed in various types of carcinoma. Using two-dimensional digest-liquid chromatography-mass spectrometry (LC-MS)/MS, we showed that the expression of proteins associated with the Warburg effect was upregulated in trastuzumab-resistant BT-474 cells that overexpressed ECM1 compared to control cells. We further demonstrated that ECM1 induced the expression of genes that promote the Warburg effect, such as glucose transporter 1 (GLUT1), lactate dehydrogenase A (LDHA), and hypoxia-inducible factor 1 α (HIF-1α). The phosphorylation status of pyruvate kinase M2 (PKM-2) at Ser37, which is responsible for the expression of genes that promote the Warburg effect, was affected by the modulation of ECM1 expression. Moreover, EGF-dependent ERK activation that was regulated by ECM1 induced not only PKM2 phosphorylation but also gene expression of GLUT1 and LDHA. These findings provide evidence that ECM1 plays an important role in promoting the Warburg effect mediated by PKM2.

Fig. 1.ECM1 induces a metabolic shift toward promoting Warburg effect. (A) The levels of glucose uptake were examined with a cell-based assay. (B) Levels of lactate production were measured using a lactate assay kit. (C) Cellular ATP content was determined with a Cell Titer-Glo luminescent cell viability assay. Error bars represent mean ± SD of triplicate experiments (*p b 0.05, ***p b 0.0005).

Fig.2. ECM1 up-regulates expression of gene sassociated with the Warburg effect. (A) Cell lysates were analyzed by western blotting using antibodies specific for ECM1, LDHA, GLUT1,and actin (as a loading control). The intensities of the bands were quantified using 1D Scan software and plotted. (BandC) mRNA levels of each gene were determined by real-time PCR using specific primers. (D) HIF-1α-dependent transcriptional activities were examined using a hypoxia response element (HRE) reporter indual luciferase assays. Error bars represent mean ± SD of triplicate experiments (*p b 0.05, **p b 0.005, ***p b 0.0005).

Fig.3. ECM1-dependent upregulation of gene expression is not mediated byEgr-1.

Fig.4. ECM1 activates PKM2 via EGF-mediated ERK activation

Fig. 5. TheWarburg effect is attenuated by silencing of PKM2 in breast cancer cells

Recently, a non-glycolytic function of PKM2 was reported. Phosphorylated PKM2 at Ser37 is translocated into the nucleus after EGFR and ERK activation and regulates the expression of cyclin D1, c-Myc, LDHA, and GLUT1[19,37]. Here, we showed that ECM1 regulates the phosphorylation level and translocation of PKM2 via the EGFR/ ERK pathway. As we previously showed that ECM1 enhances the EGF response and increases EGFR expression through MUC1-dependent stabilization [17], it seemed likely that activation of the EGFR/ERK pathway by ECM1 is linked to PKM2 phosphorylation. Indeed, we show here that ECM1 regulates the phosphorylation of PKM2 at Ser37 and enhances the Warburg effect through the EGFR/ERK pathway. HIF-1α is known to be responsible for alterations in cancer cell metabolism [38] and our current studies showed that the expression level of HIF-1α is up-regulated by ECM1 (Fig. 2C and D). To determine the mechanism by which ECM1 upregulated HIF-1α expression, we focused on the induction of Egr-1 by EGFR/ERK signaling [39]. However, although Egr-1 expression was regulated by ECM1 we failed to find evidence that Egr-1 affected the expression of genes involved in the Warburg effect (Fig. 3C). Moreover, ERK-dependent PKM2 activation did not regulate HIF-1α expression in BT-474 cells (Fig. 4D and5B). These results suggested that the upregulation of HIF-1α by ECM1 is not mediated by the EGFR/ERK pathway.

Conclusions

In the current study we showed that ECM1 altered metabolic phenotypes of breast cancer cells toward promoting the Warburg effect.

Phosphorylation and nuclear translocation of PKM2 were induced by ECM1 through the EGFR/ERK pathway. Moreover, phosphorylated PKM2 increased the expression of metabolic genes such as LDHA and GLUT1, and promoted glucose uptake and lactate production. These findings provide a new perspective on the distinct functions of ECM1 in cancer cell metabolism. Supplementary data to this article can be found online at
http://dx.doi.org/10.1016/j.cellsig.2014.11.004

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2.1.2.10 Glutamine Oxidation Maintains the TCA Cycle and Cell Survival during impaired Mitochondrial Pyruvate Transport

Chendong Yang, B Ko, CT. Hensley,…, J Rutter, ME. Merritt, RJ. DeBerardinis
Molec Cell  6 Nov 2014; 56(3):414–424
http://dx.doi.org/10.1016/j.molcel.2014.09.025

Highlights

  • Mitochondria produce acetyl-CoA from glutamine during MPC inhibition
    •Alanine synthesis is suppressed during MPC inhibition
    •MPC inhibition activates GDH to supply pools of TCA cycle intermediates
    •GDH supports cell survival during periods of MPC inhibition

Summary

Alternative modes of metabolism enable cells to resist metabolic stress. Inhibiting these compensatory pathways may produce synthetic lethality. We previously demonstrated that glucose deprivation stimulated a pathway in which acetyl-CoA was formed from glutamine downstream of glutamate dehydrogenase (GDH). Here we show that import of pyruvate into the mitochondria suppresses GDH and glutamine-dependent acetyl-CoA formation. Inhibiting the mitochondrial pyruvate carrier (MPC) activates GDH and reroutes glutamine metabolism to generate both oxaloacetate and acetyl-CoA, enabling persistent tricarboxylic acid (TCA) cycle function. Pharmacological blockade of GDH elicited largely cytostatic effects in culture, but these effects became cytotoxic when combined with MPC inhibition. Concomitant administration of MPC and GDH inhibitors significantly impaired tumor growth compared to either inhibitor used as a single agent. Together, the data define a mechanism to induce glutaminolysis and uncover a survival pathway engaged during compromised supply of pyruvate to the mitochondria.

Yang et al, Graphical Abstract

Yang et al, Graphical Abstract

Graphical abstract

Figure 1. Pyruvate Depletion Redirects Glutamine Metabolism to Produce AcetylCoA and Citrate (A) Top: Anaplerosis supplied by [U-13C]glutamine. Glutamine supplies OAA via a-KG, while acetylCoA is predominantly supplied by other nutrients, particularly glucose. Bottom: Glutamine is converted to acetyl-CoA in the absence of glucosederived pyruvate. Red circles represent carbons arising from [U-13C]glutamine, and gray circles are unlabeled. Reductive carboxylation is indicated by the green dashed line. (B) Fraction of succinate, fumarate, malate, and aspartate containing four 13C carbons after culture of SFxL cells for 6 hr with [U-13C]glutamine in the presence or absence of 10 mM unlabeled glucose (Glc). (C) Mass isotopologues of citrate after culture of SFxL cells for 6 hr with [U-13C]glutamine and 10 mM unlabeled glucose, no glucose, or no glucose plus 6 mM unlabeled pyruvate (Pyr). (D) Citrate m+5 and m+6 after culture of HeLa or Huh-7 cells for 6 hr with [U-13C]glutamine and 10 mM unlabeled glucose, no glucose, or no glucose plus 6 mM unlabeled pyruvate. Data are the average and SD of three independent cultures. *p < 0.05; **p < 0.01; ***p < 0.001.

Figure 2. Isolated Mitochondria Convert Glutamine to Citrate (A) Western blot of whole-cell lysates (Cell) and preparations of isolated mitochondria (Mito) or cytosol from SFxL cells. (B) Oxygen consumption in a representative mitochondrial sample. Rates before and after addition of ADP/GDP are indicated. (C) Mass isotopologues of citrate produced by mitochondria cultured for 30 min with [U-13C] glutamine and with or without pyruvate.

Figure 3. Blockade of Mitochondrial Pyruvate Transport Activates Glutamine-Dependent Citrate Formation (A) Dose-dependent effects of UK5099 on citrate labeling from [U-13C]glucose and [U-13C]glutamine in SFxL cells. (B) Time course of citrate labeling from [U-13C] glutamine with or without 200 mM UK5099. (C) Abundance of total citrate and citrate m+6 in cells cultured in [U-13C]glutamine with or without 200 mM UK5099. (D) Mass isotopologues of citrate in cells cultured for 6 hr in [U-13C]glutamine with or without 10 mM CHC or 200 mM UK5099. (E) Effect of silencing ME2 on citrate m+6 after 6 hr of culture in [U-13C]glutamine. Relative abundances of citrate isotopologues were determined by normalizing total citrate abundance measured by mass spectrometry against cellular protein for each sample then multiplying by the fractional abundance of each isotopologue. (F) Effect of silencing MPC1 or MPC2 on formation of citrate m+6 after 6 hr of culture in [U-13C]glutamine. (G) Citrate isotopologues in primary human fibroblasts of varying MPC1 genotypes after culture in [U-13C]glutamine. Data are the average and SD of three independent cultures. *p < 0.05; **p < 0.01; ***p < 0.001. See also Figure S1.

Figure 4. Kinetic Analysis of the Metabolic Effects of Blocking Mitochondrial Pyruvate Transport (A) Summation of 13C spectra acquired over 2 min of exposure of SFxL cells to hyperpolarized [1-13C] pyruvate. Resonances are indicated for [1-13C] pyruvate (Pyr1), the hydrate of [1-13C]pyruvate (Pyr1-Hydr), [1-13C]lactate (Lac1), [1-13C]alanine (Ala1), and H[13C]O3 (Bicarbonate). (B) Time evolution of appearance of Lac1, Ala1, and bicarbonate in control and UK5099-treated cells. (C) Relative 13C NMR signals for Lac1, Ala1, and bicarbonate. Each signal is summed over the entire acquisition and expressed as a fraction of total 13C signal. (D) Quantity of intracellular and secreted alanine in control and UK5099-treated cells. Data are the average and SD of three independent cultures. *p < 0.05; ***p < 0.001. See also Figure S2.

Figure 5. Inhibiting Mitochondrial Pyruvate Transport Enhances the Contribution of Glutamine to Fatty Acid Synthesis (A) Mass isotopologues of palmitate extracted from cells cultured with [U-13C] glucose or [U-13C]glutamine, with or without 200 mM UK5099. For simplicity, only even-labeled isotopologues (m+2, m+4, etc.) are shown. (B) Fraction of lipogenic acetyl-CoA derived from glucose or glutamine with or without 200 mM UK5099. Data are the average and SD of three independent cultures. ***p < 0.001. See also Figure S3.

Figure 6. Blockade of Mitochondrial Pyruvate Transport Induces GDH (A) Two routes by which glutamate can be converted to AKG. Blue and green symbols are the amide (g) and amino (a) nitrogens of glutamine, respectively. (B) Utilization and secretion of glutamine (Gln), glutamate (Glu), and ammonia (NH4+) by SFxL cells with and without 200 mM UK5099. (C) Secretion of 15N-alanine and 15NH4+ derived from [a-15N]glutamine in SFxL cells expressing a control shRNA (shCtrl) or either of two shRNAs directed against GLUD1 (shGLUD1-A and shGLUD1-B). (D) Left: Phosphorylation of AMPK (T172) and acetyl-CoA carboxylase (ACC, S79) during treatment with 200 mM UK5099. Right: Steady-state levels of ATP 24 hr after addition of vehicle or 200 mM UK5099. (E) Fractional contribution of the m+6 isotopologue to total citrate in shCtrl, shGLUD1-A, and shGLUD1-B SFxL cells cultured in [U-13C]glutamine with or without 200 mM UK5099. Data are the average and SD of three independent cultures. *p < 0.05; **p < 0.01; ***p < 0.001. See also Figure S4.

Figure 7. GDH Sustains Growth and Viability during Suppression of Mitochondrial Pyruvate Transport (A) Relative growth inhibition of shCtrl, shGLUD1A, and shGLUD1-B SFxL cells treated with 50 mM UK5099 for 3 days. (B) Relative growth inhibition of SFxL cells treated with combinations of 50 mM of the GDH inhibitor EGCG, 10 mM of the GLS inhibitor BPTES, and 200 mM UK5099 for 3 days. (C) Relative cell death assessed by trypan blue staining in SFxL cells treated as in (B). (D) Relative cell death assessed by trypan blue staining in SF188 cells treated as in (B) for 2 days. (E) (Left) Growth of A549-derived subcutaneous xenografts treated with vehicle (saline), EGCG, CHC, or EGCG plus CHC (n = 4 for each group). Data are the average and SEM. Right: Lactate abundance in extracts of each tumor harvested at the end of the experiment. Data in (A)–(D) are the average and SD of three independent cultures. NS, not significant; *p < 0.05; **p < 0.01; ***p < 0.001. See also Figure S5.

Mitochondrial metabolism complements glycolysis as a source of energy and biosynthetic precursors. Precursors for lipids, proteins, and nucleic acids are derived from the TCA cycle. Maintaining pools of these intermediates is essential, even under circumstances of nutrient limitation or impaired supply of glucose-derived pyruvate to the mitochondria. Glutamine’s ability to produce both acetyl-CoA and OAA allows it to support TCA cycle activity as a sole carbon source and imposes a greater cellular dependence on glutamine metabolism when MPC function or pyruvate supply is impaired. Other anaplerotic amino acids could also supply both OAA and acetyl-CoA, providing flexible support for the TCA cycle when glucose is limiting. Although fatty acids are an important fuel in some cancer cells (Caro et al., 2012), and fatty acid oxidation is induced upon MPC inhibition, this pathway produces acetyl-CoA but not OAA. Thus, fatty acids would need to be oxidized along with an anaplerotic nutrient in order to enable the cycle to function as a biosynthetic hub. Notably, enforced MPC overexpression also impairs growth of some tumors (Schell et al., 2014), suggesting that maximal growth may require MPC activity to be maintained within a narrow window. After decades of research on mitochondrial pyruvate transport, molecular components of the MPC were recently reported (Halestrap, 2012; Schell and Rutter, 2013). MPC1 and MPC2 form a heterocomplex in the inner mitochondrial membrane, and loss of either component impairs pyruvate import, leading to citrate depletion (Bricker et al., 2012; Herzig et al., 2012). Mammalian cells lacking functional MPC1 display normal glutamine-supported respiration (Bricker et al., 2012), consistent with our observation that glutamine supplies the TCA cycle in absence of pyruvate import. We also observed that isolated mitochondria produce fully labeled citrate from glutamine, indicating that this pathway operates as a self-contained mechanism to maintain TCA cycle function. Recently, two well-known classes of drugs have unexpectedly been shown to inhibit MPC. First, thiazolidinediones, commonly used as insulin sensitizers, impair MPC function in myoblasts (Divakaruni et al.,2013). Second, the phosphodiesterase inhibitor Zaprinast inhibits MPC in the retina and brain (Du et al., 2013b). Zaprinast also induced accumulation of aspartate, suggesting that depletion of acetyl-CoA impaired the ability of a new turn of the TCA cycle to be initiated from OAA; as a consequence, OAA was transaminated to aspartate. We noted a similar phenomenon in cancer cells, suggesting that UK5099 elicits a state in which acetyl-CoA supply is insufficient to avoid OAA accumulation. Unlike UK5099, Zaprinast did not induce glutamine-dependent acetyl-CoA formation. This may be related to the reliance of isolated retinas on glucose rather than glutamine to supply TCA cycle intermediates or the exquisite system used by retinas to protect glutamate from oxidation (Du et al., 2013a). Zaprinast was also recently shown to inhibit glutaminase (Elhammali et al., 2014), which would further reduce the contribution of glutamine to the acetyl-CoA pool.

Comment by reader –

The results from these studies served as a good
reason to attempt the vaccination of patients using p53-
derived peptides, and a several clinical trials are currently
in progress. The most advanced work used a long
synthetic peptide mixture derived from p53 (p53-SLP; ISA
Pharmaceuticals, Bilthoven, the Netherlands) (Speetjens
et al., 2009; Shangary et al., 2008; Van der Burg et al.,
2001). The vaccine is delivered in the adjuvant setting
and induces T helper type cells.

Read Full Post »


Larry H. Bernstein, MD, FCAP, Author and Curator

Isozymes

An example of an isozyme is glucokinase, a variant of hexokinase which is not
inhibited by glucose 6-phosphate.  Its different regulatory features and lower
affinity for glucose (compared to other hexokinases), allows it to serve different
functions in cells of specific organs, such as

  • control of insulinrelease by the beta cells of the pancreas, or
  • initiation ofglycogen synthesis by liver
  • Both of these processes must only occur when glucose is abundant,or
    problems occur.

Isozymes or Isoenzymes are proteins with different structure which catalyze
the same reaction. Frequently they are oligomers made with different
polypeptide chains, so they usually differ in regulatory mechanisms and in
kinetic characteristics.

From the physiological point of view, isozymes allow the existence of similar
enzymes with different characteristics, “customized” to specific tissue
requirements or metabolic conditions.

One example of the advantages of having isoenzymes for adjusting the
metabolism to different conditions and/ or in different organs is the following:

Glucokinase and Hexokinase are typical examples of isoenzymes. In fact,
there are four Hexokinases: I, II, III and IV. Hexokinase I is present in all
mammalian tissues, and Hexokinase IV, aka Glucokinase, is found mainly
in liver, pancreas  and brain.

Both enzymes catalyze the phosphorylation of Glucose:

Glucose + ATP —–à Glucose 6 (P) + ADP

Hexokinase I has a low Km and is inhibited by glucose 6 (P).  Glucokinase
is not inhibited by Glucose 6 (P) and his Km is high. These two facts
indicate that the activity of glucokinase depends on the availability
of substrate and not on the demand of the product.

Since Glucokinase is not inhibited by glucose 6 phosphate, in
conditions of high concentrations of glucose this enzyme
continues phosphorylating glucose, which can be used for
glycogen synthesis in liver. Additionally, since Glucokinase
has a high Km, its activity does not compromise the supply
of glucose to other organs; in other words, if Glucokinase
had a low Km, and since it is not inhibited by its product, it
would continue converting glucose to glucose 6 phosphate
in the liver,  making glucose unavailable for other organs
(remember that after meals, glucose arrives first to the liver
through the portal system).

The enzyme Lactate Dehydrogenase is made of two (H-
and M-)  sub units, combined in different Permutations
and 
Combinations  depending on the tissue in which it
is present as shown in table,

Type Composition Location
LDH1 HHHH Heart and Erythrocyte
LDH2 HHHM Heart and Erythrocyte
LDH3 HHMM Brain and Kidney
LDH4 HMMM Skeletal Muscle and Liver
LDH5 MMMM Skeletal Muscle and Liver
  • While isozymes may be almost identical in function
    (defined by Michaelis constant, KM)
  • they differ in amino acidsubstitutions that change the
    electric charge of the enzyme (such as replacing
    aspartic acid with glutamic acid)
  • The sum of zwitterion charges result in identifyjng
    difference inmigratiion toward the anode by gel
    electrophoresis
    , and this forms the basis for the use
    of isozymes as molecular markers.
  • To identify isozymes, a crude protein extract is made by
    grinding animal or plant tissue with an extraction buffer,
    and the components of extract are separated according
    to their charge by gel electrophoresis.
  • They were classically purified by ion-exchange column
    chromatography after first precipitation with ammonium
    sulfate, followed by dialysis.

The cytochrome P450 isozymes play important roles in
metabolism and steroidogenesis. The multiple forms of
phosphodiesterase also play major roles in various
biological processes.

These isoforms of the enzyme are unequally distributed
in the various cells of an organism.

Further the main isoenzymes may have closely grouped
“isoforms” having unclear significance.

There are many examples of isoenzymes in cell
metabolism that distinguish cells:

  • Adenylate kinase (AL in liver, and myokinase) – that
    are distinguished by reactivity with sulfhydryl reagents
  • Pyruvate kinase
  • AMPK, and Calmodulin kinase
  • Malate, isocitrate, alcohol, and aldehyde dehydrogenase
  • Nitric oxide synthase (i, e, and n)…

References[edit]

Hunter, R. L. and C.L. Markert. (1957) Histochemical
demonstration of enzymes separated by zone electrophoresis
in starch gels. Science 125: 1294-1295

Uzunov, P. and Weiss, B.(1972) “Separation of multiple
molecular forms of cyclic adenosine 3′,5′-monophosphate
phosphodiesterase in rat cerebellum by polyacrylamide
gel electrophoresis.”  Biochim. Biophys. Acta 284:220-226.

Uzunov, P., Shein, H.M. and Weiss, B.(1974) “Multiple
forms of cyclic 3′,5′-AMP phosphodiesterase
of rat cerebrum and cloned astrocytoma and
neuroblastoma cells.” Neuropharmacology 13:377-391.

Weiss, B., Fertel, R., Figlin, R. and Uzunov, P. (1974)
“Selective alteration of the activity of the multiple forms
of adenosine 3′,5′-monophosphate phosphodiesterase
of rat cerebrum.” Mol. Pharmacol.10:615-625.

Lactate dehydrogenase

In cells, the immediate energy sources involve glucose oxidation. In anaerobic metabolism, the donor of the phosphate group is adenosine triphosphate (ATP), and the reaction is catalyzed via the hexokinase or glucokinase: Glucose +ATP-Mg²+ = Glucose-6-phosphate (ΔGo = – 3.4 kcal/mol with hexokinase as the co-enzyme for the reaction.).
In the following step, the conversion of G-6-phosphate into F-1-6-bisphosphate is mediated by the enzyme phosphofructokinase with the co-factor ATP-Mg²+. This reaction has a large negative free energy difference and is irreversible under normal cellular conditions. In the second step of glycolysis, phosphoenolpyruvic acid in the presence of Mg²+ and K+ is transformed into pyruvic acid. In cancer cells or in the absence of oxygen, the transformation of pyruvic acid into lactic acid alters the process of glycolysis.
The energetic sum of anaerobic glycolysis is ΔGo = -34.64 kcal/mol. However a glucose molecule contains 686kcal/mol and, the energy difference (654.51 kcal) allows the potential for un-controlled reactions during carcinogenesis. The transfer of electrons from NADPH in each place of the conserved unit of energy transmits conformational exchanges in the mitochondrial ATPase. The reaction ADP³+ P²¯ + H²–à ATP + H2O is reversible. The terminal oxygen from ADP binds the P2¯ by forming an intermediate pentacovalent complex, resulting in the formation of ATP and H2O. This reaction requires Mg²+ and an ATP-synthetase, which is known as the H+-ATPase or the Fo-F1-ATPase complex. Intracellular calcium induces mitochondrial swelling and aging. [12].
The known marker of monitoring of treatment in cancer diseases, lactate dehydrogenase (LDH) is an enzyme that is localized to the cytosol of human cells and catalyzes the reversible reduction of pyruvate to lactate via using hydrogenated nicotinamide deaminase (NADH) as co-enzyme.
The causes of high LDH and high Mg levels in the serum include neoplastic states that promote the high production of intracellular LDH and the increased use of Mg²+ during molecular synthesis in processes pf carcinogenesis (Pyruvate acid>> LDH/NADH >>Lactate acid + NAD), [13].
LDH is released from tissues in patients with physiological or pathological conditions and is present in the serum as a tetramer that is composed of the two monomers LDH-A and LDH-B, which can be combined into 5 isoenzymes: LDH-1 (B4), LDH-2 (B3-A1), LDH-3 (B2-A2), LDH-4 (B1-A3) and LDH-5 (A4). The LDH-A gene is located on chromosome 11, whereas the LDH-B gene is located on chromosome 12. The monomers differ based on their sensitivity to allosteric modulators. They facilitate adaptive metabolism in various tissues. The LDH-4 isoform predominates in the myocardium, is inhibited by pyruvate and is guided by the anaerobic conversion to lactate.
Total LDH, which is derived from hemolytic processes, is used as a marker for monitoring the response to chemotherapy in patients with advanced neoplasm with or without metastasis. LDH levels in patients with malignant disease are increased as the result of high levels of the isoenzyme LDH-3 in patients with hematological malignant diseases and of the high level of the isoenzymes LDH-4 and LDH-5, which are increased in patients with other malignant diseases of tissues such as the liver, muscle, lungs, and conjunctive tissues. High concentrations of serum LDH damage the cell membrane [11, 31].

Relation between LDH and Mg as Factors of Interest in the Monitoring and Prognoses of Cancer

Aurelian Udristioiu, Emergency County Hospital Targu Jiu Romania, Clinical Laboratory Medical Analyses, E-mail: aurelianu2007@yahoo.com

Lactate Dehydrogenase (LDH) is ubiquitous in animals and
man, and  it occurs in different organs of the body, each
region having a unique conformation of the subunits, but
the significance was once disputed. Perhaps the experiments
of Jakob and Monod on the lac 1 operon put to rest any
notions that isoenzymes and their conformational forms are
something of no real significance.  This concept does not
necessarily apply in all cases of isoenzyme differences, by
which I mean that there may be a difference in reactivity at
the active site.

For that matter, Jakob and Monod discovered and elucidated
allosterism.

300px-Enzyme_Model  allosterism
In biochemistryallosteric regulation is the regulation of a
protein by binding an effector molecule at a site other than
the protein’s active site.

The site the effector binds to is termed the allosteric site.
Allosteric sites allow effectors to bind to the protein, often
resulting in a conformational change. Effectors that enhance
the protein’s activity are referred to as allosteric activators,
whereas  those that decrease the protein’s activity are called
allosteric inhibitors.

Allosteric regulations are a natural example of control loops,
such as feedback from downstream products or feedforward
 from upstream substrates. Long-range allostery is especially
important in cell signaling. Allosteric regulation
is also particularly important in the cell’s ability to adjust
enzyme activity.

The term allostery comes from the Greek allos (ἄλλος), “other,”
and stereos (στερεὀς), “solid (object).” This is in reference
to the fact that the regulatory site of an allosteric protein is
physically distinct from its active site.

Jacob and Monod model of transcriptional regulation of the lac operon by lac repressor

Jacob and Monod model of  lac repressor

Most allosteric effects can be explained by the concerted
MWC model put forth by Monod, Wyman, and Changeux[2]
or by the sequential model described by Koshland, Nemethy,
and Filmer.[3] Both postulate that enzyme subunits exist in
one of two conformations, tensed (T) or relaxed (R), and
that relaxed subunits bind substrate more readily than
those in the tense state. The two models differ most in
their assumptions about subunit interaction and the pre-
existence of both states.

Allosteric_Regulation Model

Allosteric_Regulation Model

  1.  Monod, J. Wyman, J.P. Changeux. (1965). On the nature of
    allosteric transitions:A plausible model. J. Mol. Biol.;12:88-118.
  2. E. Jr Koshland, G. Némethy, D. Filmer (1966). Comparison of
    experimental binding data and theoretical models in proteins
    containing subunits. Biochemistry. Jan;5(1):365-8

The sequential model (2) of allosteric regulation holds that subunits
are not connected in such a way  that a  conformational change in
one induces a similar change in the others. Thus, all enzyme
subunits do not necessitate the  same conformation. Moreover,
the sequential model dictates that molecules of substrate
bind via an
 induced fit  protocol. In general, when a subunit
randomly collides with a molecule of substrate, the active site,
in essence, forms a  glove around its substrate.

While such an induced fit converts a subunit from the tensed
state to relaxed state, it does not propagate the conformational
change to adjacent subunits. Instead, substrate-binding at
one subunit  only slightly  alters the structure of other
subunits so that their binding sites are more receptive to
substrate.
To summarize:

  • subunits need not exist in the same conformation
  • molecules of substrate bind via induced-fit protocol
  • conformational changes are not propagated to all
    subunits

The discovery of morpheeins has revealed a previously
unforeseen mechanism to target universally essential
enzymes for species-specific drug design and discovery.
A morpheein-based inhibitor would function by  binding
to and stabilizing  the inactive morpheein form of the
enzyme, thereby shifting the equilibrium to favor that form (3).

  1. K. Jaffe, S.H. Lawrence (2008). “Expanding the
    concepts in protein structure-function relationships
    and  enzyme kinetics: Teaching using morpheeins”
    .
    Biochemistry and Molecular Biology  Education36 (4)
    : 274–283. http://dx.doi.org:/10.1002/bmb.20211.
    PMC 2575429PMID 19578473

Important related points are:

Non-regulatory allostery

A non-regulatory allosteric site refers to any non-regulatory
component of an enzyme (or any protein), that is not  itself
an amino acid. For instance, many enzymes require sodium
binding to ensure proper function. However, the sodium
does not necessarily act as a regulatory subunit; the sodium
is always present and there are no known biological processes
to add/remove sodium to regulate enzyme activity. Non-
regulatory allostery could comprise any other  ions besides
sodium (calcium, magnesium, zinc), as well as other chemicals
and possibly vitamins.

Lactate and malate dehydrogenases

LDH is a key enzyme in glycolysis. Anaerobic glycolysis is the
conversion of pyruvate into lactate acid in the absence
of oxygen. This pathway is important to glycolysis in two main
ways. The first is that

  • if pyruvate were to build up glycoysis
  • the generation of ATP would slow.

The second is anaerobic respiration

  • allows for the regeneration of NAD+ from NADH.

NAD+ is required when glyceraldehyde-3-phosphate
dehydrogenase oxidizes glyceraldehyde-3-phosphate in
glycolysis, which generates NADH. Lactate dehydrogenase
is responsible for the anaerobic conversion of NADH to
NAD+. Click here to see the residues which form
inter
actions with pyruvate in the Lactate Dehydrogenase
from Cryptosporidium  parvum (2fm3). (Wikipedia)

Glycolysis ends with the synthesis of pyruvate.  But, to be
self-functioning, it must end with lactate.  Why?  Anaerobic
means “without oxygen”.  This is tantamount to saying
“without mitochondria”.

  1. The mitochondria are especially adept at oxidizing
    NADH to NAD+. NAD+ is needed to keep the glyceraldehyde-
    3-PO4 dehydrogenase reaction functioning.
  2. If glycolysis is to continue when no oxygen is present or in
    short supply (as in a working muscle), an alternative means
    of oxidizing NADH must occur.

Pyruvate has 2 metabolic fates:

  • it can either be converted into lactate or to acetyl-CoA .
    Note that in animals and plants the electrons in  NADH
    are transferred  to pyruvate which reduces the carbonyl
    carbon in the pyruvate molecule to an alcohol. The
    reaction is catalyzed by the enzyme lactate dehydrogenase.
    Lactate (or L-lactate to be more precise)  is thus  a
    “waste product”, since it has no metabolic fate other
    than to be converted back into pyruvate in a reverse of
    the  forward reaction.
  • More importantly, the NAD+ feeds back to the glyceraldehyde-
    3-PO4 dehydrogenase reaction, which  allows glycolysis
    to continue.  Were it not for lactate formation, glycolysis
    as a self-functioning pathway could not exist.

In yeast a slightly different end of glycolysis becomes apparent.
Yeast do not synthesize lactate.  They do, however, oxidize
NADH back to NAD+ anaerobically.  How do they do this?  The
answer is they make ethanol.  In the reaction the pyruvate is
converted into acetaldehyde.  The reaction is catalyzed by a
lyase enzyme, pyruvate decarboxylase, which removes the
carboxyl group as a CO2.  Acetaldehyde is formed because
the electron pair that bonds the –COO group is not removed
by the decarboxylation.  A proton is plucked from the
environment giving the final product, acetaldehyde.
Acetaldehyde is now the substrate that will oxidize NADH to
NAD+ and in the process ethanol is formed.

There is another advantage to the pyruvate-lactate interchange.
The lactate formed by lactate  dehydrogenase  can  be
reconverted. This allows a cell to synthesize glucose from lactate.
Converting lactate to glucose is a major feature of gluconeogenesis,
an anabolic pathway that synthesizes glucose from smaller
precursors such as lactate. This is important because acetyl-CoA
cannot be converted back to pyruvate and hence cannot be a
source of carbons  for glucose biosynthesis.

ADP.  ADP is required in the 3-phosphoglycerate kinase reaction
and in the pyruvate kinase reaction.  It is formed from ATP in the
hexokinase reaction and the phosphofructokinase-I reaction.

NADH, ADP and PO4.   NADH oxidation is important in glycolysis.
NADH is converted into NAD+ in the mitochondria.  That
reaction is promoted by O2 ; NAD+ stays in the mitochondria.
Also in the mitochondria, ATP is formed by condensing ADP
with PO4.  Thus, O2 allows mitochondria to out-compete the
cytosol for ADP,  NADH and PO4, all limiting  substrates or
coenzymes.

In vertebrates, gluconeogenesis takes place mainly in the liver
and, to a lesser extent, in the cortex of kidneys. In many
animals, the process occurs during periods of fasting,
starvationlow-carbohydrate diets, or intense exercise.
The process is highly endergonic until it is coupled to the
hydrolysis of ATP or GTP, effectively making the process
exergonic. For example, the pathway leading from pyruvate
to glucose-6-phosphate requires 4 molecules of  ATP and
2 molecules of GTP to proceed spontaneously. Gluco-
neogenesis is a target of therapy for type II diabetes,
such as metformin, which inhibits glucose formation
and stimulates glucose uptake by cells.

Lactate is formed at the endstage of glycolysis with insufficient
oxygen is transported to the liver where it is converted into
pyruvate by the Cori cycle using the enzyme lactate
dehydrogenase
. In this reaction lactate loses two electrons
(becomes oxidized) and is converted to pyruvate. NAD+
gains two electrons (is reduced) and is converted to NADH.

Both lactate and NAD+ bind to the active site of the enzyme
lactate dehydrogenase and both lactate and NAD+ participate
in the catalysis reaction. In fact, catalysis could not occur
unless the coenzyme NAD+ bound to the active site.

lactat-pyr.LDH

lactat-pyr.LDH

http://academic.brooklyn.cuny.edu/biology/bio4fv/page/couple.gif

What is not shown:

  1. The liver LDH is composed of predominantly M-type subunits.
  2. The forward reaction is regulated in the H-type LDH, but not
    the M-type   enzyme by the formation of a ternary complex
    of LDH-ox. NAD-lactate
  3. The formation and breakup of the ternary complex is
    dependent on the pyruvate in the forward reaction in a
    concentration dependent manner.
  4. The M-type LDH doesn’t have this tight binding of the LDH –
    NAD+ – lactate  (see catalysis below)
  5. As lactate concentration builds in the circulation from heavy
    muscle production (M-type), or from circulatory insufficiency,
    the circulating lactic acid reaches the liver.
  6. The lactic acid is taken up by the liver, and the high
    concentration of lactic acid drives the backward reaction,
    unrestricted.

Pyruvate, the first designated substrate of the gluconeogenic
pathway, can then be used to generate glucose. Transamination
or deamination of amino acids facilitates entering of their
carbon skeleton into the cycle directly  (as pyruvate or
oxaloacetate), or indirectly via the citric acid cycle.  It is
known that odd-chain fatty acids can be  oxidized to yield
propionyl-CoA, a precursor for succinyl-CoA, which can
be converted to  pyruvate and  enter  into gluconeogenesis.

gluconeogenesis

gluconeogenesis

http://upload.wikimedia.org/wikipedia/commons/thumb/6/63/Amino_acid_catabolism.svg/300px-Amino_acid_catabolism.svg.png

Catalysis

Studies have shown that the reaction mechanism of LDH follows an ordered sequence.

mechanism of LDH reaction

mechanism of LDH reaction

In the forward reaction

  1. NADH must bind to the enzyme  Several residues are
    involved in the binding of NADH
    . Once the NADH is
    bound to the enzyme,
  2. pyruvatebinds (substrate oxamate is shown; the CH3
    group is replaced by NH2 to form oxamate). (see the
    direction of the arrow)
  3. binds to the enzyme between the nicotinamide ring
    and several LDH residues.-
  4. transfer of a hydride ion then happens quickly
  5. in either direction giving a mixture of the two ternary
    complexes,
  6. enzyme-NAD+-lactate and enzyme-NADH-pyruvate .
  7. finally L-lactate dissociates from the enzyme followed
    by NAD+[2].

What is not shown is:

  1. The dissocation of NAD+ and lactate from the H-type LDHs
    is  dependent on the pyruvate  in the forward reaction in a
    concentration dependent manner
  2. This results in inhibition of the reaction as it proceeds as
    a result of the abortive ternary complex that forms in about
    500 msec carried out in the Aminco-Morrow stop flow analyzer.
  3. The regulatory effect of the tighter binding of the LDH (H)-
    NAD+-lactate is not seen with the M-type LDH.
  4. The result of this is that the H-type LDH is regulated by the
    formation of oxidized coenzyme  bound with reduced substrate.

Genetics and Mutagenesis of Fish 1973, pp 243-276.
Developmental and Biochemical Genetics of Lactate
Dehydrogenase Isozymes in Fishes
.
G. S. WhittE. T. MillerJ. B. Shaklee
 http://link.springer.com/article/10.1007%2F978-3-642-
65700-9_23/lookinside/000.png

In the teleost there are only three of the isoenzymes.  LDH-1,
3, and 5 (H4, H2M2, M4).

 teleost

Lactic dehydrogenase isozymes in lens and cornea 
Larry BernsteinMichael KerriganHarry Maisel
Experimental Eye Research Oct 1966; 5, (4): Pp 309–314, IN23–IN28
http://dx.doi.org:/10.1016/S0014-4835(66)80041-6

Lactic dehydrogenase isozymes of bovine and rabbit lens and
cornea were analyzed by starch gel electrophoresis.
Although there was a progressive loss of enzyme activity in
the lenses of both species with increasing age, the loss of
isozymes was more clearly evident in the bovine lens. In
the adult bovine lens, 

  • lactic dehydrogenase isozyme Iwas predominant,
  • while in the adult rabbit lens, isozymes 3–5were mainly present.

The mobility of lens isozymes was identical to that of isozymes
in other tissues. Furthermore, the isozymes were not  localized
to any major specific lens crystallin.

Lactate Dehydrogenase Isozyme Patterns of Human
Platelets and Bovine Lens Fibers

Elliot S. Vesell
Science 24 Dec 1965; 150(3704): pp.1735-1737   
http://dx.doi.org:/10.1126/science

Since the platelets and lens fibers, like mature human erythrocytes,
lack a nucleus, the results strengthen the case for a

  • previously developed association between LDH-5 and the
    cell nucleus.

These three cell types are mainly anaerobic, and therefore

  • their isozyme patterns are incompatible with the theory
    that anaerobic `  tissues exhibit predominantly LDH-5
    and aerobic tissues mainly LDH-1.

Lactate dehydrogenase isozymes and their relationship
to lens cell differentiation 

James A. StewartJohn Papaconstantinou
Biochimica et Biophysica Acta (BBA) – General Subjects
26 May 1966; 121,(1): Pp 69–78
http://dx.doi.org:/10.1016/0304-4165(66)90349-7

Changes in the activity of lactate dehydrogenase (LDH) (l-lactate:
NAD+ oxidoreductase EC 1.1.1.27) isozymes are associated with
the growth and differentiation of bovine lens cells. Calf and adult
lens epithelial cells contain all 5 isozymes. The cathodal forms are
most active in the calf-epithelial cells; the anodal forms are most
active in the fiber cells
. This transition from cathodal to anodal
forms of lactate dehydrogenase in the epithelial cells is associated
with cellular aging.

During the differentiation of an epithelial cell to a fiber cell, in calf
and adult lenses there is an enhancement of 

  • the transition from cathodal forms to anodal forms. 

The regulation of lactate dehydrogenase subunit synthesis may
be associated, therefore, with

  • the replicative activity of these cells.

In cells having the greatest replicative activity (calf epithelial
cells) the cathodal isozymes are most active; in cells having a
decreased mitotic activity (adult epithelial cells) the anodal
isozymes are most active. The non-replicative

  • fiber cell of calf and adult shows a transition toward the
    anodal forms.

Although lens fiber cells have a low rate of oxidative metabolism
lactate dehydrogenase-I is the most active isozyme in these
cells. Kinetically,

  • lactate dehydrogenase-I factors other than, or in addition
    to, the regulation of carbohydrate metabolism
  • are involved in regulating the synthesis of lactate dehydrogenase subunits.

Abbreviations   LDH; lactate dehydrogenase

What is not examined to resolve the discrepancy (see the next item):

The Vessell paper was a challenge to the work in Nathan
Kaplan’s lab.  However, there is sufficient complexity revealed
in these works that there is no conceptual foundation.

  1. The analogy is to the loss of cell nuclei in crystallin lens
    fiber formation with the LDH-H type subunits (aerobic?)
  2. The findings are reproduced in several laboratories.
  3. In the lens, glucose is catabolized primarily to lactic
    acid, and is not appreciably combusted to CO2
    (J Kinoshita. Glucose metabolism of Lens)
  4. However, synthetic processes, including nuclear DNA and
    cell replication requires TPNH. This is produced by means
    of the Pentose Shunt.
  5. The most favorable conditions for the lens are achieved
    by incubating in a medium containing glucose in the
    presence of oxygen. Under these conditions of
    incubation (Kinoshita)
  • the lens remains completely transparent,
  • it maintains normal levels of high energy phosphate
    bonds and cations, and
  • it shows a high rate of arginine incorporationinto protein.

incubation in the absence of glucose, but in the presence of oxygen

  • a haze is found in the lens,
  • a drop in high energy phosphate level is observed, and
  • Changes in cation levels are apparent.
  • A 50 percent decrease in the incorporation of arginine
    into lens protein is also observed.

the most unfavorable condition for the lens is an anaerobic
incubation in a medium without glucose

Pirie2 observed that a-glycerophosphate is one of the end products
of lens metabolism. Its oxidation with DPN as the cofactor could
channel its electrons directly into the ETC to produce energy without
involving the Krebs cycle. a-Glycerophosphate is formed from intermediates of the glycolytic scheme by reduction of dihydroxy-
acetone phosphate, one of the triose phosphates produced in
glycolysis.

the dehydrogenase of the mitochondria catalyzes the transfer
of elections to form DPNH by the following reactions:

a-glycerophosphate + DPN+ ± dihydroxyacetone ……..

phosphate + DPNH.

The DPNH is channeled into the oxidative phosphorylation
mechanism to form ATP. The dihydroxyacetone phosphate
then diffuses out into the soluble cytoplasm, interacts with
the glycolytic intermediates by the reversal of the above reaction,

  • and the cyclic mechanism is begunover again.

That this type of electron transport system functions in the
lens was proposed by Pirie.
http://www.iovs.org/content/4/4/619.full.pdf

Lactate dehydrogenase activity and its isoenzymes in
concentric layers of adult bovine and calf lenses.
  
Sempol DOsinaga EZigman SKorc IKorc BSans ARadi R, et al.
Curr Eye Res. 1987 Apr;6(4):555-60.

The activity of lactate dehydrogenase (LDH) and its isoenzyme
pattern were studied in four concentric layers of adult
bovine and calf lenses. In both groups the specific activity of
the total LDH diminished progressively toward the internal
nuclear layer; the decrease was greater in the adult lenses.
The enzyme activities in the cortical layers of the calf lens
were lower than in the adult lens, but in the inner nuclear layers,
the opposite was found. All of the 5 LDH isoenzymes were found
in each layer. In both groups of animals the LDH1 isoenzyme
prevailed, followed by LDH2. No differences were found in the
percentage of each isoenzyme in the different lens layers.
The differences in the activitie(s) of LDH found may be due

  • to post-translational or post-synthetic modifications which
    may occur during the aging process.

Structural basis for altered activity of M- and H-isozyme
forms of human lactate dehydrogenase.

Read JA1, Winter VJEszes CMSessions RBBrady RL.
Author information  Proteins. 2001 May 1;43(2):175-85

Lactate dehydrogenase (LDH) interconverts pyruvate and
lactate with concomitant interconversion of NADH and NAD(+).
Although crystal structures of a variety of LDH have previously
been described, a notable absence has been any of the
three known human forms of this glycolytic enzyme. We have
now determined the crystal structures of two isoforms of
human LDH-the M form, predominantly found in muscle; and
the H form, found mainly in cardiac muscle. Both structures
have been crystallized as ternary complexes in the presence
of the NADH cofactor and oxamate, a substrate-like inhibitor.

Although each of these isoforms has different kinetic properties,
the domain structure, subunit association, and active-site regions
are indistinguishable between the two structures.

The pK(a) that governs the K(M) for pyruvate for the two isozymes
is found to differ by about 0.94 pH units, consistent with variation in
pK(a) of the active-site histidine.

The close similarity of these crystal structures suggests the distinctive
activity of these enzyme isoforms is likely to result

  • directly from variation of charged surface residues peripheral to the active site,
  • a hypothesis supported by electrostatic calculations based on each structure.

Proteins 2001;43:175-185.

Mechanistic aspects of biological redox reactions involving NADH.
Part 4. Possible mechanisms and corresponding intermediates for
the catalytic reaction in L-lactate dehydrogenase

J Molec Structure: THEOCHEM,25 Feb 1993; 279, Pp 99-125
Kathryn E. Norris, Jill E. Gready

The catalytic step in the conversion of pyruvate to L-lactate in the
enzyme L-lactate dehydrogenase involves the transfer of both a
proton and a hydride ion (A.R. Clarke, T. Atkinson and J.J. Holbrook,
TIBS, 14 (1989) 101.) However, it is not known whether the
reaction is concerted or, if a multistep process, the order in
which the transfers of the proton and the hydride ions take
place. Four possible non-concerted mechanisms can be
proposed, which differ in the order of the transfers of the
proton and hydride ion and the protonation state of the substrate
carboxylate group during the transfers. The energies and
optimized geometries of the corresponding intermediates,
protonated pyruvate, protonated pyruvic acid, deprotonated
L-lactate and deprotonated L-lactic acid, are computed using
the semiempirical AM 1 and ab initio SCF/3–21 G – methods.
These calculations are complementary to the study of
the substrates for the enzyme discussed in a previous paper
(K.E. Norris and J.E. Gready, J. Mol. Struct. (Theochem),
258 (1992) 109.) The structures and energetics of protonated
pyruvate and deprotonated L-lactate provide some
important insights into the requirements for enzymic reaction
and the characteristics of the transition state.

Pyruvate production by Enterococcus casseliflavus A-12
from gluconate in an alkaline medium

J Fermentation and Bioengineering, 1992; 73(4):287-291
H Yanase, N Mori, M Masuda, K Kita, M Shimao, N Kato

A newly isolated lactic acid bacterium, Enterococcus casseliflavus
A-12, produced pyruvic acid (16 g/l) during aerobic culture in
an alkaline medium containing sodium gluconate (50 g/l) as
the carbon source. The production was dependent on the pH
of the culture, the optimum initial pH being 10.0. With static
culture, the organism produced lactic acid (2.7 g/l) from both
gluconate and glucose. Pyruvate did not accumulate in growing
cultures on glucose, but resting cells obtained from a culture
on gluconate produced pyruvate from glucose as well as
gluconate. The enzyme profiles of the organism, which
grew on gluconate and glucose, suggested that gluconate
was metabolized via the Entner-Doudoroff and Embdem-
Meyerhof-Parnas pathways in aerobic culture, and that glucose
was oxidized mainly via the latter pathway under both aerobic
and anaerobic conditions. Gluconokinase, a key enzyme in
the aerobic metabolism of gluconate, was partially purified
from this strain and characterized.

A specific, highly active malate dehydrogenase by redesign
of a lactate dehydrogenase framework

HM WilksKW HartR FeeneyCR DunnH MuirheadWN Chiaet al.

Department of Biochemistry, University of Bristol, United Kingdom.
Science 16 Dec1988: 242(4885),  pp. 1541-1544
http://dx.doi.org:/10.1126/science.3201242

 Three variations to the structure of the nicotinamide adenine
dinucleotide (NAD)-dependent L-lactate dehydrogenase
from Bacillus stearothermophilus were made to try to
change the substrate specificity from lactate to malate:
Asp197—-Asn, Thr246—-Gly, and Gln102—-Arg).

Each modification shifts the specificity from lactate to malate, although

  • only the last (Gln102—-Arg) provides an effective and
    highly specific catalyst for the new substrate.

This synthetic enzyme has a ratio of catalytic rate (kcat) to
Michaelis constant (Km) for oxaloacetate of 4.2 x 10(6)M-1 s-1,

  • equal to that of native lactate dehydrogenase for its natural
    substrate, pyruvate, and a maximum velocity (250 s-1),
    which is double that reported for a natural malate from B.
    stearothermophilus.

Malate dehydrogenase: distribution, function and properties.

Musrati RA1, Kollárová MMernik NMikulásová D.
Author information
Gen Physiol Biophys. 1998 Sep;17; (3):193-210.

Malate dehydrogenase (MDH) (EC 1.1.1.37) catalyzes the
conversion of oxaloacetate and malate. This reaction is
important in cellular metabolism, and it is coupled with
easily detectable cofactor oxidation/reduction. It is a
rather ubiquitous enzyme, for which several isoforms
have been identified, differing in their subcellular
localization and their specificity for the cofactor NAD
or NADP. The nucleotide binding characteristics can
be altered by a single amino acid change. Multiple
amino acid sequence alignments of MDH show there is a

  • low degree of primary structural similarity, apart from
    several positions crucial for catalysis, cofactor binding
    and the subunit interface.
  • Despite the low amino acids sequence identity their
    3-dimensional structures are very similar.
  • MDH is a group of multimeric enzymes consisting of
    identical subunits usually organized as either dimer
    or tetramers with subunit molecular weights of 30-35 kDa.

Malate dehydrogenase, mitochondrial (MDH2)

UniProt Number: P40926
Alternate Names: Malate DH

Structure and Function:
Malate dehydrogenase (MDH2) is an enzyme in the citric
acid cycle that catalyzes the conversion of malate into
oxaloacetate (using NAD+) and vice versa (this is a
reversible reaction). Malate dehydrogenase is also
involved in gluconeogenesis, the synthesis of glucose
from smaller molecules.Pyruvate in the mitochondria is acted upon by pyruvate
carboxylase  to form oxaloacetate, a citric acid cycle
intermediate.In order to get the oxaloacetate out of the mitochondria,
malate dehydrogenase reduces it to malate, and it then
traverses the inner mitochondrial membrane.Once in the cytosol, the malate is oxidized back to
oxaloacetate by cytosolic malate dehydrogenase.

Finally, phosphoenol-pyruvate carboxy kinase (PEPCK)
converts oxaloacetate to phosphoenol pyruvate.

Malate Dehydrogenase (MDH)(PDB entry 2x0i) is most known
for its role in the metabolic pathway of the tricarboxylic acid cycle,
critical to cellular respiration; The enzyme has other metabolic roles in –

  •  glyoxylate bypass,
  • amino acid synthesis,
  • glucogenesis, and
  • oxidation/reduction balance .

An oxidoreductase, MDH has been extensively studied due to its
isozymes The enzyme exists in two places inside a cell:

  • the mitochondria and cytoplasm.
  • In the mitochondria, the enzyme catalyzes the reaction of
    malate to oxaloacetate;
  • in the cytoplasm, the enzyme catalyzes oxaloacetate to
    malate to allow transport.

The enzyme malate dehydrogenase is composed of either
a dimer or tetramer depending on the location of the enzyme
and the organism it is located in. During catalysis, the enzyme
subunits are

  • non-cooperative between active sites.

The mitochondrial MDH is complexly,

  • allosterically controlled by citrate, but no other known
    metabolic regulation mechanisms have been discovered.
  • the exact mechanism of regulation has yet to be discovered.

Kinetically, the pH of optimization is 7.6 for oxaloacetate
conversion and 9.6 for malate conversion. The reported
K(m) value for malate conversion is 215 uM and the V(max)
value is 87.8 uM/min.

Comment:

The mMDH and the cMDH both form ternary complex
of MDH-NAD+-OAA formed during the forward reaction,
like the LDH H-type isozyme LDH-NAD+-PYR (mot the M-type).
However, the binding of the Enz-coenzyme-substrate is not
as strong as for the H-type LDH.  .The regulatory role has
not been established.

References

  1. Minarik P, Tomaskova N, Kollarova M, Antalik M. Malate
    dehydrogenases–structure and function. Gen Physiol Biophys.
    2002 Sep;21(3):257-65. PMID:12537350
  2. Musrati RA, Kollarova M, Mernik N, Mikulasova D.
    Malate dehydrogenase: distribution, function and properties.
    Gen Physiol Biophys. 1998 Sep;17(3):193-210. PMID:9834842
  3. Boernke WE, Millard CS, Stevens PW, Kakar SN, Stevens FJ,
    Donnelly MI. Stringency of substrate specificity of
    Escherichia coli malate dehydrogenase. Arch Biochem
    Biophys. 1995 Sep 10;322(1):43-52. PMID:7574693
    doi:http://dx.doi.org/10.1006/abbi.1995.1434
  4. Goward CR, Nicholls DJ. Malate dehydrogenase: a model
    for structure, evolution, and catalysis. Protein Sci. 1994
    Oct;3(10):1883-8. PMID:7849603
    doi:http://dx.doi.org/10.1002/pro.5560031027

Kinetic determination of malate dehydrogenase isozymes.

L H Bernstein, M B Grisham

Journal of Molecular and Cellular Cardiology (Impact Factor: 5.15).
11/1978; 10(10):931-44. http://dx.doi.org/10.1016/0022-2828(78)90339-5

Source: PubMed

ABSTRACT These studies determine the levels of malate
dehydrogenase isoenzymes in cardiac muscle by a steady
state kinetic method which depends on the differential inhibition
of these isoenzyme forms by high concentrations of oxaloacetate.
This inhibition is similar to that exhibited by lactate dehydrogenase
in the presence of high concentrations of pyruvate. The results
obtained by this method are comparable in resolution to those
obtained by CM-Sephadex fractionation and by differential
centrifugation for the analyses of mitochondrial malate
dehydrogenase and cytoplasmic malate dehydrogenase in
tissues. The use of standard curves of percent inhibition of
malate dehydrogenase activity plotted against the ratio of
mitochondrial MDH activity to the total of mMDH and cMDH
activities [ malate dehydrogenase ratio] (percent m-type) is
introduced for studies of comparative mitochondrial
function in heart muscle of different species or in different
tissues of the same species.

Calmodulin and Protein Kinase C Increase Ca21-stimulated
Secretion by Modulating Membrane-attached Exocytic Machinery

YA Chen, V Duvvuri, H Schulmani, and RH Scheller
Hughes Medical Institute, Department of Molecular and Cellular
Physiology, and the iDepartment of Neurobiology, Stanford
University School of Medicine, Stanford, California 94305-5135
JBC Sep 10, 1999; 274( 37): 26469–26476

Using a reconstituted [3H]norepinephrine
release assay in permeabilized PC12 cells, we
found that essential proteins that support the triggering
stage of Ca21-stimulated exocytosis are enriched in an
EGTA extract of brain membranes. Fractionation of this
extract allowed purification of two factors that stimulate
secretion in the absence of any other cytosolic proteins.
These are calmodulin and protein kinase Ca
(PKCa). Their effects on secretion were confirmed using
commercial and recombinant proteins. Calmodulin enhances
secretion in the absence of ATP, whereas PKC
requires ATP to increase secretion, suggesting that
phosphorylation is involved in PKC- but not calmodulin
mediated stimulation. Both proteins modulate release
events that occur in the triggering stage of exocytosis.

Endothelial nitric oxide synthase (eNOS) variants in
cardiovascular disease: pharmacogenomic implications  

Indian J Med Res  May 2011;  133:  464-466

Commentary

Manjula Bhanoori

Department of Biochemistry, University College of Science,
Osmania University, Hyderabad 500 007, India

 

The maintenance of regular vascular tone substantially
depends on the bioavailability of endothelium-derived
nitric oxide (NO) synthesized by eNOS. The essential
role of NO, as the elusive endothelium-derived relaxing
factor (EDRF), was the topic of research that won the
1998 Nobel Prize in Physiology or Medicine. The eNOS
gene, as a candidate gene in the investigations on
hypertension genetics, has attracted the attention of
several researchers because of the established role
of NO in vascular homeostasis. The eNOS variants
located in the 7q35-q36 region have been investigated
for their association with CVD, particularly hypertension.
Three variants, viz., (i) G894T substitution in exon 7
resulting in a Glu to Asp substitution at codon 298 (rs1799983),
(ii) an insertion-deletion in intron 4 (4a/b) consisting of two
alleles (the a*-deletion which has four tandem 27-bp repeats
and the b*-insertion having five repeats), and (iii) a T786C
substitution in the promoter region (rs2070744), have been
extensively studied20-22. Individual SNPs often cause only
a modest change in the resulting gene expression or function.
It is, therefore, the concurrent presence of a number of SNPs
or haplotypes within a defined region of the chromosome that
determines susceptibility to disease development and progression,
particularly in case of polygenic diseases.

Shankarishan et al24 analysed for the first time the prevalence
of eNOS exon 7 Glu298Asp polymorphism in tea garden community
of North Eastern India, who are a high risk group for CVD. This study
also included indigenous Assamese population and found no
significant difference between the distribution patterns of eNOS
exon 7 Glu298Asp variants between the communities. They have
rightly mentioned that for developing public health policies and
programmes it is necessary to know the prevalence and distribution
of the candidate genes in the population, as well as trends in
different population groups. They have also observed that the
eNOS exon 7 homozygous GG wild genotype (75.8%) was
predominant in the study population followed by heterozygous
GT genotype (21.5%) and homozygous TT genotype (2.7%).
The frequency distribution of the homozygous GG, heterozygous
GT and homozygous mutant TT genotypes were comparable to
that of the north Indian and south Indian population.

Polymorphisms in the endothelial nitric oxide synthase gene have
been associated inconsistently with cardiovascular diseases.
Varying distribution of eNOS variants among ethnic groups may
explain inter-ethnic differences in nitric oxide mediated vasodilation
and response to drugs28. Different population studies showed
association of eNOS polymorphisms with variations in NO
formation and response to drugs. Cardiovascular drugs including
statins increase eNOS expression and upregulate NO formation
and this effect may be responsible for protective, pleiotropic
effects produced by statins31. With respect to hypertension,
studies have reported interactions between diuretics and
polymorphisms in eNOS gene. Particularly, the Glu298Asp
polymorphism made a statistically significant contribution to
predicting blood pressure response to diuretics.

Neuronal Nitric Oxide Synthase and Its Interaction
With Soluble Guanylate Cyclase Is a Key Factor for
the Vascular Dysfunction of Experimental Sepsis

GM. Nardi, K Scheschowitsch, D Ammar, SK de
Oliveira, TB. Arruda; J Assreuy

Vascular dysfunction plays a central role in sepsis, and it is
characterized by hypotension and hyporesponsiveness to
vasoconstrictors. Nitric oxide is regarded as a central element
of sepsis vascular dysfunction. The high amounts of nitric
oxide produced during sepsis are mainly derived from the
inducible isoform of nitric oxide synthase 2.
We have previously shown that nitric oxide synthase 2 levels
decrease in later stages of sepsis, whereas levels and activity
of soluble guanylate cyclase increase. Therefore, we studied
the putative role of other relevant nitric oxide sources, namely,

  • the neuronal (nitric oxide synthase 1) isoform, in sepsis
  • and its relationship with soluble guanylate cyclase.

We also studied the consequences of

  • nitric oxide synthase 1 blockade in the hyporesponsiveness
    to vasoconstrictors.

1) Both nitric oxide synthase 1 and soluble guanylate cyclase
are expressed in higher levels in vascular tissues during sepsis;

2) both proteins physically interact and nitric oxide synthase 1
blockade inhibits cyclic guanosine monophosphate production;

3) pharmacological blockade of nitric oxide synthase 1 using
7-nitroindazole or S-methyl-l-thiocitrulline reverts the hypo
responsiveness to phenylephrine and increases the vaso
constrictor effect of norepinephrine and phenylephrine.

Sepsis induces increased expression and physical association
of nitric oxide synthase 1/soluble guanylate cyclase and a higher
production of cyclic guanosine monophosphate that together
may help explain sepsis-induced vascular dysfunction.

In addition, selective inhibition of nitric oxide synthase 1
restores the responsiveness to vasoconstrictors.

Therefore, inhibition of nitric oxide synthase 1 (and possibly
soluble guanylate cyclase) may represent a valuable
alternative to restore the effectiveness of vasopressor
agents during late sepsis.  (Crit Care Med 2014; XX:00–00)

Nitric Oxide Synthase Inhibitors That Interact with Both Heme
Propionate and Tetrahydrobiopterin Show High Isoform Selectivity

S Kang, W Tang, H Li, G Chreifi, P Martásek, LJ. Roman,
TL. Poulos, and RB. Silverman

†Department of Chemistry, Department of Molecular Biosciences,
Chemistry of Life Processes Institute, Center for Molecular Innovation
and Drug Discovery, Northwestern University, Evanston, Illinois
‡Departments of Molecular Biology and Biochemistry, Pharmaceutical
Sciences, and Chemistry, University of California, Irvine, California,
Department of Biochemistry, University of Texas Health Science Center,
San Antonio, Texas

Overproduction of NO by nNOS is implicated in the pathogenesis of
diverse neuronal disorders. Since NO signaling is involved in
diverse physiological functions, selective inhibition of nNOS
over other isoforms is essential to minimize side effects. A series of
α-amino functionalized aminopyridine derivatives (3−8) were
designed to probe the structure−activity relationship between ligand,
heme propionate, and H4B. Compound 8R was identified as the
most potent and selective molecule of this study, exhibiting a Ki of
24 nM for nNOS, with 273-fold and 2822-fold selectivity against
iNOS and eNOS, respectively.Although crystal structures of 8R
complexed with nNOS and eNOS revealed a similar binding mode,
the selectivity stems from the distinct electrostatic environments in
two isoforms that result in much lower inhibitor binding free energy
in nNOS than in eNOS. These findings provide a basis for further
development of simple, but even more selective and potent, nNOS
inhibitors

  • Aurelian Udristioiu

    Aurelian

    Aurelian Udristioiu

    Lab Director at Emergency County Hospital Targu Jiu

    In cells, the immediate energy sources involve glucose oxidation. In anaerobic metabolism, the donor of the phosphate group is adenosine triphosphate (ATP), and the reaction is catalyzed via the hexokinase or glucokinase: Glucose +ATP-Mg²+ = Glucose-6-phosphate (ΔGo = – 3.4 kcal/mol with hexokinase as the co-enzyme for the reaction.).
    In the following step, the conversion of G-6-phosphate into F-1-6-bisphosphate is mediated by the enzyme phosphofructokinase with the co-factor ATP-Mg²+. This reaction has a large negative free energy difference and is irreversible under normal cellular conditions. In the second step of glycolysis, phosphoenolpyruvic acid in the presence of Mg²+ and K+ is transformed into pyruvic acid. In cancer cells or in the absence of oxygen, the transformation of pyruvic acid into lactic acid alters the process of glycolysis.
    The energetic sum of anaerobic glycolysis is ΔGo = -34.64 kcal/mol. However a glucose molecule contains 686kcal/mol and, the energy difference (654.51 kcal) allows the potential for un-controlled reactions during carcinogenesis. The transfer of electrons from NADPH in each place of the conserved unit of energy transmits conformational exchanges in the mitochondrial ATPase. The reaction ADP³+ P²¯ + H²–à ATP + H2O is reversible. The terminal oxygen from ADP binds the P2¯ by forming an intermediate pentacovalent complex, resulting in the formation of ATP and H2O. This reaction requires Mg²+ and an ATP-synthetase, which is known as the H+-ATPase or the Fo-F1-ATPase complex. Intracellular calcium induces mitochondrial swelling and aging. [12].
    The known marker of monitoring of treatment in cancer diseases, lactate dehydrogenase (LDH) is an enzyme that is localized to the cytosol of human cells and catalyzes the reversible reduction of pyruvate to lactate via using hydrogenated nicotinamide deaminase (NADH) as co-enzyme.
    The causes of high LDH and high Mg levels in the serum include neoplastic states that promote the high production of intracellular LDH and the increased use of Mg²+ during molecular synthesis in processes pf carcinogenesis (Pyruvate acid>> LDH/NADH >>Lactate acid + NAD), [13].
    LDH is released from tissues in patients with physiological or pathological conditions and is present in the serum as a tetramer that is composed of the two monomers LDH-A and LDH-B, which can be combined into 5 isoenzymes: LDH-1 (B4), LDH-2 (B3-A1), LDH-3 (B2-A2), LDH-4 (B1-A3) and LDH-5 (A4). The LDH-A gene is located on chromosome 11, whereas the LDH-B gene is located on chromosome 12. The monomers differ based on their sensitivity to allosteric modulators. They facilitate adaptive metabolism in various tissues. The LDH-4 isoform predominates in the myocardium, is inhibited by pyruvate and is guided by the anaerobic conversion to lactate.
    Total LDH, which is derived from hemolytic processes, is used as a marker for monitoring the response to chemotherapy in patients with advanced neoplasm with or without metastasis. LDH levels in patients with malignant disease are increased as the result of high levels of the isoenzyme LDH-3 in patients with hematological malignant diseases and of the high level of the isoenzymes LDH-4 and LDH-5, which are increased in patients with other malignant diseases of tissues such as the liver, muscle, lungs, and conjunctive tissues. High concentrations of serum LDH damage the cell membrane [11, 31].

    Relation between LDH and Mg as Factors of Interest in the Monitoring and Prognoses of Cancer

    Aurelian Udristioiu, Emergency County Hospital Targu Jiu Romania, Clinical Laboratory Medical Analyses, E-mail: aurelianu2007@yahoo.com

    Larry Bernstein likes this

  • Larry Bernstein

    Larry Bernstein

    CEO/CSO at Triplex Consulting

    The inhibition be pyruvate is related by a ternary complex formed by NAD+ formed in the catalytic forward reaction Pyruvate + NADH –> Lactate + NAD(+). The reaction can be followed in an Aminco-Morrow stop-flow analyzer and occurs in ~ 500 msec. The reaction does not occur with the muscle type LDH, and it is regulatory in function. I did not know about the role of intracellular Mg(2+) in the catalysis, as my own work was in Nate Kaplan’s lab in 1970-73.

    This difference in the behavior of the isoenzyme types was considered to be important then in elucidating functional roles, but it was challenged by Vessell earlier. The isoenzymes were first described by Clement Markert at Yale. I think, but don’t know, that the Mg++ would have a role in driving the forward reaction, but I can’t conceptualize how it might have any role in the difference between muscle and heart.

    I didn’t quite know why oncologists used it specifically. Cancer cells exhibit the reliance on the anaerobic (muscle) type enzyme, which is also typical of liver, but with respect to the adenylate kinases – the liver AK and muscle AK (myokinase) are different. That difference was discovered by Masahiro Chiga, and differences in the reaction with sulfhydryl reagents were identified by Percy Russell.

    Oddly enough, Vessell had a point. The RBC has the heart type predominance, not the M-type. He thought that it was related to the loss of nuclei from the reticulocyte. I did not buy that, and I had worked on the lens of the eye at the time.

  • Aurelian Udristioiu

    Aurelian

    Aurelian Udristioiu

    Lab Director at Emergency County Hospital Targu Jiu

    Very interesting scientific comments. Thanks. !

  • Aurelian Udristioiu

    Aurelian

    Aurelian Udristioiu

    Lab Director at Emergency County Hospital Targu Jiu

    The IDH1 and IDH2 genes are mutated in > 75% of different malignant diseases. Two distinct alterations are caused by tumor-derived mutations in IDH1 or IDH2,
    IDH1 and IDH2 mutations have been observed in myeloid malignancies, including de novo and secondary AML (15%–30%), and in pre-leukemic clone malignancies, including myelodysplastic syndrome and myeloproliferative neoplasm (85% of the chronic phase and 20% of transformed cases in acute leukemia.
    Aurelian Udristioiu, M.D
    City Targu Jiu, Romania
    AACC, NACB, Member, USA.

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Buffering of genetic modules involved in tricarboxylic acid cycle metabolism provides homeomeostatic regulation

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

Leaders in Pharmaceutical Intelligence

This posting is the fifth in a series on metabolomics.  The first covered general principles.  Proteomics has not been covered and will be returned to.  But we have opened a door.  We have now looked at a comparison of two lymphocytic cell lines, and then the measurement of external effluxes to define internal metabolic conditions in yeast, with a view to delineating relationships between internal metabolic pathways and genetic variants under metabolic constraints.  These studies were confined to the experimental conditions, and could not measure metabolic fluxes, but I consider a study of the fluxes referred to in the comment by Dr. Jose Eduardo des Salles (JEDS) Roselino, who has brought up the concept, not yet specifically discussed – homeostasis.  It is part of a series of communications over several months.  

In the last article I might not have provided answers to some of the questions posed up front.  One of them refers to whether one finds a relationship to the Pasteur effect.  In both studies, leukemia cells and yeast, the cells are eukariotic, not prokaryotic, although the studies were preceded by other studies of bacteria.  It is important to remember that there are differences between prokaryotes and eukaryotes, and these studies encompassed aerobiuc and anaerobic glycolysis, mitochochondrial pathways, and cell death pathways, as well as energy balance, which involves ATP and a series of linked hydrogen transfers in the electron transport chain (ETC).  In the first two papers, we could infer the comparison between differences in oxidative phosphorylation and lactic aciid formation between two strains of cells, whether they be yeast or lymphocytic leukemia.  This is where the observation of Otto Warburg refers back to the work of Pasteur 60 years prior to his discovery.  

In this study we find that metabolic fluxes can be and are measured in Saccharomyces Cerevisiae, and the internal metabolites are measured extensively.  JEDS refers me to Schroedinger’s (Physics Nobel, Quantum Field Theory) classic work, “What is Life?” and his famous CATS, or Rabbits ( a Twilight Zone where objects can be two places at the same time: Schroedinger’s Rabbits: Colin Bruce, Joseph Henry Press, Washington, DC.) That is for another time.  I have also previously referred to the work of Ilya Prigogine (Chemistry Nobel; self organizing systems).  We can set up studies, but we cannot identify the initial state. These two major scientists understood the limits of our ability to study life.

The focus here is on homeostasis.  Homeostasis (Wikipedia), also spelled homoeostasis (from Greek: ὅμοιος, “hómoios”, “similar”,[1] and στάσις, stásis, “standing still”[2]), is the property of a system in which variables are regulated so that internal conditions remain stable and relatively constant. Examples of homeostasis include the regulation of temperature and the balance between acidity and alkalinity (pH). It is a process that maintains the stability of the human body’s internal environment in response to changes in external conditions. The concept was described by Claude Bernard in 1865.  The term was originally used to refer to processes within living organisms, it is frequently applied to automatic control systems.

Buffering of deoxyribonucleotide pool homeostasis by threonine metabolism

John L. Hartman IV *

Author Affiliations   

 Communicated by Leland H. Hartwell, Fred Hutchinson Cancer Research Center, Seattle, WA, June 4, 2007 (received for review January 21, 2007)

Synergistically interacting gene mutations reveal buffering relationships that provide growth homeostasis through their compensation of one another.

Abstract

This analysis in Saccharomyces cerevisiae revealed genetic modules involved in

  • tricarboxylic acid cycle regulation (RTG1RTG2RTG3),
  • threonine biosynthesis (HOM3HOM2HOM6THR1,THR4),
  • amino acid permease trafficking (LST4LST7), and
  • threonine catabolism (GLY1).

These modules contribute to a molecular circuit that

  • regulates threonine metabolism and
  • buffers deficiency in deoxyribonucleotide biosynthesis.

Phenotypic, genetic, and biochemical evidence for this buffering circuit was obtained

  • through analysis of deletion mutants,
  • titratable alleles of ribonucleotide reductase genes, and
  • measurements of intracellular deoxyribonucleotide pool concentrations.

This circuit provides experimental evidence, in eukaryotes, for the presence of a

  • high-flux backbone of metabolism,

which was previously predicted from 

  • in silicomodeling of global metabolism in bacteria.

This part of the high-flux backbone appears to

  • buffer deficiency in ribonucleotide reductase
  • by enabling a compensatory increase in
  • de novopurine biosynthesis
  • that provides additional rate-limiting substrates for
  • dNTP production and DNA synthesis.

Hypotheses regarding unexpected connections

  • between these metabolic pathways
  • were facilitated by genome-wide, and
  • quantitative phenotypic assessment of interactions.

Validation of these hypotheses substantiates

  • the added benefit of quantitative phenotyping
  • for identifying subtleties in gene interactionnetworks
  • that modulate cellular phenotypes.

Keywords: genetic buffering, high-flux backbone of metabolism, protein trafficking, ribonucleotide reductase, mitochondria-to-nucleus retrograde signaling pathway

Introduction 

Cells are complex genetic systems, having evolved

  • compensatory molecular networks
  • that provide growth homeostasis (robustness).

Conceptually, gene interactions

  • underlie robustness by buffering
  • environmental or genetic perturbations (13).

Synergistic effects on the phenotype resulting from

  • two genetic deficiencies or chemical inhibition
  • in combination with a genetic deficiency
  1. reveal buffering relationships
  2. when the double limitation
  3. is more severe than either single limitation.

Genome-wide phenotypic analysis,

  • as possible with RNAi or
  • use of the complete set of
    yeast gene deletion mutants,
  • has enabled new approaches
  • to investigate buffering relationships
    systematically (245).

It has been shown that

  • quantitative (strength) and
  • qualitative (pattern) aspects of
    gene interaction profiles reveal
    • how genes organize
    • in a pathway or cellular process (46).

such sets of genes represent genetic modules that

  • contribute buffering capacity to the cell,
    • providing insight into
    • how molecular circuitry

is arranged to achieve robustness (78).

Comprehensive and quantitative methods

  • for genotype–phenotype analysis are available
    • to gain a more global and precise understanding
    • of buffering networks (469).

These methods permit unbiased

  • investigation of growth homeostasis,
  • systematically revealing
    • how combinations of genetic and
    • environmental variables

result in phenotypic complexity.

High-throughput genotype–phenotype data

  • offer an opportunity to use
  • the extensive and growing genome annotations

to discover new connections between

  • previously annotated genes and pathways,
  • with respect to physiological homeostasis.

Systematic, experimentally derived understanding of

  • genetic interaction networks

will advance efforts to

  • map natural phenotypic variation,
  • thereby aiding the dissection

of genetic disease complexity (10).

This work tests a model constructed after

  • finding threonine biosynthesis
  • to play a role in
  • buffering growth inhibition with

the deoxyribonucleotide (dNTP) biosynthesis
inhibitor, hydroxyurea (HU) (4).

HU is a chemotherapy agent that

  • limits cell proliferation by inhibition of
    ribonucleotide reductase (RNR)
    • leading to dNTP pool deficiency and
    • slow DNA synthesis (11).

The results provide

  • genetic,
  • biochemical, and
  • phenotypic evidence

that growth homeostasis

  • is maintained by
  • a molecular circuit
    • that regulates threonine metabolism
    • to buffer depletion of dNTP pools.

These findings shed light on

  • systems-level observations about
  • cellular metabolism, including
    • function of a high-flux backbone of metabolism (12)
    • and gating of DNA synthesis by
      • oscillation of global transcription
      • and redox metabolism (1314).

FUNCTIONAL INTERACTIONS BETWEEN DNTP AND THREONINE METABOLISM.

This work focused on understanding genetic modules

  • found to buffer RNR deficiency (4).

Synergistic interactions between HU and

  • threonine biosynthesis genes, were uncovered ( 1a).
  • but not genes that function in the synthesis of other amino acids

Deletion ofAAT2 (aspartate aminotransferase) was also synergistic,

  • suggesting buffering by tricarboxylic acid (TCA) cycle flux
  • as AAT2converts the TCA cycle intermediate,
    • oxaloacetate è aspartate
    • the substrate for synthesis of homoserine
    • and ultimately threonine (yeastgenome.org). 

RTG1RTG2, and RTG3, transcription factors

  • regulating transcription of TCA cycle genes
  • in response to mitochondrial stress
    • were also synergistic with hydroxyurea growth limitation
  • further implicating TCA cycle involvement ( 1b).

The RTG and threonine biosynthesis modules were

  • independently confirmed to buffer HU-induced stress
    by Panet al. (17).

Synergistic interaction between HU and

  • deletion alleles ofLST4 and LST7 
  • implicated extracellular uptake of threonine
  • as an alternative mechanism
  • to augment threonine flux ( 1cand ​and22a)
    • becauseLST4 and LST7 regulate
    • delivery of amino acid permeases
      • between the vacuole and
      • plasma membrane compartments of the cell (18).

To confirm that chemical–genetic

  • interactions with HU
  • were caused by its known inhibitory effect
  • on dNTP biosynthesis,
    • a more specific method was used.

Integrating plasmids were

  • introduced into mutant strains
    • to placeRNR1 or RNR2 
  • under transcriptional control by doxycycline (19).

Deletion of homoserine or threonine biosynthesis genes

  • was found to be synergistic with
  • repression of RNR activity by
  • using doxycycline in these mutants ( 1d),
    • confirming that interactions with HU
    • were caused by its inhibitory effect on RNR.

 Media supplementation with amino acids

  • tested whether uptake of extracellular threonine
    • suppresses the growth limitation of mutations
  • in threonine biosynthesis in the presence of HU.

Threonine was found to selectively suppress

  • interaction between HU and
  • disruption of threonine biosynthesis,
  • in a concentration-dependent manner ( 2b–d).

This finding led to the prediction that

  • disabling both threonine biosynthesis and
  • threonine uptake
    • would be synergistic
  • in the presence of HU growth limitation.

 Double deletion mutants of

  • the four possible combinations of
  • thr1or thr4 and lst4 or lst7 were created.

 All combinations were synthetic lethal

  • even in the absence of HU

This is consistent with the hypothesis that lst4 and lst7 

  • compensate threonine biosynthetic deficiency
  • through regulation of extracellular uptake ( 3).

A slow-growth phenotype observed

  • for thehom6 deletion mutant
    • was exacerbated by extracellular threonine,
  • even in the absence of HU (Fig. 2b).

 The hom6deletion mutant is unique

  • among threonine biosynthesis mutants
  • in that the resulting intermediate metabolite is toxic (20)
    (aspartate β-semialdehyde)

Whether this toxicity could be related to its different phenotype

  • in the context of HU perturbation is unexplained.

BIOSYNTHESIS AND EXTRACELLULAR UPTAKE OF THREONINE CONTRIBUTE TO DNTP POOL HOMEOSTASIS.

To test the effect of threonine metabolism on dNTP pools

  • pools were measured in threonine metabolism deletion mutants
  • perturbed by doxycycline-conditional repression
    • of RNR2transcription ( 4).

Although rnr2 deletion is lethal in a haploid,

  • repression of RNR2transcription
  • only reduced the growth rate

when an otherwise non-growth-inhibitory concentration (5 mM) of HU was present (data not shown).

In contrast, RNR1repression was

  • growth-limiting without HU (see  1d) and
  • did not sensitize growth to 5 mM HU
    (data not shown).

The specificity of low-dose HU for

  • growth inhibition in combination with
  • repression of RNR2
  • is explained by the mechanism of action of HU. 

HU scavenges a tyrosyl radical

  • that is present on the Rnr2p and
  • that is required as a cofactor
  • for ribonucleotide reduction (21).

 Non-growth-inhibitory concentrations of HU

  • paradoxically induced increased steady-state
  • dNTP pool concentrations.

The increase in pools was sustained over time

  • and additive with the effect of modulating RNR
    transcriptional levels ( 4a).
  • As a result, growth inhibition,
  • caused byRNR2 repression
  • combined with low-dose HU treatment,
  • occurred with dNTP levels slightly higher than
  • those in the untreated wild-type (WT) control strain
    (endogenousRNR2 promoter).

A possible explanation is that increases in dNTP pools

  • are required for growth fitness
  • in the setting of DNA damage, which is
  • known to involve RNR regulation (22).

 Fig. 1.

HU chemical–genetic interactions. Interactions for three genetic modules are depicted.

HU chemical–genetic interactions. Interactions for three genetic modules are depicted.

HU chemical–genetic interactions. Interactions for three genetic modules are depicted.
The WT control is compared with deletion strains representative of each module,
with respect to their area under the growth curve (AUGC) vs. perturbing drug …

Fig. 2.

Extracellular threonine suppresses interactions between HU and threonine biosynthesis zpq0290770000002

Extracellular threonine suppresses interactions between HU and threonine biosynthesis.
(a) A model explaining interactions between HU and genes involved in threonine metabolism.
In the context of dNTP pool deficiency, threonine metabolism is up-regulated …

To confirm that chemical–genetic interactions with HU

  • were caused by its known inhibitory effect on dNTP biosynthesis,
  • a more specific method was used.

Integrating plasmids were introduced

  • into a variety of mutant strains to place 
  • RNR1or RNR2 under transcriptional control
    by doxycycline (19).

Deletion of homoserine or threonine biosynthesis

  • genes was found to be synergistic with
  • repression of RNR activity by using doxycycline
  • in these mutants ( 1d), confirming that
    • interactions with HU were caused by
      its inhibitory effect on RNR.

Media supplementation with amino acids was used

  • to test whether uptake of extracellular threonine
  • suppresses the growth limitation of mutations
  • in threonine biosynthesis in the presence of HU.

Threonine selectively

  • suppresses interaction between HU and
  • disruption of threonine biosynthesis,
    • in a concentration-dependent manner
      ( 2b–d).

This finding led to the prediction that disabling

  • both threonine biosynthesis and threonine uptake
  • would be synergistic with HU growth limitation.

To test this hypothesis, double deletion mutants of

  • the four possible combinations of
    • thr1or thr4 and lst4 or lst7 were created.

All combinations were synthetic lethal

  • even in the absence of HU,
  • consistent with the hypothesis that
    • lst4andlst7 compensate threonine
      biosynthetic deficiency

through regulation of extracellular uptake (Fig. 3).

A slow-growth phenotype observed for

  • the hom6deletion mutant was exacerbated
  • by extracellular threonine, even
  • in the absence of HU ( 2b).

The hom6deletion mutant is unique among

  • threonine biosynthesis mutants in that
  • the resulting intermediate metabolite is toxic (20)
    (aspartate β-semialdehyde), although
    • whether this toxicity could be related
      to its different phenotype
  • in the context of HU perturbation is unexplained.

Fig. 3.

Deficiency in amino acid permease trafficking (LST4 or LST7) is synthetic lethal with deletion of threonine biosynthesis (THR1 or THR4).

Deficiency in amino acid permease trafficking (LST4 or LST7) is synthetic lethal with deletion of threonine biosynthesis (THR1 or THR4).

Deficiency in amino acid permease trafficking (LST4 or LST7) is synthetic lethal
with deletion of threonine biosynthesis (THR1 or THR4). Interactions between
permease trafficking (LST4 and LST7) and threonine biosynthesis (THR1 and THR4)
were assessed …

BIOSYNTHESIS AND EXTRACELLULAR UPTAKE OF
THREONINE CONTRIBUTE TO DNTP POOL HOMEOSTASIS
.

To test the effect of threonine metabolism on dNTP pools,

  • pools were measured in threonine metabolism deletion mutants
  • perturbed by doxycycline-conditional repression of RNR2transcription ( 4).

Although rnr2 deletion is lethal in a haploid,

  • repression of RNR2transcription only
  • reduced the growth rate when an otherwise
    • non-growth-inhibitory concentration (5 mM)
  • of HU was present (data not shown).

In contrast, RNR1repression was

  • growth-limiting without HU (see  1d)
    • and did not sensitize growth
    • to 5 mM HU (data not shown).

The specificity of low-dose HU for growth inhibition

  • in combination with repression of RNR2
  • is explained by the mechanism of action of HU.

HU scavenges a tyrosyl radical

  • present on the Rnr2p
  • that is required as a cofactor
    • for ribonucleotide reduction (21).

Fig. 4.

Effect of threonine metabolism on dNTP pool homeostasis

Effect of threonine metabolism on dNTP pool homeostasis

Effect of threonine metabolism on dNTP pool homeostasis.
(a) Intracellular dNTP pool concentrations are depicted 90 (black)
and 360 (gray) min after exposure to the perturbations  indicated
by each block. Block 1 is the unperturbed WT (BY4741) strain in …

Non-growth-inhibitory concentrations of HU

  • paradoxically induced increased steady-state
    dNTP pool concentrations.

The increase in pools was sustained over time

  • and additive with the effect of modulating
    RNR transcriptional levels ( 4a).

As a result, growth inhibition, caused by RNR2 repression

  • combined with low-dose HU treatment, occurred
    • with dNTP levels slightly higher than those
    • in the untreated wild-type (WT) control strain
      (endogenous RNR2promoter).

A possible explanation is that increases in dNTP pools are

  • required for growth fitness in the setting of DNA damage,
  • which is known to involve RNR regulation (22).

However, production of DNA damage
(requiring increased dNTP pools for DNA repair)

  • would have been expected only at HU concentrations
  • high enough to arrest DNA synthesis in the first place (23).

The observation that low concentrations of HU

  • led to increased pools could be explained
  • if DNA damage occurs by a mechanism
    • independent of the effect of HU
    • on cytoplasmic pools.

A possible mechanism could involve

  • dNTP pool concentrations at replication forks
  • being affected differentially from
    • cytoplasmic pools;
  • this is not thought to occur
    in eukaryotic cells (24).

Thus, the paradoxical effect of

  • low HU concentrations
  • on increasing dNTP pools
  • remains unexplained.

dNTP pools were increased

  • by expression ofRNR2  from the Tet promoter
    (in the absence of repression with doxycycline),
  • presumably because of overexpression
  • relative to the endogenousRNR2 

Dox-conditional repression of RNR2 

  • reduced dNTP pools in a
  • concentration-dependent fashion ( 4a)
    • so that synergism from deletion of
      threonine metabolism genes could be tested.

The rtg2hom2thr1, and lst4 deletion mutants

  • all exacerbated the reduction in dNTP pools
    • afterRNR2 repression ( 4b).

The contribution of RTG2 for

  • dNTP pool maintenance
  • was less than that of HOM2,THR1, or LST4,
  • consistent with their effects on growth ( 1).

 Consistent with low dNTP pools

  • causing cell cycle arrest in each of the mutants,
    • median cell size increased
    • the relative number of cells and
    • total cell volume
      (median cell size × median cell volume)
    • decreased as pools became depleted ( 4c).

The scs7 (functions in sphingolipid metabolism) deletion strain

  • maintained dNTP pools comparable with WT,
  • despite a greater fitness defect ( 4b and c),
    • indicating a specific role of threonine metabolic genes
    • in homeostatic regulation of dNTP pools.

THREONINE ALDOLASE IS RATE-LIMITING FOR DNTP METABOLISM IN SACCHAROMYCES CEREVISIAE.

The genetic, phenotypic, and biochemical results

  • are consistent with a model whereby
    • TCA cycle regulation (RTG genes),
    • threonine biosynthesis (HOM and THR genes), and
    • permease trafficking (LST genes) pathways
    • coordinately buffer dNTP pool depletion by
      • up-regulating threonine metabolism.

The model postulates that threonine catabolism

  • contributes glycine to augment
  • de novopurine synthesis ( 2a).

HU has been shown to preferentially deplete

  • dATP pools in mammalian cells (2526), and
  • there was a tendency for purine pools to fluctuate
    (particularly dATP)
    • acutely whenever threonine metabolism and
    • RNR activity were perturbed in combination
      ( 4aand b).

However, allosteric regulation of RNR would

  • distribute this effect across all pools (21).

Threonine aldolase, encoded by GLY1 (EC 4.1.2.5),

  • cleaves threonine into glycine and acetaldehyde (27).

Notably, the gly1 deletion mutant exhibited slow growth
(data not shown)

  • even with glycine supplementation.

This phenotype was found to be the result of

  • limitation of dNTP metabolism.

Basal dNTP pools were reduced

  • in the gly1deletion mutant,

Pools fell dramatically

  • after treatment with 10 mM HU,

and normal homeostatic increases in dNTP concentrations

  • after treatment with 50 mM HU were delayed,
  • particularly dATP pools (Fig. 5). 

CHA1 (EC 4.2.1.13) and ILV1 (EC 4.3.1.19) are

  • deaminases that convert threonine to 2-oxybutanoate
  • or other metabolic intermediates such as
    • homoserine, cystathionine, or propionyl-CoA.

However, deletion of neither CHA1 nor ILV1 

  • modified the growth response to HU (4).

Fig. 5.

Threonine aldolase contributes to normal dNTP metabolism

Threonine aldolase contributes to normal dNTP metabolism

Threonine aldolase contributes to normal dNTP metabolism. Intracellular dNTP pools are shown for the WT control strain (BY4741) and gly1 (threonine aldolase) deletion mutant before (Left) and 120 or 360 min after perturbation with 10 mM (Center) or 50 

DISCUSSION

Computational analysis of global metabolism

  • inEscherichia coli has suggested
  • that threonine flux is of particular importance.

These studies propose that

  • threonine synthesis and
  • its degradation to glycine
    • for purine biosynthesis
  • are part of a high-flux backbone (HFB)
  • of metabolism (12).

The HFB was defined by a

  • subset of all metabolic reactions
  • found to have sufficient flux for
    • providing growth homeostasis
  • in response to growth-limiting perturbations
    (such shifting to a poor carbon source).

Utilization of threonine for buffering

  • dNTP metabolism and growth homeostasis
  • provides experimental evidence for
  • the presence of the HFB in eukaryotes.

Discovery of new connections between

  • dNTP and threonine metabolism
  1. demonstrates the value of quantitative high-throughput
    cellular phenotyping for identifying 
  2. functional redundancies in gene networks
    • by measuring interactions between
    • genetic module metabolism.

The ability to detect relatively small effects

  • of individual modules and
  • to order their relative quantitative impact
    • aided hypotheses about how
    • these modules might relate to one another (4).

By this approach, genes involved in

  1. TCA cycle regulation,
  2. threonine biosynthesis,
  3. amino acid permease trafficking,
  4. threonine catabolism, and
  5. ribonucleotide reduction
  • were found to function as a modular circuit
  • to maintain robust dNTP pools
  • for DNA synthesis
    • even though these modules
    • appear to function independently
      in other contexts (1835).

In natural (outbred) populations,

  • compensatory networks also buffer
  • genetic and chemical growth perturbations;

however, the amount of genotypic and phenotypic variation

  • renders dissection of interactions relatively intractable.

By contrast, systematic analysis of yeast deletion mutants

  • exposes interactions on a fixed genetic background
    • but does not survey natural variation.

Recently, segregants from a cross of S288C
(the background used for systematic gene deletion)

  • and a natural isolate
  • have been genotyped at high resolution (3637).

Quantitative high-throughput cellular phenotyping,

  • applied in parallel to these strains and
  • the comprehensive collection of
  • yeast gene deletion mutants, would
    • provide a dual strategy to
    • deconstruct gene networks
    • that buffer growth perturbations, by
    • systematic analysis of all deletion mutants
    • in parallel with surveying for natural occurrence.

Quantitative genetic dissection of

  • buffering networks in yeast thus
  • provides a way to model genotype–phenotype variation
  • on a genomic scale, providing insight into
    • functional interactions between conserved pathways
    • that potentially modulate human disease.

Cell Proliferation Measurements. 

Experiments represented in Figs. 1 and ​and22 were performed in Hartwell complete agar medium. High-throughput kinetic phenotyping (by imaging and image analysis) and area under the growth curve (AUGC) calculations were performed as described previously (4). AUGC encapsulates the overall growth phenotype of a strain with respect to time under a particular condition. AUGC is affected by initial population size (no. of cells transferred in a spot culture), lag time (delay before log-linear growth), maximum specific rate (actual log-linear rate), total efficiency (saturation density), and duration of the assay. For assessing the strength of a genetic interaction, the change in the AUGC conferred by a particular deletion allele relative to its WT control allele is considered with respect to perturbation intensity, e.g., concentration of HU, as depicted in Fig. 1. AUGC values for all mutants perturbed with 0, 50, and 150 mM HU are available at (http://genomebiology.com/2004/5/7/R49/additional).

dNTP Pool Sample Collections. 

Strains were grown overnight in liquid medium at 30°C to a concentration of ≈3 × 106 cells/ml and diluted to prewarmed medium with HU or doxycycline to achieve the desired cell and drug concentrations in a final volume of 30 ml. Each time point was grown separately and harvested when the cell concentration was ≈3 × 106 cells per ml. Twenty milliliters of culture was collected by vacuum filtration and immediately washed with ice-cold medium, and filters were transferred to 2 ml of ice-cold medium (dNTP concentrations remain stable in iced medium for several hours). Cells were removed from the filter by vortexing, the sample was divided in half for duplicate readings, cells were pelleted, medium removed by aspiration, and cells were lysed with 40 μl of 0.1 M perchloric acid and then snap-frozen.

Cell Volume Measurements. 

Cell volumes were measured by size analysis with a Coulter Counter (Beckman–Coulter, Fullerton, CA). The total cell volume of each culture (median cell size × total cell number) was used for calculating intracellular dNTP pool concentrations. Before vacuum filtration and lysis of each culture for mass spectrometry analysis, 200 μl was collected into 10 ml of ice-cold isoton (Beckman–Coulter). Samples were sonicated at low power to separate nonspecifically adherent cells. To calculate relative changes in total cell volume (Fig. 4c), values for each strain were first normalized against self at time zero and then divided by the corresponding normalized WT (BY4741) values.

HPLC. 

Samples were thawed by microcentrifugation (18,000 × g) for 15 min at 4°C. Sixteen microliters of lysate was added to 8 μl of 3× mobile-phase buffer [60 mM acetic acid/0.075% dimethylhydroxylamine (Sigma, St. Louis, MO)/pH adjusted to 7 with ammonium hydroxide], and 10 μl was injected onto an Agilent C-8 Zorbax column (part 883700-906) with a linear 5–30% methanol gradient from 2 to 11 min, 30–50% from 11 to 12 min, with final reequilibration for 5 min in 5% methanol (flow rate of 0.3 ml/min). Retention times of 4.5 (dTTP), 7.5 (dGTP and dTTP), and 9.5 min (dATP) were observed. dNTP-depleted lysate was obtained by lysis of saturation-density cultures after 30-min incubation in room temperature water. Dilution of standards in this lysate improved dCTP chromatography. Trace amounts of dNTPs remaining in the diluent were subtracted for standard curve calculations.

Mass Spectrometry. 

Mass spectrometry was performed with electron spray ionization in negative ion mode. Two instruments were used: (i) an Agilent 1100 MSD [dNTPs were monitored as single ions at m/z 466 (dCTP)], 481 (dTTP), 490 (dTTP), and 506 (dGTP). The drying gas was N2 at 340°C at 10 liters/min, and nebulizing pressure 25 psi (1 psi = 6.89 kPa). The fragmentor was set at 90 eV and capillary voltage 3500. (ii) An ABI API-4000 Q-trap triple quadrupole instrument was used [mass transition to a 189 fragment was monitored for each of the dNTP species, as described previously (39); N2 gas was used for nebulization, drying, and collision and the ionization chamber temperature was 250°C]. New standard curves were created for every assay.

Calculation of Intracellular dNTP Concentrations. 

Sample concentrations were determined from standard curves and adjusted to account for dilution by lysis and total cell volume [volume added for lysis + 2(tcv)] μL /tcv (μL). Standard curves showed high linear correlation (R2 > 0.998), and variation from duplicate mass spec measurements was generally <10%.

ABBREVIATIONS: AUGC, area under the growth curve; dNTP, deoxyribonucleotide; HU, hydroxyurea; RNR, ribonucleotide reductase; TCA, tricarboxylic acid..

The requirement reported here of mitochondrial-to-nucleus retrograde signaling for dNTP pool homoeostasis in yeast may be of importance to a recent report that mutations in p53R2 cause human mitochondrial depletion syndromes (MDS) (4041). If compensatory/buffering relationships between RNR and retrograde signaling in yeast are evolutionarily conserved, then genetic variation in retrograde signaling may modulate MDS disease phenotypes resulting from deficiency in p53R2 activity.

ARTICLE INFORMATION

Proc Natl Acad Sci U S A. Jul 10, 2007; 104(28): 11700–11705.

Published online Jul 2, 2007. doi:  10.1073/pnas.0705212104

PMCID: PMC1913885

Genetics

John L. Hartman, IV*

Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294

*To whom correspondence should be addressed. E-mail: ude.bau@namtrahj

Communicated by Leland H. Hartwell, Fred Hutchinson Cancer Research Center, Seattle, WA, June 4, 2007.

Author contributions: J.L.H. designed research, performed research, contributed new reagents/analytic tools,
analyzed data, and wrote the paper.

Received January 21, 2007

Buffering of deoxyribonucleotide pool homeostasis by threonine metabolism

John L. Hartman, IV

Additional article information

NOTE ADDED IN PROOF.

Note Added in Proof.

The requirement reported here of mitochondrial-to-nucleus retrograde signaling for dNTP pool homoeostasis in yeast may be of importance
to a recent report that mutations in p53R2 cause human mitochondrial depletion syndromes (MDS) (4041). If compensatory/buffering
relationships between RNR and retrograde signaling in yeast are evolutionarily conserved, then genetic variation in retrograde signaling
may modulate MDS disease phenotypes resulting from deficiency in p53R2 activity.

FOOTNOTES

The author declares no conflict of interest.

ARTICLE INFORMATION

Proc Natl Acad Sci U S A. Jul 10, 2007; 104(28): 11700–11705.

Published online Jul 2, 2007. http://dx.doi.org:/10.1073/pnas.0705212104

PMCID: PMC1913885

Genetics

John L. Hartman, IV*

Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294

*To whom correspondence should be addressed. E-mail: ude.bau@namtrahj

Communicated by Leland H. Hartwell, Fred Hutchinson Cancer Research Center, Seattle, WA, June 4, 2007.

Author contributions: J.L.H. designed research, performed research, contributed new reagents/analytic tools, analyzed data, and wrote the paper.

Received January 21, 2007  Copyright © 2007 by The National Academy of Sciences of the USA

This article has been cited by other articles in PMC.

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

 REFERENCES

  1. Hartman JL, IV, Garvik B, Hartwell L. Science. 2001;291:1001–1004. [PubMed]
  2. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, et al. Science. 2004;303:808–813. [PubMed]
  3. Lehner B, Crombie C, Tischler J, Fortunato A, Fraser AG. Nat Genet. 2006;38:896–903.[PubMed]
  4. Hartman JL, IV, Tippery NP. Genome Biol. 2004;5:R49. [PMC free article] [PubMed]
  5. Parsons AB, Brost RL, Ding H, Li Z, Zhang C, Sheikh B, Brown GW, Kane PM, Hughes TR, Boone C. Nat Biotechnol. 2004;22:62–69. [PubMed]
  6. Collins SR, Schuldiner M, Krogan NJ, Weissman JS. Genome Biol. 2006;7:R63.[PMC free article] [PubMed]
  7. Csete ME, Doyle JC. Science. 2002;295:1664–1669. [PubMed]
  8. Hartwell LH, Hopfield JJ, Leibler S, Murray AW. Nature. 1999;402:C47–C52. [PubMed]
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  12. Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL. Nature. 2004;427:839–843.[PubMed]

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Carbohydrate Metabolism

Author and Curator: Larry H. Bernstein, MD, FCAP

This is the portion of the discussion in a series of articles that began with signaling and signaling pathways. There are features on the functioning of enzymes and proteins, on sequential changes in a chain reaction, and on conformational changes that we shall return to.  These are critical to developing a more complete understanding of life processes.  I have indicated that many of the protein-protein interactions or protein-membrane interactions and associated regulatory features have been referred to previously, but the focus of the discussion or points made were different.  Even though I considered placing this after the discussion of proteins and how they play out their essential role, I needed to lay out the scope of metabolic reactions and pathways, and their complementary changes. These may not appear to be adaptive, if the circumstances and the duration is not clear. The metabolic pathways map in total is in interaction with environmental conditions – light, heat, external nutrients and minerals, and toxins – all of which give direction and strength to these reactions. I shall again take from Wikipedia, as needed, and also follow mechanisms and examples from the literature, which give insight into the developments in cell metabolism. A developing goal is to discover how views introduced by molecular biology and genomics don’t clarify functional cellular dynamics that are not related to the classical view.  The work is vast.

  1. Signaling and signaling pathways
  2. Signaling transduction tutorial.
  3. Carbohydrate metabolism
  4. Lipid metabolism
  5. Protein synthesis and degradation
  6. Subcellular structure
  7. Impairments in pathological states: endocrine disorders; stress hypermetabolism; cancer.

Carbohydrate metabolism

Carbohydrate metabolism denotes the various biochemical processes responsible for the formation, breakdown and interconversion of carbohydrates in living organisms.

The most important carbohydrate is glucose, a simple sugar (monosaccharide) that is metabolized by nearly all known organisms. Glucose and other carbohydrates are part of a wide variety of metabolic pathways across species: plants synthesize carbohydrates from carbon dioxide and water by photosynthesis storing the absorbed energy internally, often in the form of starch or lipids. Plant components are consumed by animals and fungi, and used as fuel for cellular respiration. Oxidation of one gram of carbohydrate yields approximately 4 kcal of energy and from lipids about 9 kcal. Energy obtained from metabolism (e.g. oxidation of glucose) is usually stored temporarily within cells in the form of ATP.[1] Organisms capable of aerobic respiration metabolize glucose and oxygen to release energy with carbon dioxide and water as byproducts.

Complex carbohydrates contain three or more sugar units linked in a chain, with most containing hundreds to thousands of sugar units. They are digested by enzymes to release the simple sugars.
I shall not go into the digestion, breakdown and absorption of these sugar molecules. Carbohydrates are used for short-term fuel, and the most important is glucose.  Even though they are simpler to metabolize than fats or those amino acids (components of proteins) that can be used for fuel, they do not produce as effect an energy yield measured by ATP.  In animals, The concentration of glucose in the blood is linked to the pancreatic endocrine hormone, insulin.

Carbohydrates are typically stored as long polymers of glucose molecules with glycosidic bonds for structural support (e.g. chitin, cellulose) or for energy storage (e.g. glycogen, starch). However, the strong affinity of most carbohydrates for water makes storage of large quantities of carbohydrates inefficient due to the large molecular weight of the solvated water-carbohydrate complex. In most organisms, excess carbohydrates are regularly catabolised to form acetyl-CoA, which is a feed stock for the fatty acid synthesis pathway; fatty acids, triglycerides, and other lipids are commonly used for long-term energy storage. The hydrophobic character of lipids makes them a much more compact form of energy storage than hydrophilic carbohydrates. However, animals, including humans, lack the necessary enzymatic machinery and so do not synthesize glucose from lipids, though glycerol can be converted to glucose.[6]

Metabolic pathways in eukaryotes

  • Carbon fixation, or photosynthesis, in which CO2 is reduced to carbohydrate.  [omitted]
  • Glycolysis – the metabolism of glucose molecules to obtain ATP and pyruvate[7] by way of first splitting a six-carbon into two three csrbon chains, which are converted to lactic acid from pyruvate in the lactic dehydrogenase reaction. The reverse conversion is by a separate unidirectional reaction back to pyruvate after moving through pyruvate dehydrogenase complex.[8]
  • Krebs, tricarboxylic acic, or citric acid cycle
    • Typically, a breakdown of one molecule of glucose by aerobic respiration (i.e. involving both glycolysis and Kreb’s cycle) is about 33-35 ATP.[1] This is categorized as:
  • Glycogenolysis – the breakdown of glycogen into glucose, which provides a glucose supply for glucose-dependent tissues.
    • Glycogenolysis in liver provides circulating glucose short term.
    • Glycogenolysis in muscle is obligatory for muscle contraction.
    •     Anaerobic breakdown by glycolysis – yielding 8-10 ATP
    •     Aerobic respiration by kreb’s cycle – yielding 25 ATP
  • The pentose phosphate pathway (shunt) converts hexoses into pentoses and regenerates NADPH.[9] NADPH is an essential antioxidant in cells which prevents oxidative damage and acts as precursor for production of many biomolecules.
  • Glycogenesis – the conversion of excess glucose into glycogen as a cellular storage mechanism; achieving low osmotic pressure.
  • Gluconeogenesisde novo synthesis of glucose molecules from simple organic compounds. An example in humans is the conversion of a few amino acids in cellular protein to glucose.
    Metabolic use of glucose is highly important as an energy source for muscle cells and in the brain, and red blood cells.

Glucoregulation

The hormone insulin is the primary glucose regulatory signal in animals. It mainly promotes glucose uptake by the cells,  and causes liver to store excess glucose as glycogen. Its absence turns off glucose uptake, reverses electrolyte adjustments, begins glycogen breakdown and glucose release into the circulation by some cells, begins lipid release from lipid storage cells, etc. The level of circulatory glucose (known informally as “blood sugar”) is the most important signal to the insulin-producing cells. Because the level of circulatory glucose is largely determined by the intake of dietary carbohydrates, diet controls major aspects of metabolism via insulin. In humans, insulin is made by beta cells in the pancreas, fat is stored in adipose tissue cells, and glycogen is both stored and released as needed by liver cells. Regardless of insulin levels, no glucose is released to the blood from internal glycogen stores from muscle cells.

The hormone glucagon, on the other hand, opposes that of insulin, forcing the conversion of glycogen in liver cells to glucose, and then release into the blood. Muscle cells, however, lack the ability to export glucose into the blood. The release of glucagon is precipitated by low levels of blood glucose. Other hormones, notably growth hormone, cortisol, and certain catecholamines (such as epinepherine) have glucoregulatory actions similar to glucagon.  These hormones are referred to as stress hormones because they are released under the influence of catabolic proinflammatory (stress) cytokines – interleukin-1 (IL1) and tumor necrosis factor α (TNFα).

metabolic pathways

metabolic pathways

Glycemic control in DM

Glycemic control in DM

  1. Catabolic proinflammatory cytokines. Argilés JM1López-Soriano FJ. Curr Opin Clin Nutr Metab Care.1998 May;1(3):245-51.
  2. Tumor necrosis factor as a mediator of shock, cachexia and inflammation. Cerami A. Blood Purif. 1993; 11(2):108-17.
  3. Mediators of cytokine-induced insulin resistance in obesity and other inflammatory settings. Marette A. Curr Opin Clin Nutr Metab Care. 2002 Jul; 5(4):377-83.
  4. Inflammation: the link between insulin resistance, obesity and diabetes. Dandona P, Aljada A, Bandyopadhyay A. Trends Immunol. 2004 Jan; 25(1):4-7
  5. Proinflammatory cytokines and skeletal muscle. Späte U1, Schulze PC. Curr Opin Clin Nutr Metab Care. 2004 May;7(3):265-9.
  6. Insulin-like growth factor-1 and muscle wasting in chronic heart failure. Schulze PC, Späte U. Int J Biochem Cell Biol. 2005 Oct; 37(10):2023-35.
  7. IGF-I stimulates muscle growth by suppressing protein breakdown and expression of atrophy-related ubiquitin ligases, atrogin-1 and MuRF1. Sacheck JM, Ohtsuka A, McLary SC, Goldberg AL. Am J Physiol Endocrinol Metab. 2004 Oct; 287(4):E591-601. Epub 2004 Apr 20.

Glycolysis – Animation and Notes

By Sweety Mehta – Sept 20, 2011  in: Animations, Biochemistry Animations, Biochemistry Notes

http://pharmaxchange.info/press/2011/09/glycolysis-animation-and-notes/

Cellular respiration involves breaking the bonds of glucose to produce energy in the form of ATP (adenosine triphosphate). The total energy produced during glucose metabolism is described at Energetics of Cellular Respiration. Glycolysis is the most critical phase in glucose metabolism during cellular respiration. The term “glycolysis” literally means breakdown of glucose and sugars. Biochemically, it involves the breakdown of glucose to pyruvate (or pyruvic acid) via a series of enzymes. Glycolysis does not require molecular oxygen and is hence considered anaerobic. Therefore, it is a common pathway for all living organisms.

Glycolysis is followed by

Kreb’s cycle in the stages of cellular respiration.

Glycolysis is said to occur in two phases:

  1. The Preparatory Phase: From glucose till formation of Glyceraldehyde 3-Phosphate (GADP)
  2. The Pay-off Phase: From Glyceraldehyde-3-Phosphate (GADP) to the final product pyruvate

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glycolysis

The animation below gives an outline of the entire pathway of glucose metabolism by glycolysis

Note – The animation is best played in full screen. To go forward in the animation, press the Play button. To skip the whole section press the forward button. To go back press the rewind button.

The Preparatory Phase

In this stage of the cycle, ATP or energy is actually consumed and is hence also known as the investment phase of glycolysis.

Step 1, involves the conversion of glucose to glucose-6-phosphate (G6P) with the help of the enzyme hexokinase and the consumption of 1 molecule of ATP. This reaction helps keep the concentration of glucose low in the cell, allowing for more absorption of glucose into it. Additionally, G6P is not transported out of the cell as there are no G6P transporters on the cell.

Step 2 involves the rearrangement of glucose-6-phosphate to fructose-6-phosphate (F6P) with the help of the enzyme phosphohexose isomerase in a reversible manner. Fructose can directly enter the glycolysis pathway at this point. This isomerization to a keto-sugar such as fructose is essential for carbanion stabilization required for the next step.

Step 3 involves the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate (F1,6BP) by the use of 1 molecule of ATP and the enzyme phosphofructokinase-1 (PPK1). This phosphorylation step destabilizes the molecule and helps drive the next reaction which ensures breakdown of the molecule to a 3-carbon unit.

Step 4 involves the breakdown of fructose-1,6-biphosphate (6 carbons) to two molecules of 3-carbon units i.e. glyceralde 3-phosphate (GADP) and Dihydroxyacetone phosphate (DHAP). The GADP can be interconverted to DHAP by enzyme triose phosphate isomerase.

The Pay-Off Phase

In this stage of the cycle, ATP or energy is produced either in the form of ATP alone or in the form of NADH + H+ which can be later converted to ATP via the electron transport chain (ETS). In this since energy is restored it is known as the pay-off phase of glycolysis. All steps in this phase occur with 2 molecules of the substrates each as indicated in the brackets by the name of the molecules.

Step 1, involves the dehydrogenation of glyceraldehyde-3-phosphate (GADP) to 1,3-biphophoglycerate (1,3BPG) by the use of 2 molecules of inorganic phosphate (Pi) with the production of 2 molecules of NADH + H+ in the presence of the enzyme glyceraldehyde 3-phosphate dehydrogenase.

Step 2, in this step dephosphorylation of 1,3-biphosphoglycerate (1,3BPG) to 3-phospoglycerate (3PG) produces 2 molecules of ATP by the enzyme phosphoglycerate kinase.

Step 3, involves the isomerisation of 3-phosphoglycerate (3PG) to 2-phosphoglycerate (2PG) by the enzyme phosphoglycerate mutase in a reversible manner.

Step 4 involves the enolization of 2-phosphoglycerate (2PG) to phosphoenolpyruvate (PEP) with the loss of one molecule of water in the presence of enzyme enolase.

Step 5 is the final step of the glycolysis pathway and it involves the dephosphorylation of the phosphoenolpyruvate (PEP) to pyruvate by enzyme pyruvate kinase to produce 2 more molecules of ATP.

Net Yield of Glycolysis

  1. The preparatory phase consumes 2 ATP
  2. The pay-off phase produces 4 ATP.
  3. The gross yield of glycolysis is therefore
    4 ATP – 2 ATP = 2 ATP
  4. The pay-off phase also produces 2 molecules of NADH + H+ which can be further converted to a total of 5 molecules of ATP* by the electron transport chain (ETC) during oxidative phosphorylation.
  5. Thus the net yield during glycolysis is 7 molecules of ATP.

* This is calculated assuming one NADH molecule gives 2.5 molecules of ATP during oxidative phosphorylation.

References

  1. David L. Nelson and Michael M. Cox, Lehninger Principles of Biochemistry, 4th Ed.
  2. Jeremy M. Berg, John L. Tymockzo and Luber Stryer, Biochemistry, 7th Ed.

Tags: cellular respiration, electron transport chain, etc, glucose, glycolysis, metabolism, pay-off phase

Kreb’s Cycle or Citric Acid Cycle or Tricarboxylic Acid Cycle (with Animation)

By Sweety Mehta  – Sept 21, 2013  in: Animations, Biochemistry Animations, Biochemistry Notes
http://pharmaxchange.info/press/2013/09/krebs-cycle-citric-acid-cycle-tricarboxylic-acid-cycle-animation/

Introduction

Cellular respiration involves 3 stages for the breakdown of glucose – glycolysis, Kreb’s cycle and the electron transport system. The total energy produced during glucose metabolism is described at Energetics of Cellular Respiration. We have seen the glycolysis pathway with animation previously. The Kreb’s cycle is named after Adolf Krebs who studied the utilization of oxygen in a pigeon. It is also commonly known as the citric acid cycle or the tricarboxylic acid cycle. Kreb’s cycle is a very important step in the metabolic pathway as it produces about 60-70% of ATP for release of energy in the body. It directly or indirectly connects with all the other individual pathways in the body too. It takes place in the mitochondria as all the enzymes and co-enzymes required are present there.

The Kreb’s Cycle occurs in two stages:

1. Conversion of Pyruvate to Acetyl CoA

Glycolysis of 1 molecule of glucose produces 2 molecules of pyruvate. Each pyruvate in the presence of pyruvate dehydrogenase (PDH) complex in the mitochondria gets converted to acetyl CoA which in turn enters the Kreb’s cycle. This reaction is called as oxidative  decarboxylation as the carboxyl group is removed from the pyruvate molecule in the form of CO2 thus yielding 2-carbon acetyl group which along with the coenzyme A forms acetyl CoA.

The pyruvate dehydrogenase complex (PDH) comprises of three enzymes – pyruvate dehydrogenase, dihydrolipoyl transacetylase and dihydrolipoyl dehydrogenase each one playing an important role in the reaction as shown below. The PDH requires the sequential action of five co-factors or co-enzymes for the combined action of dehydrogenation and decarboxylation to take place. These five are TPP (thiamine phosphate), FAD (flavin adenine dinucleotide), NAD (nicotinamide adenine dinucleotide), coenzyme A (denoted as CoA-SH at times to depict role of -SH group) and lipoamide.

Conversion of pyruvate to acetyl CoA by the pyruvate dehydrogenase complex

pyruvate_dehydrogenase_complex_new2

Conversion of pyruvate to acetyl CoA by the pyruvate dehydrogenase complex

Pyruvate reacts with the TPP (Thiamine Phosphate) bound part of pyruvate dehydrogenase and undergoes decarboxylation to give hydroxyethyl-TPP.

This hydroxyethyl-TPP in turn gets oxidised to acetyl lipoamide by the same enzyme pyruvate dehydrogenase by the transfer of two electrons. These electrons then reduce the disulfide bond of the enzyme dihydrolipoyl transacetylase with the transfer of the acetyl group as highlighted in purple.

Dihydrolipoyl transacetylase catalyses the transesterification forming acetyl CoA by transfer of acetyl group to coenzyme A.

When acetyl CoA is being formed, at the same time reduced lipoamide is getting converted to oxidised lipoamide due to enzyme dihydrolipoyl dehydrogenase by the transfer of 2 hydrogen atoms to FAD.

Dihydrolipoyl dehydrogenase transfers the reduced equivalents (2 hydrogen atoms) to FAD thus forming FADH2. FADH2 in turn transfers a hydride ion to NAD+ to form NADH+H+.

2. Acetyl CoA Enters the Kreb’s Cycle

The acetyl CoA produced from the pyruvate dehydrogenase complex enters the Kreb’s cycle.

The animation below describes the Kreb’s cycle in detail followed by the discussion. A static image of the cycle can be found next to the discussion for reference. Press the play button to progress in the animation.

Discussion

Krebs1 cycle

The Kreb’s Cycle or Citric Acid Cycle or Tricarboxylic Acid Cycle in a static image version of the animation.

Acetyl CoA condenses with oxaloacetate (4C) to form a citrate (6C) by transferring its acetyl group in the presence of enzyme citrate synthase. The CoA liberated in this reaction is ready to participate in the oxidative decarboxylation of another molecule of pyruvate by PDH complex.

  • Citrate is then isomerised to Isocitrate by the enzyme aconitase through the formation of the intermediate cis-aconitate. This is a reversible reaction as aconitase has an iron-sulfur center which can promote reversible addition of H2O to the double bond of enzyme-bound cis-aconitate in 2 different ways, one forming citrate and the other isocitrate.
  • Isocitrate undergoes oxidative decarboxylation by the enzyme isocitrate dehydrogenase to form oxalosuccinate (intermediate- not shown) which in turn forms α-ketoglutarate (also known as oxoglutarate) which is a five carbon compound. CO2 and NADH are released in this step.
  • α-ketoglutarate (5C) undergoes oxidative decarboxylation once again to form succinyl CoA (4C) catalysed by the enzyme α-ketoglutarate dehydrogenase complex. α-ketoglutarate dehydrogenase complex is similar to PDH complex and is made up of 3 enzymes and is dependent on five co-enzymes TPP, FAD, NAD, bound lipoate and conenzyme A. In this step once again NADH and CO2 are liberated. So in all 2 molecules of NADH and 2 molecules of CO2 is produced till now.
  • Succinyl CoA is then converted to succinate by succinate thiokinase or succinyl coA synthetase in a reversible manner. This reaction involves an intermediate step in which the enzyme gets phosphorylated and then the phosphoryl group which has a high group transfer potential is transferred to GDP to form GTP. This GTP is converted to ATP by the enzyme nucleoside diphosphate kinase by donating its phosphoryl group to ADP. This reaction which involves the formation of GTP is a substrate level phosphorylation as it happens by using the energy formed by the oxidative decarboxylation of α-ketoglutarate.
  • Succinate then gets oxidised reversibly to fumarate by succinate dehydrogenase. The enzyme contains iron-sulfur clusters and covalently bound FAD which when undergoes electron exchange in the mitochondria causes the production of FADH2.
  • Fumarate is then by the enzyme fumarase converted to malate by hydration(addition of H2O) in a reversible manner.
  • Malate is then reversibly converted to oxaloacetate by malate dehydrogenase which is NAD linked and thus produces NADH.
  • The oxaloacetate produced is now ready to be utilized in the next cycle by the citrate synthase reaction and thus the equilibrium of the cycle shifts to the right.
Schrodingers_cat

Schrodingers_cat

Energetics of the Kreb’s Cycle

Keeping in mind that 1 molecule of glucose would produce 2 molecules of pyruvate via glycolysis. Hence the net energy produced by the Kreb’s cycle for each molecule of pyruvate is doubled for each molecule of glucose. Thus net energy yield in Kreb’s cycle can be summarized as follows for each molecule of glucose:

Reaction                                                              Number of ATP or                                        Number of ATP
reduced coenzyme formed                        ultimately formed

2 Pyruvate → 2 acetyl CoA                                  2 NADH                                                             5

2 Isocitrate → 2 α- ketoglutarate                     2 NADH                                                              5

2 α- ketoglutarate → 2 succinyl CoA             2 NADH                                                               5

2 Succinyl CoA → 2 succinate                           2 ATP                                                                  2

2 Succinate → 2 fumarate                               2 FADH2                                                               3

2 Malate → 2 oxaloacetate                            2 NADH                                                                  5

TOTAL                                                                                                                                                 25 ATP

* Note- This is calculated as 2.5 ATP per NADH and 1.5 ATP per FADH2. This is because there are multiple electron transport shuttle pathways through which these can be broken to ATP.

Regulation of Kreb’s Cycle

The amount of ADP and ATP largely control the citric acid cycle along with the activity of three key enzymes within the cycle:

Availability of ADP: ADP is a key substrate which finally gets converted to ATP that is essential for the energetics of the cell. A drop in ADP levels would result in inhibition of the electron transport system leading to accumulation of NADH and FADH2. These in turn inhibit the enzymes below.

Citrate Synthase: inhibited by ATP, acetyl CoA, NADH, and succinyl CoA.
Isocitrate Dehydrogenase: activated by ADP, and inhibited by NADH and ATP.
α-ketoglutarate dehydrogenase: inhibited by NADH and succinyl CoA.

Recommended Texts

David L. Nelson and Michael M. Cox, Lehninger Principles of Biochemistry 6th Edition
Jeremy M. Berg, John L. Tymockzo and Luber Stryer, Biochemistry 7th Edition

Tags: acetyl coA, animation, cellular respiration, citric acid cycle, energy, kreb’s cycle, pyruvate, pyruvate dehydrogenase, TCA cycle, tricarboxylic acid cycle

Energetics of Cellular Respiration (Glucose Metabolism)

By Sweety Mehta   – Oct 9, 2013 in: Biochemistry Notes, Notes
http://pharmaxchange.info/press/2013/10/energetics-of-cellular-respiration-glucose-metabolism/

energetics-of-cellular-respiration

electron transport chain in the mitochondrion energetics-of-cellular-respiration

Important Note: The NADH formed in the cytosol can yield variable amounts of ATP depending on the shuttle system utilized to transport them into the mitochondrial matrix. This NADH, formed in the cytosol, is impermeable to the mitochondrial inner-membrane where oxidative phosphorylation takes place. Thus to carry this NADH to the mitochondrial matrix there are special shuttle systems in the body. The most active shuttle is the malate-aspartate shuttle via which 2.5 molecules of ATP are generated for 1 NADH molecule. This shuttle is mainly used by the heart, liver and kidneys. The brain and skeletal muscles use the other shuttle known as glycerol 3-phosphate shuttle which synthesizes 1.5 molecules of ATP for 1 NADH.

Note: The above calculations are done considering that one NADH molecules produces 2.5 ATP and one FADH2 molecule produces 1.5 ATP in the ETS cycle (See full reasoning above). This is because the Kreb’s cycle occurs within the mitochondria and therefore does not require any shuttle pathway for the transport of the NADH into the mitochondrial matrix. Hence there is optimal conversion of NADH to ATP.

Development of the acetylation problem: a personal account

FRITZ LI P M A N N  Nobel Prize  1953

After my  apprenticeship with Otto Meyerhof, a first interest on my own became the phenomenon we call the Pasteur effect, this peculiar depression of the wasteful fermentation in the respiring cell. By looking for a chemical explanation of this economy measure on the cellular level, I was prompted into a study of the mechanism of pyruvic acid oxidation, since it is at the pyruvic stage where respiration branches off from fermentation. For this study I chose as a  promising system a relatively simple looking pyruvic acid oxidation enzyme in a certain strain of Lactobacillus delbrueckii1.

The most important event during this whole period, I now feel, was the accidental observation that in the L. delbrueckii system, pyruvic acid oxidation was completely dependent on the presence of inorganic phosphate. This observation was made in the course of attempts to replace oxygen by methylene blue. To measure the methylene blue reduction manometrically,
I had to switch to a bicarbonate buffer instead of the otherwise routinely used In bicarbonate, to my surprise, as shown in Fig. 1, pyruvate oxidation was very slow, but the addition of a little phosphate caused a remarkable increase in rate. The next figure, Fig. 2, shows the phosphate effect more drastically, using a preparation from which all phosphate was removed by washing with acetate buffer. Then it appeared that the reaction was really fully dependent on phosphate.

In spite of such a phosphate dependence, the phosphate balance measured by the ordinary Fiske-Subbarow procedure did not at first indicate any phosphorylative step. Nevertheless, the suspicion remained that phosphate in  some manner was entering into the reaction and that a phosphorylated intermediary was formed. As a first approximation, a coupling of this pyruvate oxidation with adenylic acid phosphorylation was attempted. And,indeed, addition of adenylic acid to the pyruvic oxidation system brought out a net  disappearance of inorganic phosphate, accounted for as adenosine triphosphate (Table 11).

I  now concluded that the missing link in the reaction chain was acetyl phosphate. In partial confirmation it was shown that a crude preparation of acetyl phosphate, synthesized by the old method of Kämmerer and Carius 2 would transfer phosphate to adenylic acid (Table 2). However, it still took quite some time from then on to identify acetyl phosphate definitely as the initial product of the pyruvic oxidation in this system3,4

At the time when these observations were made, about a dozen years ago,there was, to say the least, a tendency to believe that phosphorylation was rather specifically coupled with the glycolytic reaction. Here, however, we had found a coupling of phosphorylation with a respiratory system. This observation immediately suggested a rather sweeping biochemical significance, of transformations of electron transfer potential, respiratory or fermentative, to phosphate bond energy and therefrom to a wide range of biosynthetic reactions7.

There was a further unusual feature in this pyruvate oxidation system in that the product emerging from the process not only carried an energy-rich phosphoryl radical such as already known, but the acetyl phosphate was even more impressive through its energy-rich acetyl. It rather naturally became a contender for the role of “active” acetate, for the widespread existence of which the isotope experience had already furnished extensive evidence. I became, therefore, quite attracted by the possibility that acetyl phosphate could serve two rather different purposes, either to transfer its phosphoryl group into the phosphate pool, or to supply its active acetyl for biosynthesisof carbon structures. Thus acetyl phosphate should be able to serve as acetyldonor as well as phosphoryl donor, transferring, as shown in Fig. 3, on either side of the oxygen center, such as indicated by Bentley’s early experiments on cleavage7a of acetyl phosphate in H218O.

Phosphate dependence of pyruvate oxidation

Phosphate dependence of pyruvate oxidation

These two novel aspects of the energy problem, namely

(1) the emergence of an energy-rich phosphate bond from a purely
respiratory reaction; and

(2) the presumed derivation of a metabolic building-block through this same
reaction, prompted me to propose not only

  • the generalization of the phosphate bond as a versatie energy distributing system, but also to
    aim from there towards
  • a general concept of transfer of activated groupings by carrier as the fundamental reaction in
    biosynthesis8,9.

Although in the related manner the appearance of acetyl phosphate as a
metabolic intermediary first

  •  focused attention to possible mechanisms for the metabolic elaboration of  group activation,

it soon turned out that the relationship between acetyl phosphate and
acetyl transfer was much more complicated than anticipated.

Acetyl phosphate as acetyl and phosphoryl donor.

Although acetylation was found with rabbit liver homogenate, the
reaction was rather weak. In search of a more active system,   Pigeon
liver homogenate was tried and found to harbour an exceedingly potent
acetylation system (Ref. 11, cf. also Ref. 12). This finding of a particularly
active acetylation reaction in cell-free pigeon liver preparations was most
fortunate and played a quite important part in the development of the
acetylation problem.

[portion of lecture]

The pentose phosphate pathway is the major source for the NADPH
required for anabolic processes.
Pentose Phosphate Pathway

http://chemwiki.ucdavis.edu/Biological_Chemistry/Metabolism/Pentose_
Phosphate_Pathway

  • There are three distinct phases each of which has a distinct outcome.
  • Depending on the needs of the organism the metabolites of that outcome
    can be fed into many other pathways.
  • Gluconeogenesis is directly connected to the pentose phosphate pathway.
  • As the need for glucose-6-phosphate (the beginning metabolite in the pentose
    phosphate pathway) increases so does the activity of gluconeogenesis.

 pentose-phosphate-pathway

http://images.tutorvista.com/content/respiration/pentose-phosphate-pathway.jpeg

Introduction

The main molecule in the body that makes anabolic processes possible is NADPH.  Because of the structure of this molecule it readily donates hydrogen ions to metabolites thus reducing them and making them available for energy harvest at a later time. The PPP is the main source of synthesis for NADPH.  The pentose phosphate pathway (PPP) is also responsible for the production of Ribose-5-phosphate which is an important part of nucleic acids. Finally the PPP can also be used to produce glyceraldehyde-3-phosphate which can then be fed into the TCA and ETC cycles allowing for the harvest of energy. Depending on the needs of the cell certain enzymes can be regulated and thus increasing or decreasing the production of desired metabolites. The enzymes reasonable for catalyzing the steps of the PPP are found most abundantly in the liver (the major site of gluconeogenesis) more specifically in the cytosol. The cytosol is where fatty acid synthesis takes place which is a NADPH dependent process.

 

Oxidation Phase

  • The beginning molecule for the PPP is glucose-6-P which is the second intermediate metabolite in glycolysis. Glucose-6-P is oxidized in the presence of glucose-6-P dehydrogenase and NADP+.  This step is irreversible and is highly regulated.  NADPH and fatty acyl-CoA are strong negative inhibitors to this enzyme.  The purpose of this is to decrease production of NADPH when concentrations are high or the synthesis of fatty acids is no longer necessary.
  • The metabolic product of this step is gluconolactone which is hydrolytrically unstable.  Gluconolactonase causes gluconolactone to undergo a ring opening hydrolysis.  The product of this reaction is the more stable sugar acid, 6-phospho-D-gluconate.
  • 6-phospho-D-gluconate is oxidized by NADP+ in the presence of 6-phosphogluconate dehydrogenase which yields ribulose-5-phosphate.
  • The oxidation phase of the PPP is solely responsible for the production of the NADPH to be used in anabolic processes.

Isomerization Phase

  •  Ribulose-5-phosphate can then be isomerized by phosphopentose isomerase to produce ribose-5-phosphate.  Ribose-5-phosphate is one of the main building blocks of nucleic acids and the PPP is the primary source of production of ribose-5-phosphate.
  • If production of ribose-5-phosphate exceeds the needs of required ribose-5-phosphate in the organism, then phosphopentose epimerase catalyzes a chiralty rearrangement about the center carbon creating xylulose-5-phosphate.
  • The products of these two reactions can then be rearranged to produce many different length carbon chains.  These different length carbon chains have a variety of metabolic fates.

Rearrangement Phase 

  •  There are two main classes of enzymes responsible for the rearrangement and synthesis of the different length carbon chain molecules.  These are transketolase and transaldolase.
  • Transketolase is responsible for the cleaving of a two carbon unit from xylulose-5-P and adding that two carbon unit to ribose-5-P thus resulting in glyceraldehyde-3-P and sedoheptulose-7-P.
  • Transketolase is also responsible for the cleaving of a two carbon unit from xylulose-5-P and adding that two carbon unit to erythrose-4-P resulting in glyceraldehyde-3-P and fructose-6-P.
  • Transaldolase is responsible for cleaving the three carbon unit from sedoheptulose-7-P and adding that three carbon unit to glyceraldehyde-3-P thus resulting in erythrose-4-P and fructose-6-P.
  • The end results of the rearrangement phase is a variety of different length sugars which can be fed into many other metabolic processes.  For example, fructose-6-P is a key intermediate of glycolysis as well as glyceraldehyde-3-P.

References

  1. Garrett, H., Reginald and Charles Grisham. Biochemistry. Boston: Twayne Publishers, 2008.
  2. Raven, Peter. Biology. Boston: Twayne Publishers, 2005.

Glycogen Metabolism

Glycogen is a readily mobilized storage form of glucose. It is a very large, branched polymer of glucose residues (Figure 21.1) that can be broken down to yield glucose molecules when energy is needed. Most of the glucose residues in glycogen are linked by α-1,4-glycosidic bonds. Branches at about every tenth residue are created by α-1,6-glycosidic bonds. Recall that α-glycosidic linkages form open helical polymers, whereas β linkages produce nearly straight strands that form structural fibrils, as in cellulose (Section 11.2.3).

http://www.ncbi.nlm.nih.gov/books/NBK21190/bin/ch21f1.jpg

Figure 21.1

Glycogen Structure ch21f1

Glycogen Structure. In this structure of two outer branches of a glycogen molecule, the residues at the nonreducing ends are shown in red and residue that starts a branch is shown in green. The rest of the glycogen molecule is represented by R.

Glycogen is not as reduced as fatty acids are and consequently not as energy rich. Why do animals store any energy as glycogen? Why not convert all excess fuel into fatty acids? Glycogen is an important fuel reserve for several reasons. The controlled breakdown of glycogen and release of glucose increase the amount of glucose that is available between meals. Hence, glycogen serves as a buffer to maintain blood-glucose levels. Glycogen’s role in maintaining blood-glucose levels is especially important because glucose is virtually the only fuel used by the brain, except during prolonged starvation. Moreover, the glucose from glycogen is readily mobilized and is therefore a good source of energy for sudden, strenuous activity. Unlike fatty acids, the released glucose can provide energy in the absence of oxygen and can thus supply energy for anaerobic activity.

Gluconeogenesis
ChemWiki: The Dynamic Chemistry E-textbook > Biological Chemistry > Metabolism > Gluconeogenesis

Gluconeogenesis is much like glycolysis only the process occurs in reverse. However, there are exceptions. In glycolysis there are three highly exergonic steps (steps 1,3,10). These are also regulatory steps which include the enzymes hexokinase, phosphofructokinase, and pyruvate kinase. Biological reactions can occur in both the forward and reverse direction. If the reaction occurs in the reverse direction the energy normally released in that reaction is now required. If gluconeogenesis were to simply occur in reverse the reaction would require too much energy to be profitable to that particular organism. In order to overcome this problem, nature has evolved three other enzymes to replace the glycolysis enzymes hexokinase, phosphofructokinase, and pyruvate kinase when going through the process of gluconeogenesis:

  1. The first step in gluconeogenesis is the conversion of pyruvate to phosphoenolpyruvic acid (PEP). In order to convert pyruvate to PEP there are several steps and several enzymes required. Pyruvate carboxylase, PEP carboxykinase and malate dehydrogenase are the three enzymes responsible for this conversion. Pyruvate carboxylase is found on the mitochondria and converts pyruvate into oxaloacetate. Because oxaloacetate cannot pass through the mitochondria membranes it must be first converted into malate by malate dehydrogenase. Malate can then cross the mitochondria membrane into the cytoplasm where it is then converted back into oxaloacetate with another malate dehydrogenase. Lastly, oxaloacetate is converted into PEP via PEP carboxykinase. The next several steps are exactly the same as glycolysis only the process is in reverse.
  2. The second step that differs from glycolysis is the conversion of fructose-1,6-bP to fructose-6-P with the use of the enzyme fructose-1,6-phosphatase. The conversion of fructose-6-P to glucose-6-P uses the same enzyme as glycolysis, phosphoglucoisomerase.
  3. The last step that differs from glycolysis is the conversion of glucose-6-P to glucose with the enzyme glucose-6-phosphatase. This enzyme is located in the endoplasmic reticulum.

Glycolysis

File:Glycolysis overview.svg

Regulation

Because it is important for organisms to conserve energy, they have derived ways to regulate those metabolic pathways that require and release the most energy. In glycolysis and gluconeogenesis seven of the ten steps occur at or near equilibrium. In gluconeogenesis the conversion of pyruvate to PEP, the conversion of fructose-1,6-bP, and the conversion of glucose-6-P to glucose all occur very spontaneously which is why these processes are highly regulated. It is important for the organism to conserve as much energy as possible. When there is an excess of energy available, gluconeogenesis is inhibited. When energy is required, gluconeogenesis is activated.

  1. The conversion of pyruvate to PEP is regulated by acetyl-CoA. More specifically pyruvate carboxylase is activated by acetyl-CoA. Because acetyl-CoA is an important metabolite in the TCA cycle which produces a lot of energy, when concentrations of acetyl-CoA are high organisms use pyruvate carboxylase to channel pyruvate away from the TCA cycle. If the organism does not need more energy, then it is best to divert those metabolites towards storage or other necessary processes.
  2. The conversion of fructose-1,6-bP to fructose-6-P with the use of fructose-1,6-phosphatase is negatively regulated and inhibited by the molecules AMP and fructose-2,6-bP. These are reciprocal regulators to glycolysis’ phosphofructokinase. Phosphofructosekinase is positively regulated by AMP and fructose-2,6-bP. Once again, when the energy levels produced are higher than needed, i.e. a large ATP to AMP ratio, the organism increases gluconeogenesis and decreases glycolysis. The opposite also applies when energy levels are lower than needed, i.e. a low ATP to AMP ratio, the organism increases glycolysis and decreases gluconeogenesis.
  3. The conversion of glucose-6-P to glucose with use of glucose-6-phosphatase is controlled by substrate level regulation. The metabolite responsible for this type of regulation is glucose-6-P. As levels of glucose-6-P increase, glucose-6-phosphatase increases activity and more glucose is produced. Thus glycolysis is unable to proceed.

 

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A Synthesis of the Beauty and Complexity of How We View Cancer


A Synthesis of the Beauty and Complexity of How We View Cancer

Author: Larry H. Bernstein, MD, FCAP

Cancer Volume One – Summary

A Synthesis of the Beauty and Complexity of How We View Cancer

 

This document has covered a broad spectrum of the research, translational biology, diagnostics (both laboratory and imaging methodologies), and treatments for a variety of cancers, mainly by organs, and selectively by the most common cancers seen in human populations. A number of observations stand out on review of all the material presented. 1. The most common cancers affecting humans is spread worldwide, with some variation by region. 2. Cancers within geographic regions may be expressed differently in relationship to population migrations, the incidence of specific environmental pollutants, occurrence of insect transmitted and sexually transmitted diseases (HIV, HCV, HPV), and possibly according to age, or relationship to ultraviolet or high dose radiation exposure. 3. Cancers are expressed within generally recognized age timelines. For example, acute lymphocytic leukemia and neuroblastoma in children under 10 years age; malignant giant cell tumor and osteosarcoma in the third and fourth decade; prostate cancer and breast cancer over age 40, and are more aggressive at an earlier age, both having a strong sex hormone dependence. 4. There is dispute about the effectiveness of screening for cancer with respect to what age, excessive risk in treatment modality, and the duration of progression free survival. Despite the evidence of several years potential life extension, a long term survival of 10 years is not the expected outcome. However, the quality of life in the remaining years is a valid point in favor of progress. 5. There has been a significant reduction in toxicity of treatment, but attention has been focused on a patient-centric decision process. 6. There has been a dramatic improvement in surgical approaches, post-surgical surveillance, and in diagnosis by invasive and noninvasive methods, especially in the combination of needle biopsy and imaging techniques. 7. There is significant variation within cancer cell types with respect to disease-free survival.

The work presented has several main components: First, there is the biology and mechanisms involved in carcinogenesis related to (1) mutations; (2) carcinogenesis; (3) cell regulatory mechanisms; (4) cell signaling pathways; (5) apoptosis (6) ubitination (7) mitochondrial dysfunction; (8) cell-cell interactions; (9) cell migration; (10) metastasis. Then there are large portions covering (1) imaging; (2) specific targeted therapy; (3) nanotechology-based therapy; (4) specific organ-type cancers; (5) genomics-based testing; (6) circulating cancer cells; (7) miRNAs; (8) siRNAs; (9) cancer immunology and (10) immunotherapy.

Classically, we refer to cancer development in terms of the germ cell layers – ectoderm, mesoderm, and endoderm. These are formative in embryonic development. The most active development occurs during embryonic development, with a high growth rate of cells and also a high utilization of energy. The cells utilize oxidation for energy in this period characterized by movement of cells in differentiation and organogenesis. This was observed to be unlike the cell metabolism in carcinogenesis, which is characterized by impaired mitochondrial function and reliance on lactate production for energy – termed anaerobic glycolysis, as investigated by Meyerhof, Embden, Warburg, Szent-Gyorgy, H. Krebs, Theorell, AV Hill, B Chance, P Mitchell, P Boyer, F Lippman, and others.

In addition, the body economy has been divided into two major metabolic compartments: fat and lean body mass (LBM), which is further denoted as visceral and structural. This denotes the gut, kidneys, liver, lung, pancreas, sexual organs, endocrines, brain and fat cells in one compartment, and skeletal muscle, bone and cardiovascular in another. LBM is calculated as fat free mass. Further, brown fat is distinguished from white fat. But this was a first layer of construction of the human body. One peels away this layer to find a second layer. For example, the gut viscera have an inner (outer) epithelial layer, a muscularis, and a deep epithelium, which has circulation and fat. There is also an interstitium between the gut epithelium and muscularis. The lung has an epithelium exposed to the airspaces, then capillaries, and then epithelium, designed for exchange of O2 and CO2, the source of heat generation. The pancreas has an endocrine portion in the islets that are embedded in an exocrine secretory organ. The sexual organs have a combination of glandular structures embedded in a mesothelium.

The structural compartment is entirely accounted for by the force of contraction. If this is purely anatomical, that is not really the case when one goes into the functioning substructures of these tissues – cytoplasm, endoplasmic reticulum (ribosomal), mitochondria, liposomes, chromatin apparatus, cell membrane and vesicles. Within and between these structures are the working and interacting mechanisms of the cell in its unique role. What ties these together was first thought to be found in the dogma following the discovery of the genetic code in 1953 that begat DNA to RNA to protein.

This led to many other discoveries that made it clear that it was only a first approximation. It did not account for noncoding DNA, which became unmasked with the culmination of the Human Genome Project and concurrent advances in genomics (mtDNA, mtRNA, siRNA, exosomes, proteomics, synthetic biology, predictive analytics, and regulatory pathways directed by signaling molecules. Here is a list of signaling pathways: 1. JAK-STAT 2. GPCR 3. Endocrine 4. Cytochemical 5. RTK 6. P13K 7. NF-KB 8. MAPK 9. Ubiquitin 10. TGF-beta 11. Stem cell These signaling pathways have become the basis for the discovery of inhibitors of signaling pathways (suppressors), as well as activators, as these have been considered as specific targets for selective therapy. (.See Figure below) Of course, extensive examination of these pathways has required that all such findings are validated based on the STRENGTH of their effect on the target and in the impact of suppression.

inhibitors of signaling pathways-1

http://www.SelleckChem.com

 

Let us continue this discussion elucidating several major points.  While the early observations that drove the interest in biochemical behavior of cancer cells has been displaced, it has not faded from view.

Bioenergetics of Cancer cells

Michael J. Gonzalez (Bioenergetic_Theory_of_Carcinigenesis. http://www.academia.edu/2224071/ Bioenergetic_Theory_of_Carcinigenesis) maintains that the altered energy metabolism of tumor cells provides a viable target for a non-toxic chemotherapeutic approach.  An increased glucose consumption rate  has been observed in malignant cells. Warburg (NobelLaureate in medicine) postulated that the respiratory process of malignant cells was impaired in the malignant transformation. Szent-Györgyi (Nobel in medicine) also viewed cancer as originating from insufficient oxygen utilization. Oxygen inhibits anaerobic  metabolism (fermentation and lactic acid production). Interestingly, during cell differentiation (where cell energy level is high) there is an increased cellular production of oxidation products that appear to provide physiological stimulation for changes in gene expression that may lead to a terminal differentiated state. The failure to maintain high ATP production (high cell energy levels) may be a consequence of inactivation of key enzymes, especially those related to the Krebs cycle and the electron transport system. A distorted mitochondrial function (transmembrane potential) may result.  This  aspect could be suggestive of an important mitochondrial involvement in the carcinogenic process in addition to presenting it as a possible therapeutic target for cancer. Intermediate metabolic correction of the mitochondria is postulated as a possible non-toxic therapeutic approach for cancer.

Fermentation is the anaerobic metabolic breakdown of glucose without net oxidation. Fermentation does not release all the available energy of glucose or need oxygen as part of its biochemical reactions ;  it merely allows glycolysis  (a process that yields two ATP per mole of glucose) to continue by replenishing reduced coenzymes and yields lactate as its final product. The first step in aerobic and anaerobic energy producing pathways, it occurs in the cytoplasm of cells, not in specialized organelles, and is found in all living organisms.  Cancer cells have a fundamentally different energy metabolism compared to normal cells, that  are obligate aerobes (oxygen-requiring cells)  meeting their energy needs with oxidative metabolic processes., while cancer cells do not  require oxygen for their survival. This increase in glycolytic  flux is a metabolic strategy of tumor cells to ensure growth and    survival  in  environments  with  low   oxygen concentrations.

Radoslav Bozov has commented that the process of genomic evolution cannot be fully revealed through comparative genomicsHe states that DNA would be entropic- favorable stable state going towards absolute ZERO temp. Themodynamics measurement in subnano discrete space would go negative towards negativity. DNA is like a cold melting/growing crystal, quite stable as it appears not due to hydrogen bonding , but due to interference of C-N-O. That force is contradicted via proteins onto which we now know large amount of negative quantum redox state carbon attaches. The more locally one attempts to observe, the more hidden variables would emerge as a consequence of discrete energy spaces opposing continuity of matter/time. But stability emerges out of non-stable states, and never reaches absolute stability, for there would be neither feelings nor freedom.

Membrane potential(Vm)

Membrane potential (Vm), the voltage across the plasma membrane, arises because of the presence of differention channels/transporters with specific ion selectivity and permeability. Vm is a key biophysical signal in non-excitable cells, modulating important cellular activities, such as proliferation and differentiation. Therefore, the multiplicities of various ion channels/transporters expressed on different cells are finely tuned in order to regulate the Vm. (M Yang and WJ Brackenbury.

Membrane potential and cancer progression. Frontiers in Physiol.  2013(4); 185: 1.  http://dx.doi.org/10.3389/fphys.2013.00185)

It is well-established that cancer cells possess distinct bioelectrical properties. Notably, electrophysiological analyses in many cancer cell types have revealed a depolarized Vm that favors cell proliferation. Ion channels/transporters control cell volume and migration, and emerging data also suggest that the level of Vm has functional roles in cancer cell migration. In addition, yperpolarization is necessary for stem cell differentiation. For example, both osteogenesis and adipogenesis are hindered in human mesenchymal stem cells (hMSCs) under depolarizing conditions. Therefore, in the context of cancer, membrane depolarization might be important for the emergence and maintenance of cancer stem cells (CSCs), giving rise to sustained tumor growth. This review aims to provide a broad understanding of the Vm as a bioelectrical signal in cancer cells by examining several key types of ion channels that contribute to its regulation. The mechanisms by which Vm regulates cancer cell proliferation, migration, and differentiation will be discussed. In the long term, Vm might be avaluable clinical marker for tumor detection with prognostic value, and could even be artificially modified in order to inhibit tumor growth and metastasis.

Perspective beyond Cancer Genomics: Bioenergetics of Cancer Stem Cells

Hideshi Ishii, Yuichiro Doki, and Masaki Mori
Yonsei Med J 2010; 51(5):617-621.  http://dx.doi.org/10.3349/ymj.2010.51.5.617   pISSN: 0513-5796, eISSN: 1976-2437

Although the notion that cancer is a disease caused by genetic and epigenetic alterations is now widely accepted, perhaps more emphasis has been given to the fact that cancr is a genetic disease. It should be noted that in the post-genome sequencing project period of the 21st century, the underlined phenomenon nevertheless could not be discarded towards the complete control of cancer disaster as the whole strategy, and in depth investigation of the factors associated with tumorigenesis is required for achieving it. Otto Warburg has won a Nobel Prize in 1931 for the discovery of tumor bioenergetics, which is now commonly used as the basis of positron emission tomography (PET), a highly sensitive noninvasive technique used in cancer diagnosis. Furthermore, the importance of the cancer stem cell (CSC) hypothesis in therapy-related resistance and metastasis has been recognized during the past 2 decades. Accumulating evidence suggests that tumor bioenergetics plays a critical role in CSC regulation; this finding has opened up a new era of cancer medicine, which goes beyond cancer genomics.

Efficient execution of cell death in non-glycolytic cells requires the generation of ROS controlled by the activity of mitochondrial H+-ATP synthase.

Gema Santamaría1,#, Marta Martínez-Diez1,#, Isabel Fabregat2 and José M. Cuezva1,*
Carcinogenesis 2006 27(5):925-935      http://dx.doi.org/10.1093/carcin/bgi315

There is a large body of clinical data documenting that most human carcinomas contain reduced levels of the catalytic subunit of the mitochondrial H+-ATP synthase. In colon and lung cancer this alteration correlates with a poor patient prognosis. Furthermore, recent findings in colon cancer cells indicate that down-regulation of the H+-ATP synthase is linked to the resistance of the cells to chemotherapy. However, the mechanism by which the H+-ATP synthase participates in cancer progression is unknown. In this work, we show that inhibitors of the H+-ATP synthase delay

staurosporine-induced cell death in liver cells that are dependent on oxidative phosphorylation for energy provision whereas it has no effect on glycolytic cells. Efficient execution of cell death requires the generation of reactive oxygen species (ROS) controlled by the activity of the H+-ATP synthase in a process that is concurrent with the rapid disorganization of the cellular mitochondrial network. The generation of ROS after staurosporine treatment is highly dependent on the mitochondrial membrane potential and most likely caused by reverse electron flow to Complex I. The generated ROS promote the carbonylation and covalent modification of cellular and mitochondrial proteins. Inhibition of the activity of the H+-ATP synthase blunted ROS production, prevented the oxidation of cellular proteins and the modification of mitochondrial proteins, delaying the release of cyt c and the execution of cell death. The results in this work establish the down-regulation of the H+-ATP synthase, and thus of oxidative phosphorylation, as part of the molecular strategy adapted by cancer cells to avoid reactive oxygen species-mediated cell death. Furthermore, the results provide a mechanistic explanation to understand chemotherapeutic resistance of cancer cells that rely on glycolysis as main energy provision pathway.

see also –

The tumor suppressor function of mitochondria: Translation into the clinics

José M. CuezvaÁlvaro D. OrtegaImke Willers, et al.  
Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease  Dec 2009;  1792(12): 1145–1158  http://dx.doi.org/10.1016/j.bbadis.2009.01.006

Recently, the inevitable metabolic reprogramming experienced by cancer cells as a result of the onset of cellular proliferation has been added to the list of hallmarks of the cancer cell phenotype. Proliferation is bound to the synchronous fluctuation of cycles of an increased glycolysis concurrent with a restrained oxidative phosphorylation. Mitochondria are key players in the metabolic cycling experienced during proliferation because of their essential roles in the transduction of biological energy and in defining the life–death fate of the cell. These two activities are molecularly and functionally integrated and are both targets of commonly altered cancer genes. Moreover, energetic metabolism of the cancer cell also affords a target to develop new therapies because the activity of mitochondria has an unquestionable tumor suppressor function. In this review, we summarize most of these findings paying special attention to the opportunity that translation of energetic metabolism into the clinics could afford for the management of cancer patients. More specifically, we emphasize the role that mitochondrial β-F1-ATPase has as a marker for the prognosis of different cancer patients as well as in predicting the tumor response to therapy.

Self-Destructive Behavior in Cells May Hold Key to a Longer Life

Carl Zimmer, MY Times  October 5, 2009

In recent years, scientists have found evidence of autophagy in preventing a much wider range of diseases. Many disorders, like Alzheimer’s disease, are the result of certain kinds of proteins forming clumps. Lysosomes can devour these clumps before they cause damage, slowing the onset of diseases.

Lysosomes may also protect against cancer. As mitochondria get old, they cast off charged molecules that can wreak havoc in a cell and lead to potentially cancerous mutations. By gobbling up defective mitochondria, lysosomes may make cells less likely to damage their DNA. Many scientists suspect it is no coincidence that breast cancer cells are often missing autophagy-related genes. The genes may have been deleted by mistake as a breast cell divided. Unable to clear away defective mitochondria, the cell’s descendants become more vulnerable to mutations.

Unfortunately, as we get older, our cells lose their cannibalistic prowess. The decline of autophagy may be an important factor in the rise of cancer, Alzheimer’s disease and other disorders that become common in old age. Unable to clear away the cellular garbage, our bodies start to fail.

If this hypothesis turns out to be right, then it may be possible to slow the aging process by raising autophagy. It has long been known, for example, that animals that are put on a strict low-calorie diet can live much longer than animals that eat all they can. Recent research has shown that caloric restriction raises autophagy in animals and keeps it high. The animals seem to be responding to their low-calorie diet by feeding on their own cells, as they do during famines. In the process, their cells may also be clearing away more defective molecules, so that the animals age more slowly.

Some scientists are investigating how to manipulate autophagy directly. Dr. Cuervo and her colleagues, for example, have observed that in the livers of old mice, lysosomes produce fewer portals on their surface for taking in defective proteins. So they engineered mice to produce lysosomes with more portals. They found that the altered lysosomes of the old experimental mice could clear away more defective proteins. This change allowed the livers to work better.

 

Essentiality of pyruvate kinase, oxidation, and phosphorylation

We can move to the next level with greater clarity. Yu et al. reported an important relationship between Pyruvate kinase M2 (PKM2) and the Warburg effect of cancer cells ( M Yu, et al. PIM2 phosphorylates PKM2 and promotes Glycolysis in Cancer Cells. J Biol Chem (PMID: 24142698) http://dx.doi.org10.1074/jbc.M113.508226 ).  They found that PIM2 could directly phosphorylate PKM2 on the Thr454 residue, which resulted in an increase of PKM2 protein levels. PKM2 with a phosphorylation-defective mutation displayed a reduced effect on glycolysis compared to the wild-type, thereby co-activating HIF-1α and β-catenin, and enhanced mitochondria respiration and chemotherapeutic sensitivity of cancer cells. This indicated that PIM2-dependent phosphorylation of PKM2 is critical for regulating the Warburg effect in cancer, highlighting PIM2 as a potential therapeutic target.

In another study of the effect of 3 homoplastic mtDNA mutations on oxidative metabolism of osteosarcoma cells, there was a difference proportional to the magnitude of the defect. (Iommarini L, et al. Different mtDNA mutations modify tumor progression in dependence of the degree of respiratory complex I impairment. Hum Mol Genet. 2013 Nov 11. [Epub ahead of print]; PMID: 24163135 ).   Osteosarcoma cells carrying the most marked impairment of the gene encoding mitochondrial complex I  (CI) of oxidative phosphorylation displayed a reduced tumorigenic potential both in vitro and in vivo, when compared with cells with mild CI dysfunction. The severe CI dysfunction was an energetic defect associated with a compensatory increase in glycolytic metabolism and AMP-activated protein kinase activation.  The result suggested that mtDNA mutations may display diverse impact on tumorigenic potential depending on the type and severity of the resulting oxidative phosphorylation dysfunction. The modulation of tumor growth was independent from reactive oxygen species production but correlated with hypoxia-inducible factor 1α stabilization, indicating that structural and functional integrity of CI and oxidative phosphorylation are required for hypoxic adaptation and tumor progression.

An unrelated finding shares some agreement with what has been identified (Systematic isolation of context-dependent vulnerabilities in NSCLC. Cell, 24 Oct 2013; 155 (3): 552-566, http://dx.doi.org/10.1016/ j.cell.2013.09.041). They report  three distinct target/response-indicator pairings that are represented with significant frequencies (6%–16%) in the patient population. These include NLRP3 mutation/inflammasome activation-dependent FLIP addiction, co-occurring KRAS and LKB1 mutation-driven COPI addiction, and selective sensitivity to a synthetic indolotriazine that is specified by a seven-gene expression signature.   This is depicted in the Figure below.  The authors noted a frequency and diversity of somatic lesions detected among lung tumors can confound efforts to identify these targets.

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The forging of a cancer-metabolism link and twists in the chain (Biome 19th April 2013)

Ten years ago, Grahame Hardie and Dario Alessi discovered that the elusive upstream kinase required for the activation of AMP-activated protein kinase (AMPK) by metabolic stress that the Hardie lab had been pursuing in their research on the metabolic regulator AMPK was the tumor suppressor, LKB1, that the neighbouring Alessi lab was working on at the time. This finding represented the first clear link between AMPK and cancer.

The resulting paper [1], published in 2003 in what was then Journal of Biology (now BMC Biology), was one [1] of three [2, 3] connecting these two kinases and that helped to swell of a surge of interest in the metabolism of tumor cells that was just beginning at about that time and is still growing. (LKB1 and AMPK and the cancer-metabolism link – ten years after.  D Grahame Hardie, and Dario R Alessi.  BMC Biology 2013, 11:36.   http://dx doi.org.10.1186/1741-7007-11-36.)

 

In September 2003, both groups published a joint paper [1] in Journal of Biology (now BMC Biology) that identified the long-sought and elusive upstream kinase acting on AMP-activated protein kinase (AMPK) as a complex containing LKB1, a known tumor suppressor. Similar findings were reported at about the same time by David Carling and Marian Carlson [2] and by Reuben Shaw and Lew Cantley [3]; at the time of writing these three papers have received between them a total of over 2,000 citations. These findings provided a direct link between a protein kinase, AMPK, which at the time was mainly associated with regulation of metabolism, and another protein kinase, LKB1, which was known from genetic studies to be a tumor suppressor. While the idea that cancer is in part a metabolic disorder (first suggested by Warburg in the 1920s [4]) is well recognized today [5], this was not the case in 2003, and our paper perhaps contributed towards its renaissance.

The distinctive metabolic feature of tumor cells that enables them to meet the demands of unrestrained growth is the switch from oxidative generation of ATP to aerobic glycolysis – a phenomenon now well known as the Warburg effect. Operating this switch is one of the central functions of the AMP-activated protein kinase (AMPK) that has long been the focus of research in the Hardie lab. AMPK is an energy sensor that is allosterically tuned by competitive binding of ATP, ADP and AMP to sites on its g regulatory subunit (its portrait here, with AMP bound at two sites, was kindly provided by Bing Xiao and Stephen Gamblin). When phosphorylated by LKB1, AMPK responds to depletion of ATP by turning off anabolic reactions required for growth, and turning on catabolic reactions and oxidative phosphorylation – the reverse of the Warburg effect. In this light, it is not surprising that LKB1  is inactivated in some proportion of many different types of tumors.

AMPK as an energy sensor and metabolic switch

AMPK was discovered as a protein kinase activity that phosphorylated and inactivated two key enzymes of fatty acid and sterol biosynthesis: acetyl-CoA carboxylase (ACC) and 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR). The ACC kinase activity was reported to be activated by 5’-AMP, and the HMGR kinase activity by reversible phosphorylation, but for many years the two activities were thought to be due to distinct enzymes. However, in 1987 the DGH laboratory showed that both were functions of a single protein kinase, which we renamed AMPK after its allosteric activator, 5’-AMP. It was subsequently found that AMPK regulated not only lipid biosynthesis, but also many other metabolic pathways, both by direct phosphorylation of metabolic enzymes, and through longer-term effects mediated by phosphorylation of transcription factors and co-activators. In general, AMPK switches off anabolic pathways that consume ATP and NADPH, while switching on catabolic pathways that generate ATP (Figure 1).

 

target proteins and metabolic pathways regulated by AMPK 1741-7007-11-36-1_1

 

Summary of a selection of target proteins and metabolic pathways regulated by AMPK. Anabolic pathways switched off by AMPK are shown in the top half of the ‘wheel’ and catabolic pathways switched on by AMPK in the bottom half. Where a protein target for AMPK responsible for the effect is known, it is shown in the inner wheel; a question mark indicates that it is not yet certain that the protein is directly phosphorylated. For original references see [54].

Key to acronyms: ACC1/ACC2, acetyl-CoA carboxylases-1/-2; HMGR, HMG-CoA reductase; SREBP1c, sterol response element binding protein-1c; CHREBP, carbohydrate response element binding protein; TIF-1A, transcription initiation factor-1A; mTORC1, mechanistic target-of-rapamycin complex-1; PFKFB2/3, 6-phosphofructo-2-kinase, cardiac and inducible isoforms; TBC1D1, TBC1 domain protein-1; SIRT1, sirtuin-1; PGC-1α, PPAR-γ coactivator-1α; ULK1, Unc51-like kinase-1.

Regulation of AMPK  1741-7007-11-36-3

 

Regulation of AMPK. AMPK can be activated by increases in cellular AMP:ATP or ADP:ATP ratio, or Ca2+ concentration. AMPK is activated >100-fold on conversion from a dephosphorylated form (AMPK) to a form phosphorylated at Thr172 (AMPK-P) catalyzed by at least two upstream kinases: LKB1, which appears to be constitutively active, and CaMKKβ, which is only active when intracellular Ca2+ increases. Increases in AMP or ADP activate AMPK by three mechanisms: (1) binding of AMP or ADP to AMPK, causing a conformational change that promotes phosphorylation by upstream kinases (usually this will be LKB1, unless [Ca2+] is elevated); (2) binding of AMP or ADP, causing a conformational change that inhibits dephosphorylation by protein phosphatases; (3) binding of AMP (and not ADP), causing allosteric activation of AMPK-P. All three effects are antagonized by ATP, allowing AMPK to act as an energy sensor.

AMPK and AMPK-related kinase (ARK) family  1741-7007-11-36-4

 

Members of the AMPK and AMPK-related kinase (ARK) family. All the kinases named in the figure are phosphorylated and activated by LKB1, although what regulates this phosphorylation is known only for AMPK. Alternative names are shown, where applicable.

AMPK-activating drugs metformin or phenformin might provide protection against cancer 1741-7007-11-36-5

 

 

Three possible mechanisms to explain how the AMPK-activating drugs metformin or phenformin might provide protection against cancer. (a) Metformin acts on the liver and other insulin target tissues by activating AMPK (and probably via other targets), normalizing blood glucose; this reduces insulin secretion from pancreatic β cells, reducing the growth-promoting effects of insulin (and high glucose) on tumor cells. Since metformin does not reduce glucose levels in normoglycemic individuals, this mechanism would only operate in insulin-resistant subjects. (b) Metformin or phenformin activates AMPK in pre-neoplastic cells, restraining their growth and proliferation and thus delaying the onset of tumorigenesis; this mechanism would only operate in cells where the LKB1-AMPK pathway was intact. (c) Metformin or phenformin inhibits mitochondrial ATP synthesis in tumor cells, promoting cell death. If the LKB1-AMPK pathway was down-regulated in the tumor cells, they would be more sensitive to cell death induced by the biguanides than surrounding normal cells.

Metformin and phenformin are biguanides that inhibit mitochondrial function and so deplete ATP by inhibiting its production . AMPK is activated by any metabolic stress that depletes ATP, either by inhibiting its production (as do hypoxia, glucose deprivation, and treatment with biguanides) or by accelerating its consumption (as does muscle contraction). By switching off anabolism and other ATP-consuming processes and switching on alternative ATP-producing catabolic pathways, AMPK acts to restore cellular energy homeostasis.

Findings that AMPK is activated in skeletal muscle during exercise and that it increases muscle glucose uptake and fatty acid oxidation led to the suggestion that AMPK-activating drugs might be useful for treating type 2 diabetes. Indeed, it turned out that AMPK is activated by metformin, a drug that had at that time been used to treat type 2 diabetes for over 40 years, and by phenformin , a closely related drug that had been withdrawn for treatment of diabetes due to side effects of lactic acidosis.

If only it were so simple. Effects of metformin on cancer in type 2 diabetics could be secondary to reduction in insulin levels, and although there is evidence for direct effects of AMPK activation on the development of tumors in mice, there is also recent evidence that tumors that become established without down-regulating LKB1 survive metformin better than those that have lost it – probably because metformin poisons the mitochondrial respiratory chain, depressing ATP levels, and cells in which AMPK can still be activated in response to the challenge do better than those in which it can’t.

In their review, Hardie and Alessi chart these  twists and turns, and point to the explosion of further possibilities opened up by the discovery, since their 2003 publication, of at least one other class of kinase upstream of AMPK (the CaM kinases), and at least a dozen other downstream targets of LKB1 (AMPK-related kinases, or ARKs) – not to mention the innumerable downstream targets of AMPK; all which make half their schematic illustrations look like hedgehogs.

Analysis of respiration  in human cancer

Bioenergetic profiling of cancer cells is of great potential because it can bring forward new and effective

Therapeutic  strategies along with early diagnosis. Metabolic Control Analysis (MCA) is a methodology that enables quantification of the flux control exerted by different enzymatic steps in a metabolic network thus assessing their contribution to the system‘s function.

(T Kaambre,V Chekulayev, I Shevchuk, et al. Metabolic control analysis of respiration  in human cancer tissue.  Frontiers Physiol 2013 (4); 151:  1. http://dx.doi.org/10.3389/fphys.2013.00151)

Our main goal is to demonstrate the applicability of MCA for in situ studies of energy

Metabolism in human breast and colorectal cancer cells as well as in normal tissues .We seek to determine the metabolic conditions leading to energy flux redirection in cancer cells. A main result obtained is that the adenine nucleotide translocator exhibits the highest control of respiration in human breast cancer thus becoming a prospective therapeutic target. Additionally, we present evidence suggesting the existence of mitochondrial respiratory supercomplexes that may represent a way by which cancer cells avoid apoptosis. The data obtained show that MCA applied in situ can be insightful in cancer cell energetic research.

Metabolic control analysis of respiration in human cancer tissue. fphys-04-00151-g001

Metabolic control analysis of respiration in human cancer tissue.

Representative traces of change in the rate of oxygen consumption by permeabilized human colorectal cancer (HCC) fibers after their titration with increasing concentrations of mersalyl, an inhibitor of inorganic phosphate carrier (panel A). The values of respiration rate obtained were plotted vs. mersalyl concentration (panel B) and from the plot the corresponding flux control coefficient was calculated. Bars are ±SEM.

Oncologic diseases such as breast and colorectal cancers are still one of the main causes of premature death. The low efficiency of contemporary medicine in the treatment of these malignancies is largely mediated by a poor understanding of the processes involved in metastatic dissemination of cancer cells as well as the unique energetic properties of mitochondria from tumors. Current knowledge supports the idea that human breast and colorectal cancer cells exhibit increased rates of glucose consumption displaying Warburg phenotype,i.e.,elevated glycolysis even in the presence of oxygen (Warburg and Dickens, 1930; Warburg, 1956 ;Izuishietal., 2012). Notwithstanding,  there are some evidences that in these malignancies mitochondrial oxidative phosphorylation (OXPHOS) is the main source of ATP rather than glycolysis. Cancer cells have been classified according to their pattern of metabolic remodeling depending of the relative balance between aerobic glycolysis and OXPHOS (Bellanceetal.,2012). The first type of tumor cells is highly glycolytic, the second OXPHOS deficient and the third type of tumors dislay enhanced OXPHOS. Recent studies strongly sug gest  that cancer cells can utilize lactate, free fatty acids, ketone bodies, butyrate and glutamine as key respiratory substrate selic iting metabolic remodeling of normal surrounding cells toward aerobic glycolysis—“reverse Warburg”effect (Whitaker-Menezes et al.,2011;Salem et al.,2012;Sotgia et al.,2012;Witkiewicz et al., 2012).

In normal cells,the OXPHOS system is usually closely linked to phosphotransfer systems, including various creatine kinase(CK) isotypes,which ensure a safe operation of energetics over a broad functional range of cellular activities (Dzejaand Terzic,2003).  However, our current knowledge about the function of CK/creatine (Cr) system in human breast and colorectal cancer is insufficient. In some malignancies, for example sarcomas the CK/Cr system was shown to be strongly downregulated (Beraetal.,2008;Patraetal.,2008).  Our previous studies showed  that the mitochondrial-bound CK (MtCK) activity was significantly decreased in HL-1 tumor cells (Mongeetal.,2009), as compared to normal parent cardiac cells where the OXPHOS is the main ATP source of and the CK system is a main energy carrier. In the present study,we estimated the role of MtCK in maintaining energy homeostasis in human colorectal cancer cells. Understanding the control and regulation of energy metabolism requires analytical tools that take into account  the existing interactions between individual network components and their impact on systemic network function. Metabolic Control Analysis(MCA) is a theoretical framework relating the properties of metabolic systems to the kinetic characteristics of their individual enzymatic components (Fell,2005). An experimental approach of MCA has been already successfully applied to the studies of OXPHOS in isolated mitochondria (Tageretal.,1983; Kunzetal.,1999; Rossignoletal.,2000)  and in skinned muscle fibers (Kuznetsovetal.,1997;Teppetal.,2010).

Metabolic control analysis of respiration in human cancer tissue

Values of basal (Vo) and maximal respiration rate (Vmax, in the presence of 2 mM ADP) and apparent Michaelis Menten constant (Km) for ADP in permeabilized human breast and colorectal cancer samples as well as health tissue. – See more at: http://journal.frontiersin.org/Journal/10.3389/fphys.2013.00151/full#sthash.VBXPdodj.dpuf

Role of Uncoupling Proteins in Cancer

Adamo Valle, Jordi Oliver and Pilar Roca *
Cancers 2010; 2: 567-591;   http://dx.doi.org/10.3390/cancers2020567

Since Otto Warburg discovered that most cancer cells predominantly produce energy by glycolysis rather than by oxidative phosphorylation in mitochondria, much interest has been focused on the alterations of these organelles in cancer cells. Mitochondria have been shown to be key players in numerous cellular events tightly related with the biology of cancer. Although energy production relies on the glycolytic pathway in cancer cells, these organelles also participate in many other processes essential for cell survival and proliferation such as ROS production, apoptotic and necrotic cell death, modulation of oxygen concentration, calcium and iron homeostasis, and certain metabolic and biosynthetic pathways. Many of these mitochondrial-dependent processes are altered in cancer cells, leading to a phenotype characterized, among others, by higher oxidative stress, inhibition of apoptosis, enhanced cell proliferation, chemoresistance, induction of angiogenic genes and aggressive fatty acid oxidation. Uncoupling proteins, a family of inner mitochondrial membrane proteins specialized in energy-dissipation, has aroused enormous interest in cancer due to their relevant impact on such processes and their potential for the development of novel therapeutic strategies.

Uncoupling proteins (UCPs) are a family of inner mitochondrial membrane proteins whose function is to allow the re-entry of protons to the mitochondrial matrix, by dissipating the proton gradient and, subsequently, decreasing membrane potential and production of reactive oxygen species (ROS). Due to their pivotal role in the intersection between energy efficiency and oxidative stress UCPs are being investigated for a potential role in cancer. In this review we compile the latest evidence showing a link between uncoupling and the carcinogenic process, paying special attention to their involvement in cancer initiation, progression and drug chemoresistance.

The Warburg Effect

Uncoupling the Warburg effect from cancer

A Najafov and DR Alessi
Proc Nat Acad Sci                                      www.pnas.org/cgi/doi/10.1073/pnas.1014047107
A remarkable trademark of most tumors is their ability to break down glucose by glycolysis at a vastly higher rate than in normal tissues, even when oxygen is copious. This phenomenon, known as the Warburg effect, enables rapidly dividing tumor cells to generate essential biosynthetic building blocks such as nucleic acids, amino acids, and lipids from glycolytic intermediates to permit growth and duplication of cellular components during  division (1). An assumption dominating research in this area is that the Warburg effect is specific to cancer. Thus, much of the focus has been on uncovering mechanisms by which cancer-causing mutations influence metabolism to stimulate glycolysis.

This has lead to many exciting discoveries. For example, the p53 tumor suppressor can suppress glycolysis through its ability to control expression of key metabolic genes, such as phosphoglycerate mutase (2), synthesis of cytochrome C oxidase-2 (3), and TP53-induced glycolysis and apoptosis regulator (TIGAR) (4). Many cancer-causing mutations lead to activation of the Akt and mammalian target of rapamycin (mTOR) pathway that profoundly influences metabolism and expression of metabolic enzymes to promoteglycolysis (5).

Strikingly, all cancer cells but not nontransformed cells express a specific splice variant of pyruvate kinase, termed M2-PK, that is less active, leading to the build up of phosphoenolpyruvate (6). Recent work has revealed that reduced activity of M2-PK promotes a unique glycolytic pathway in which phosphoenolpyruvate is converted to pyruvate by a histidine-dependent phosphorylation of phosphoglycerate mutase, promoting assimilation of glycolytic products into biomass (7). However, despite these observations, one might imagine that the Warburg effect need not be specific for cancer and that any normal cell would need to stimulate glycolysis to generate sufficient biosynthetic materials to fuel expansion and division.

Recent work by Salvador Moncada’s group published in PNAS (8) and other recent work from the same group (9, 10) provides exciting evidence supporting the idea that the Warburg effect is also required for the proliferation of noncancer cells.

The key discovery was that the anaphase promoting complex/cyclosome-Cdh1(APC/C-Cdh1), a master regulator of the transition of G1 to S phase of the cell cycle, inhibits glycolysis in proliferating noncancer cells by mediating the degradation of two key metabolic enzymes, namely 6-phosphofructo-2-kinase/ fructose-2,6-bisphosphatase isoform3 (PFKFB3) (9, 10) and glutaminase-(Fig. 1) (8).

Fig. 1. Mechanism by which APC_C-Cdh1 inhibits glycolysis and glutaminolysis to suppress cell proliferation

 

Fig.  Mechanism by which APC/C-Cdh1 inhibits glycolysis and glutaminolysis to suppress cell proliferation.

APC/C-Cdh1 E3 ligase recognizes KEN-box–containing metabolic enzymes, such as PFKFB3 and glutaminase-1 (GLS1), and ubiquitinates and targets them for proteasomal degradation. This inhibits glycolysis and glutaminolysis, leading to decrease in metabolites that can be assimilated into biomass, thereby suppressing proliferation.

PFKFB3 potently stimulates glycolysis by catalyzing the formation of fructose-2,6-bisphosphate, the allosteric activatorof 6-phosphofructo-1-kinase (11). Glutaminase-1 is the first enzyme in glutaminolysis, converting glutamine to lactate, yielding biosyntheticintermediates required for cell proliferation (12).

APC/C is a cell cycle-regulated E3 ubiquitin ligase that promotes ubiquitination of a distinct set of cell cycle proteins containing either a D-box (destruction box) or a KEN-box, named after the essential Lys-Glu-Asn motif required for APC recognition (13). Among its well-known substrates are crucial cell cycle proteins, such as cyclin B1, securin, and Plk1. By ubiquitinating and targeting its substrates to 26S proteasome-mediated degradation, APC/C regulates processes in late mitotic stage, exit  from mitosis, and several events in G1 (14). The Cdh1 subunit is the KENbox binding adaptor of the APC/C ligase and is essential for G1/S transition.

Importantly, APC/C-Cdh1 is inactivated at the initiation of the S-phase of the cell cycle when DNA and cellular organelles are replicated at the time of the greatest need for generation of biosynthetic materials. APC/C-Cdh1 is reactivated later at the mitosis/G1 phase of the cell cycle when there is a lower requirement for biomassgeneration.

Both PFKFB3 (9, 10) and glutaminase-1 (8) possess a KEN-box and are rapidly degraded in nonneoplastic lymphocytes during the cell cycle when APC/C-Cdh1 is active. Consistent with destruction being mediated by APC-C-Cdh1, ablation of the KEN-box prevents degradation of PFKFB3 (9, 10) and glutaminase-1 (8). Inhibiting the proteasomal-dependent degradation with the MG132 inhibitor

markedly increases levels of ubiquitinated PFKFB3 and glutaminase-1 (8). Moreover, overexpression of Cdh1 to activate APC/C-Cdh1 decreases levels of PFKFB3 as well as glutmaninase-1 and concomitantly inhibited glycolysis, as judged by decrease in lactate production. This effect is also observed when cells were treated with a glutaminase-1 inhibitor (6-diazo-5- oxo-L-norleucine) (8). The final evidence supporting the authors’ hypothesis is that proliferation and glycolysis is inhibited after shRNA-mediated silencing of either PFKFB3 or glutaminase-1 (8).

These results are interesting, because unlike most recent work in this area, Colombo et al. (8) link the Warburg effect to the machinery of the cell cycle that is present in all cells rather than to cancer driving mutations. Further work is required to properly define the overall importance of this pathway, which has thus far only been studied in a limited number of cells. It would also be of value to undertake a more detailed analysis of how the rate of glycolysis and other metabolic pathways vary during the cell cycle of normal and cancer cells…(see full 2 page article) at PNAS.

 

The Warburg Effect Suppresses Oxidative Stress Induced Apoptosis in a Yeast Model for Cancer

C Ruckenstuhl, S Buttner, D Carmona-Gutierre, et al.
PLoS ONE 2009; 4(2): e4592.  http://dx.doi.org/10.1371/journal.pone.0004592

Colonies of Saccharomyces cerevisiae, suitable for manipulation of mitochondrial respiration and shows mitochondria-mediated cell death, were used as a model. Repression of respiration as well as ROS-scavenging via glutathione inhibited apoptosis, conferred a survival advantage during seeding and early development of this fast proliferating solid cell population. In contrast, enhancement of respiration triggered cell death.

Conclusion/Significance: The Warburg effect might directly contribute to the initiation of cancer formation – not only by enhanced glycolysis – but also via decreased respiration in the presence of oxygen, which suppresses apoptosis.

 

PIM2 phosphorylates PKM2 and promotes Glycolysis in Cancer Cells
Z Yu, L Huang, T Zhang, et al.
J Biol Chem 2013;                               http://dx.doi.org/10.1074/jbc.M113.508226

http://www.jbc.org/cgi/doi/10.1074/jbc.M113.508226

Serine/threonine protein kinase PIM2, a known oncogene is a binding partner of pyruvate kinase M2 (PKM2), a key player in the Warburg effect of cancer cells.   PIM2 interacts with PKM2 and phosphorylates PKM2 on the Thr454 residue.

The phosphorylation of PKM2 increases glycolysis and proliferation in cancer cells.

The PIM2-dependent phosphoirylation of ZPKM2 is critical for regulating the Warburg effect in cancer.

 

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

Shlomi T, Benyamini T, Gottlieb E, Sharan R, Ruppin E
PLoS Comput Biol 2011; 7(3): e1002018.    http://dx.doi.org/10.1371/journal.pcbi.1002018
The Warburg effect – a classical hallmark of cancer metabolism – is a counter-intuitive phenomenon in which rapidly proliferating cancer cells resort to inefficient ATP production via glycolysis leading to lactate secretion, instead of relying primarily on more efficient energy production through mitochondrial oxidative phosphorylation, as most normal cells do.

The causes for the Warburg effect have remained a subject of considerable controversy since its discovery over 80 years ago, with several competing hypotheses. Here, utilizing a genome-scale human metabolic network model accounting for stoichiometric and enzyme solvent capacity considerations, we show that the Warburg effect is a direct consequence of the metabolic adaptation of cancer cells to increase biomass production rate. The analysis is shown to accurately capture a three phase metabolic behavior that is observed experimentally during oncogenic progression, as well as a prominent characteristic of cancer cells involving their preference for glutamine uptake over other amino acids.

 

The metabolic advantage of tumor cells

Maurice Israël and Laurent Schwartz

Additional article information

Abstract

1- Oncogenes express proteins of “Tyrosine kinase receptor pathways”, a receptor family including insulin or IGF-Growth Hormone receptors. Other oncogenes alter the PP2A phosphatase brake over these kinases.

2- Experiments on pancreatectomized animals; treated with pure insulin or total pancreatic extracts, showed that choline in the extract, preserved them from hepatomas.

Since choline is a methyle donor, and since methylation regulates PP2A, the choline protection may result from PP2A methylation, which then attenuates kinases.

3- Moreover, kinases activated by the boosted signaling pathway inactivate pyruvate kinase and pyruvate dehydrogenase. In addition, demethylated PP2A would no longer dephosphorylate these enzymes. A “bottleneck” between glycolysis and the oxidative-citrate cycle interrupts the glycolytic pyruvate supply now provided via proteolysis and alanine transamination. This pyruvate forms lactate (Warburg effect) and NAD+ for glycolysis. Lipolysis and fatty acids provide acetyl CoA; the citrate condensation increases, unusual oxaloacetate sources are available. ATP citrate lyase follows, supporting aberrant transaminations with glutaminolysis and tumor lipogenesis. Truncated urea cycles, increased polyamine synthesis, consume the methyl donor SAM favoring carcinogenesis.

4- The decrease of butyrate, a histone deacetylase inhibitor, elicits epigenic changes (PETEN, P53, IGFBP decrease; hexokinase, fetal-genes-M2, increase)

5- IGFBP stops binding the IGF – IGFR complex, it is perhaps no longer inherited by a single mitotic daughter cell; leading to two daughter cells with a mitotic capability.

6- An excess of IGF induces a decrease of the major histocompatibility complex MHC1, Natural killer lymphocytes should eliminate such cells that start the tumor, unless the fever prostaglandin PGE2 or inflammation, inhibit them…

Introduction

The metabolic network of biochemical pathways forms a system controlled by a few switches, changing the finality of this system. Specific substrates and hormones control such switches. If for example, glycemia is elevated, the pancreas releases insulin, activating anabolism and oxidative glycolysis, energy being required to form new substance or refill stores. If starvation decreases glycemia, glucagon and epinephrine activate gluconeogenesis and ketogenesis to form nutriments, mobilizing body stores. The different finalities of the system are or oriented by switches sensing the NADH/NAD+, the ATP/AMP, the cAMP/AMP ratios or the O2 supply… We will not describe here these metabolic finalities and their controls found in biochemistry books.

Many of the switches depend of the phosphorylation of key enzymes that are active or not. Evidently, there is some coordination closing or opening the different pathways. Take for example gluconeogenesis, the citrate condensation slows down, sparing OAA, which starts the gluconeogenic pathway. In parallel, one also has to close pyruvate kinase (PK); if not, phosphoenolpyruvate would give back pyruvate, interrupting the pathway. Hence, the properties of key enzymes acting like switches on the pathway specify the finality of the system. Our aim is to show that tumor cells invent a new specific finality, with mixed glycolysis and gluconeogenesis features. This very special metabolism gives to tumor cells a selective advantage over normal cells, helping the tumor to develop at the detriment of the rest of the body.

I Abnormal metabolism of tumors, a selective advantage

The initial observation of Warburg 1956 on tumor glycolysis with lactate production is still a crucial observation [1]. Two fundamental findings complete the metabolic picture: the discovery of the M2 pyruvate kinase (PK) typical of tumors [2] and the implication of tyrosine kinase signals and subsequent phosphorylations in the M2 PK blockade [35].

A typical feature of tumor cells is a glycolysis associated to an inhibition of apoptosis. Tumors over-express the high affinity hexokinase 2, which strongly interacts with the mitochondrial ANT-VDAC-PTP complex. In this position, close to the ATP/ADP exchanger (ANT), the hexokinase receives efficiently its ATP substrate [6,7]. As long as hexokinase occupies this mitochondria site, glycolysis is efficient. However, this has another consequence, hexokinase pushes away from the mitochondria site the permeability transition pore (PTP), which inhibits the release of cytochrome C, the apoptotic trigger [8]. The site also contains a voltage dependent anion channel (VDAC) and other proteins. The repulsion of PTP by hexokinase would reduce the pore size and the release of cytochrome C. Thus, the apoptosome-caspase proteolytic structure does not assemble in the cytoplasm. The liver hexokinase or glucokinase, is different it has less interaction with the site, has a lower affinity for glucose; because of this difference, glucose goes preferentially to the brain.

Further, phosphofructokinase gives fructose 1-6 bis phosphate; glycolysis is stimulated if an allosteric analogue, fructose 2-6 bis phosphate increases in response to a decrease of cAMP. The activation of insulin receptors in tumors has multiple effects, among them; a decrease of cAMP, which will stimulate glycolysis.

Another control point is glyceraldehyde P dehydrogenase that requires NAD+ in the glycolytic direction. If the oxygen supply is normal, the mitochondria malate/aspartate (MAL/ASP) shuttle forms the required NAD+ in the cytosol and NADH in the mitochondria. In hypoxic conditions, the NAD+ will essentially come via lactate dehydrogenase converting pyruvate into lactate. This reaction is prominent in tumor cells; it is the first discovery of Warburg on cancer.

At the last step of glycolysis, pyruvate kinase (PK) converts phosphoenolpyruvate (PEP) into pyruvate, which enters in the mitochondria as acetyl CoA, starting the citric acid cycle and oxidative metabolism. To explain the PK situation in tumors we must recall that PK only works in the glycolytic direction, from PEP to pyruvate, which implies that gluconeogenesis uses other enzymes for converting pyruvate into PEP. In starvation, when cells need glucose, one switches from glycolysis to gluconeogenesis and ketogenesis; PK and pyruvate dehydrogenase (PDH) are off, in a phosphorylated form, presumably following a cAMP-glucagon-adrenergic signal. In parallel, pyruvate carboxylase (Pcarb) becomes active. Moreover, in starvation, much alanine comes from muscle protein proteolysis, and is transaminated into pyruvate. Pyruvate carboxylase first converts pyruvate to OAA and then, PEP carboxykinase converts OAA to PEP etc…, until glucose. The inhibition of PK is necessary, if not one would go back to pyruvate. Phosphorylation of PK, and alanine, inhibit the enzyme.

Well, tumors have a PK and a PDH inhibited by phosphorylation and alanine, like for gluconeogenesis, in spite of an increased glycolysis! Moreover, in tumors, one finds a particular PK, the M2 embryonic enzyme [2,9,10] the dimeric, phosphorylated form is inactive, leading to a “bottleneck “. The M2 PK has to be activated by fructose 1-6 bis P its allosteric activator, whereas the M1 adult enzyme is a constitutive active form. The M2 PK bottleneck between glycolysis and the citric acid cycle is a typical feature of tumor cell glycolysis.

We also know that starvation mobilizes lipid stores from adipocyte to form ketone bodies, they are like glucose, nutriments for cells. Growth hormone, cAMP, AMP, activate a lipase, which provides fatty acids; their β oxidation cuts them into acetyl CoA in mitochondria and in peroxisomes for very long fatty acids; forming ketone bodies. Normally, citrate synthase slows down, to spare acetyl CoA for the ketogenic route, and OAA for the gluconeogenic pathway. Like for starvation, tumors mobilize lipid stores. But here, citrate synthase activity is elevated, condensing acetyl CoA and OAA [1113]; citrate increases, ketone bodies decrease. Consequently, ketone bodies will stop stimulating Pcarb. In tumors, the OAA needed for citrate synthase will presumably come from PEP, via reversible PEP carboxykinase or other sources. The quiescent Pcarb will not process the pyruvate produced by alanine transamination after proteolysis, leaving even more pyruvate to lactate dehydrogenase, increasing the lactate released by the tumor, and the NAD+ required for glycolysis.

Above the bottleneck, the massive entry of glucose accumulates PEP, which converts to OAA via mitochondria PEP carboxykinase, an enzyme requiring biotine-CO2-GDP. This source of OAA is abnormal, since Pcarb, another biotin-requiring enzyme, should have provided OAA. Tumors may indeed contain “morule inclusions” of biotin-enzyme [14] suggesting an inhibition of Pcarb, presumably a consequence of the maintained citrate synthase activity, and decrease of ketone bodies that normally stimulate Pcarb. The OAA coming via PEP carboxykinase and OAA coming from aspartate transamination or via malate dehydrogenase condenses with acetyl CoA, feeding the elevated tumoral citric acid condensation starting the Krebs cycle. Thus, tumors have to find large amounts of acetyl CoA for their condensation reaction; it comes essentially from lipolysis and β oxidation of fatty acids, and enters in the mitochondria via the carnitine transporter. This is the major source of acetyl CoA; since PDH that might have provided acetyl CoA remains in tumors, like PK, in the inactive phosphorylated form. The blockade of PDH [15] was recently reversed by inhibiting its kinase [16,17].

The key question is then to find out why NADH, a natural citrate synthase inhibitor did not switch off the enzyme in tumor cells. Probably, the synthesis of NADH by the dehydrogenases of the Krebs cycle and malate/aspartate shuttle, was too low, or the oxidation of NADH via the respiratory electron transport chain and mitochondrial complex1 (NADH dehydrogenase) was abnormally elevated. Another important point concerns PDH and α ketoglutarate dehydrogenase that are homologous enzymes, they might be regulated in a concerted way; when PDH is off, α ketoglutarate dehydrogenase might be also be slowed. Moreover, this could be associated to an upstream inhibition of aconinase by NO, or more probably to a blockade of isocitrate dehydrogenase, which favors in tumor cells, the citrate efflux from mitochondria, and the ATP citrate lyase route.

Normally, an increase of NADH inhibits the citrate condensation, favoring the ketogenic route associated to gluconeogenesis, which turns off glycolysis. Apparently, this regulation does not occur in tumors, since citrate synthase remains active. Moreover, in tumor cells, the α ketoglutarate not processed by
α ketoglutarate dehydrogenase converts to glutamate, via glutamate dehydrogenase, in this direction the reaction forms NAD+, backing up the LDH production. Other sources of glutamate are glutaminolysis, which increases in tumors [2].

The Figure Figure11 shows how tumors bypass the PK and PDH bottlenecks and evidently, the increase of glucose influx above the bottleneck, favors the supply of substrates to the pentose shunt, as pentose is needed for synthesizing ribonucleotides, RNA and DNA. The Figure Figure11 represents the stop below the citrate condensation. Hence, citrate quits the mitochondria to give via ATP citrate lyase, acetyl CoA and OAA in the cytosol of tumor cells. Acetyl CoA supports the synthesis of fatty acids and the formation of triglycerides. The other product of the ATP citrate lyase reaction, OAA, drives the transaminase cascade (ALAT and GOT transaminases) in a direction that consumes GLU and glutamine and converts in fine alanine into pyruvate and lactate plus NAD+. This consumes protein body stores that provide amino acids and much alanine (like in starvation).

The Figure Figure11 indicates that malate dehydrogenase is a source of NAD+ converting OAA into malate, which backs-up LDH. Part of the malate converts to pyruvate (malic enzyme) and processed by LDH. Moreover, malate enters in mitochondria via the shuttle and gives back OAA to feed the citrate condensation. Glutamine will also provide amino groups for the “de novo” synthesis of purine and pyrimidine bases particularly needed by tumor cells. The Figure Figure11 indicates that ASP shuttled out of the mitochondrial, joins the ASP formed by cytosolic transaminases, to feed the synthesis of pyrimidine bases via ASP transcarbamylase, a process also enhanced in tumor cells. In tumors, this silences the argininosuccinate synthetase step of the urea cycle [1820].

This blockade also limits the supply of fumarate to the Krebs cycle. The latter, utilizes the α ketoglutarate provided by the transaminase reaction, since α ketoglutarate coming via aconitase slows down. Indeed, NO and peroxynitrite increase in tumors and probably block aconitase. The Figure Figure11 indicates the cleavage of arginine into urea and ornithine. In tumors, the ornithine production increases, following the polyamine pathway. Ornithine is decarboxylated into putrescine by ornithine decarboxylase, then it captures the backbone of S adenosyl methionine (SAM) to form polyamines spermine then spermidine, the enzyme controlling the process is SAM decarboxylase. The other reaction product, 5-methlthioribose is then decomposed into methylthioribose and adenine, providing purine bases to the tumor. We shall analyze below the role of SAM in the carcinogenic mechanism, its destruction aggravates the process.

metabolic pathways 1476-4598-10-70-1
Cancer metabolism. Glycolysis is elevated in tumors, but a pyruvate kinase (PK) “bottleneck” interrupts phosphoenol pyruvate (PEP) to pyruvate conversion. Thus, alanine following muscle proteolysis transaminates to pyruvate, feeding lactate dehydrogenase,

In summary, it is like if the mechanism switching from gluconeogenesis to glycolysis was jammed in tumors, PK and PDH are at rest, like for gluconeogenesis, but citrate synthase is on. Thus, citric acid condensation pulls the glucose flux in the glycolytic direction, which needs NAD+; it will come from the pyruvate to lactate conversion by lactate dehydrogenase (LDH) no longer in competition with a quiescent Pcarb. Since the citrate condensation consumes acetyl CoA, ketone bodies do not form; while citrate will support the synthesis of triglycerides via ATP citrate lyase and fatty acid synthesis… The cytosolic OAA drives the transaminases in a direction consuming amino acid. The result of these metabolic changes is that tumors burn glucose while consuming muscle protein and lipid stores of the organism. In a normal physiological situation, one mobilizes stores for making glucose or ketone bodies, but not while burning glucose! Tumor cell metabolism gives them a selective advantage over normal cells. However, one may attack some vulnerable points.

Cancer metabolism. Glycolysis is elevated in tumors, but a pyruvate kinase (PK) “bottleneck” interrupts phosphoenol pyruvate (PEP) to pyruvate conversion. Thus, alanine following muscle proteolysis transaminates to pyruvate, feeding lactate dehydrogenase, converting pyruvate to lactate, (Warburg effect) and NAD+ required for glycolysis. Cytosolic malate dehydrogenase also provides NAD+ (in OAA to MAL direction). Malate moves through the shuttle giving back OAA in the mitochondria. Below the PK-bottleneck, pyruvate dehydrogenase (PDH) is phosphorylated (second bottleneck). However, citrate condensation increases: acetyl-CoA, will thus come from fatty acids β-oxydation and lipolysis, while OAA sources are via PEP carboxy kinase, and malate dehydrogenase, (pyruvate carboxylase is inactive). Citrate quits the mitochondria, (note interrupted Krebs cycle). In the cytosol, ATPcitrate lyase cleaves citrate into acetyl CoA and OAA. Acetyl CoA will make fatty acids-triglycerides. Above all, OAA pushes transaminases in a direction usually associated to gluconeogenesis! This consumes protein stores, providing alanine (ALA); like glutamine, it is essential for tumors. The transaminases output is aspartate (ASP) it joins with ASP from the shuttle and feeds ASP transcarbamylase, starting pyrimidine synthesis. ASP in not processed by argininosuccinate synthetase, which is blocked, interrupting the urea cycle. Arginine gives ornithine via arginase, ornithine is decarboxylated into putrescine by ornithine decarboxylase. Putrescine and SAM form polyamines (spermine spermidine) via SAM decarboxylase. The other product 5-methylthioadenosine provides adenine. Arginine deprivation should affect tumors. The SAM destruction impairs methylations, particularly of PP2A, removing the “signaling kinase brake”, PP2A also fails to dephosphorylate PK and PDH, forming the “bottlenecks”. (Black arrows = interrupted pathways).

 II Starters for cancer metabolic anomaly

1. Lessons from oncogenes

Following the discovery of Rous sarcoma virus transmitting cancer [21], we have to wait the work of Stehelin [22] to realize that this retrovirus only transmitted a gene captured from a previous host. When one finds that the transmitted gene encodes the Src tyrosine kinase, we are back again to the tyrosine kinase signals, similar to those activated by insulin or IGF, which control carbohydrate metabolism, anabolism and mitosis.

An up regulation of the gene product, now under viral control causes tumors. However, the captured viral oncogene (v-oncogene) derives from a normal host gene the proto-oncogene. The virus only perturbs the expression of a cellular gene the proto-oncogene. It may modify its expression, or its regulation, or transmit a mutated form of the proto-oncogene. Independently of any viral infection, a similar tumorigenic process takes place, if the proto-oncogene is translocated in another chromosome; and transcribed under the control of stronger promoters. In this case, the proto-oncogene becomes an oncogene of cellular origin (c-oncogene). The third mode for converting a prot-oncogene into an oncogene occurs if a retrovirus simply inserts its strong promoters in front of the proto-oncogene enhancing its expression.

It is impressive to find that retroviral oncogenes and cellular oncogenes disturb this major signaling pathway: the MAP kinases mitogenic pathways. At the ligand level we find tumors such Wilm’s kidney cancer, resulting from an increased expression of insulin like growth factor; we have also the erbB or V-int-2 oncogenes expressing respectively NGF and FGF growth factor receptors. The receptors for these ligands activate tyrosine kinase signals, similarly to insulin receptors. The Rous sarcoma virus transmits the src tyrosine kinase, which activates these signals, leading to a chicken leukemia. Similarly, in murine leukemia, a virus captures and retransmits the tyrosine kinase abl. Moreover, abl is also stimulated if translocated and expressed with the bcr gene of chromosome 22, as a fusion protein (Philadelphia chromosome). Further, ahead Ras exchanging protein for GTP/GDP, and then the Raf serine-threonine kinases proto-oncogenes are known targets for oncogenes. Finally, at the level of transcription factors activated by MAP kinases, one finds cjun, cfos or cmyc. An avian leucosis virus stimulates cmyc, by inserting its strong viral promoter. The retroviral attacks boost the mitogenic MAP kinases similarly to inflammatory cytokins, or to insulin signals, that control glucose transport and gycolysis.

In addition to the MAP kinase mitogenic pathway, tyrosine kinase receptors activate PI3 kinase pathways; PTEN phosphatase counteracts this effect, thus acting as a tumor suppressor. Recall that a DNA virus, the Epstein-Barr virus of infectious mononucleose, gives also the Burkitt lymphoma; the effect of the virus is to enhance PI3 kinase. Down stream, we find mTOR (the target of rapamycine, an immune-suppressor) mTOR, inhibits PP2A phosphatase, which is also a target for the simian SV40 and Polyoma viruses. Schematically, one may consider that the different steps of MAP kinase pathways are targets for retroviruses, while the different steps of PI3 kinase pathway are targets for DNA viruses. The viral-driven enhanced function of these pathways mimics the effects of their prolonged activation by their usual triggers, such as insulin or IGF; one then expects to find an associated increase of glycolysis. The insulin or IGF actions boost the cellular influx of glucose and glycolysis. However, if the signaling pathway gets out of control, the tyrosine kinase phosphorylations may lead to a parallel PK blockade [35] explaining the tumor bottleneck at the end of glycolysis. Since an activation of enyme kinases may indeed block essential enzymes (PK, PDH and others); in principle, the inactivation of phosphatases may also keep these enzymes in a phosphorylated form and lead to a similar bottleneck and we do know that oncogenes bind and affect PP2A phosphatase. In sum, a perturbed MAP kinase pathway, elicits metabolic features that would give to tumor cells their metabolic advantage.

2. The methylation hypothesis and the role of PP2A phosphatase

In a remarkable comment, Newberne [23] highlights interesting observations on the carcinogenicity of diethanolamine [24] showing that diethanolamine decreased choline derivatives and methyl donors in the liver, like does a choline deficient diet. Such conditions trigger tumors in mice, particularly in the B6C3F1 strain. Again, the historical perspective recalled by Newberne’s comment brings us back to insulin. Indeed, after the discovery of insulin in 1922, Banting and Best were able to keep alive for several months depancreatized dogs, treated with pure insulin. However, these dogs developed a fatty liver and died. Unlike pure insulin, the total pancreatic extract contained a substance that prevented fatty liver: a lipotropic substance identified later as being choline [25]. Like other lipotropes, (methionine, folate, B12) choline supports transmethylation reactions, of a variety of substrates, that would change their cellular fate, or action, after methylation. In the particular case concerned here, the removal of triglycerides from the liver, as very low-density lipoprotein particles (VLDL), requires the synthesis of lecithin, which might decrease if choline and S-adenosyl methionine (SAM) are missing. Hence, a choline deficient diet decreases the removal of triglycerides from the liver; a fatty liver and tumors may then form. In sum, we have seen that pathways exemplified by the insulin-tyrosine kinase signaling pathway, which control anabolic processes, mitosis, growth and cell death, are at each step targets for oncogenes; we now find that insulin may also provoke fatty liver and cancer, when choline is not associated to insulin.

We must now find how the lipotropic methyl donor controls the signaling pathway. We know that after the tyrosine kinase reaction, serine-threonine kinases take over along the signaling route. It is thus highly probable that serine-threonine phosphatases will counteract the kinases and limit the intensity of the insulin or insulin like signals. One of the phosphatases involved is PP2A, itself the target of DNA viral oncogenes (Polyoma or SV40 antigens react with PP2A subunits and cause tumors). We found a possible link between the PP2A phosphatase brake and choline in works on Alzheimer’s disease [26]. Indeed, the catalytic C subunit of PP2A is associated to a structural subunit A. When C receives a methyle, the dimer recruits a regulatory subunit B. The trimer then targets specific proteins that are dephosphorylated [27].

In Alzheimer’s disease, the poor methylation of PP2A is associated to an increase of homocysteine in the blood [26]. The result of the PP2A methylation failure is a hyperphosphorylation of Tau protein and the formation of tangles in the brain. Tau protein is involved in tubulin polymerization, controlling axonal flow but also the mitotic spindle. It is thus possible that choline, via SAM, methylates PP2A, which is targeted toward the serine-threonine kinases that are counteracted along the insulin-signaling pathway. The choline dependent methylation of PP2A is the brake, the “antidote”, which limits “the poison” resulting from an excess of insulin signaling. Moreover, it seems that choline deficiency is involved in the L to M2 transition of PK isoenzymes [28].

3. Cellular distribution of PP2A

In fact, the negative regulation of Ras/MAP kinase signals mediated by PP2A phosphatase seems to be complex. The serine-threonine phosphatase does more than simply counteracting kinases; it binds to the intermediate Shc protein on the signaling cascade, which is inhibited [29]. The targeting of PP2A towards proteins of the signaling pathway depends of the assembly of the different holoenzymes. The carboxyl methylation of C-terminal leucine 309 of the catalytic C unit, permits to a dimeric form made of C and a structural unit A, to recruit one of the many regulatory units B, giving a great diversity of possible enzymes and effects. The different methylated ABC trimers would then find specific targets. It is consequently essential to have more information on methyl transferases and methyl esterases that control the assembly or disassembly of PP2A trimeric forms.

A specific carboxyl methyltransferase for PP2A [30] was purified and shown to be essential for normal progression through mitosis [31]. In addition, a specific methylesterase that demethylates PP2A has been purified [32]. Is seems that the methyl esterase cancels the action of PP2A, on signaling kinases that increase in glioma [33]. Evidently, the cellular localization of the methyl transferase (LCMT-1) and the phosphatase methyl esterase (PME-1) are crucial for controlling PP2A methylation and targeting. Apparently, LCMT-1 mainly localizes to the cytoplasm and not in the nucleus, where PME-1 is present, and the latter harbors a nuclear localization signal [34]. From these observations, one may suggest that PP2A gets its methyles in the cytoplasm and regulates the tyrosine kinase-signaling pathway, attenuating its effects.

A methylation deficit should then decrease the methylation of PP2A and boost the mitotic insulin signals as discussed above for choline deficiency, steatosis and hepatoma. At the nucleus, where PME-1 is present, it will remove the methyl, from PP2A, favoring the formation of dimeric AC species that have different targets, presumably proteins involved in the cell cycle. It is interesting to quote here the structural mechanism associated to the demethylation of PP2A. The crystal structures of PME-1 alone or in complex with PP2A dimeric core was reported [35] PME-1 binds directly to the active site of PP2A and this rearranges the catalytic triad of PME-1 into an active conformation that should demethylate PP2A, but this also seems to evict a manganese required for the phosphatase activity. Hence, demethylation and inactivation would take place in parallel, blocking mitotic actions.

However, another player is here involved, the so-called PTPA protein, which is a PP2A phosphatase activator. Apparently, this activator is a new type of cis/trans of prolyl isomerase, acting on Pro190 of the catalytic C unit isomerized in presence of Mg-ATP [36], which would then cancel the inactivation mediated by PME-1. Following the PTPA action, the demethylated phosphatase would become active again in the nucleus, and stimulate cell cycle proteins [37,38] inducing mitosis. Unfortunately, the ligand of this new prolyl isomerase is still unknown. Moreover, we have to consider that other enzymes such as cytochrome P450 have also demethylation properties.

In spite of deficient methylations and choline dehydrogenase pathway, tumor cells display an enhanced choline kinase activity, associated to a parallel synthesis of lecithin and triglycerides.

The hypothesis to consider is that triglycerides change the fate of methylated PP2A, by targeting it to the nucleus, there a methylesterase demethylates it; the phosphatase attacks new targets such as cell cycle proteins, inducing mitosis. Moreover, the phosphatase action on nuclear membrane proteins may render the nuclear membrane permeable to SAM the general methyl donor; promoters get methylated inducing epigenetic changes.

The relative decrease of methylated PP2A in the cytosol, not only cancels the brake over the signaling kinases, but also favors the inactivation of PK and PDH, which remain phosphorylated, contributing to the metabolic anomaly of tumor cells.

In order to prevent tumors, one should then favor the methylation route rather than the phosphorylation route for choline metabolism. This would decrease triglycerides, promote the methylation of PP2A and keep it in the cytosol, reestablishing the brake over signaling kinases.

Hypoxia is an essential issue to discuss

Many adequate “adult proteins” replace their fetal isoform: muscle proteins utrophine, switches to dystrophine; enzymes such as embryonic M2 PK [39] is replaced by M1. Hypoxic conditions seem to trigger back the expression of the fetal gene packet via HIF1-Von-Hippel signals. The mechanism would depend of a double switch since not all fetal genes become active after hypoxia. First, the histones have to be in an acetylated form, opening the way to transcription factors, this depends either of histone deacetylase (HDAC) inhibition or of histone acetyltransferase (HAT) activation, and represents the main switch. Second, a more specific switch must be open, indicating the adult/fetal gene couple concerned, or more generally the isoform of a given gene that is more adapted to the specific situation. When the adult gene mutates, an unbound ligand may indeed indicate, directly or indirectly, the particular fetal copy gene to reactivate [40]. In anoxia, lactate is more difficult to release against its external gradient, leading to a cytosolic increase of up-stream glycolytic products, 3P glycerate or others. These products may then be a second signal controlling the specific switch for triggering the expression of fetal genes, such as fetal hemoglobin or the embryonic M2 PK; this takes place if histones (main switch) are in an acetylated form.

Growth hormone-IGF actions, the control of asymmetrical mitosis

When IGF – Growth hormone operate, the fatty acid source of acetyl CoA takes over. Indeed, GH stimulates a triglyceride lipase in adipocytes, increasing the release of fatty acids and their β oxidation. In parallel, GH would close the glycolytic source of acetyl CoA, perhaps inhibiting the hexokinase interaction with the mitochondrial ANT site. This effect, which renders apoptosis possible, does not occur in tumor cells. GH mobilizes the fatty acid source of acetyl CoA from adipocytes, which should help the formation of ketone bodies, but since citrate synthase activity is elevated in tumors, ketone bodies do not form.

Compounds for correcting tumor metabolism

The figure figure1 indicates interrupted and enhanced metabolic pathways in tumor cells.

In table table1,1, the numbered pathways represent possible therapeutic targets; they cover several enzymes. When the activity of the pathway is increased, one may give inhibitors; when the activity of the pathway decreases, we propose possible activators

Table - metabolic  targets

Table 1 Mol Cancer. 2011; 10 70. Published online Jun 7, 2011. doi  10.1186_1476-4598-10-70

The origin of Cancers by means of metabolic selection

The disruption of cells by internal or external compounds, releases substrates stimulating the tyrosine kinase signals for anabolism proliferation and stem cell repair, like for most oncogenes. If such signals are not limited, there is a parallel blockade of key metabolic enzymes by activated kinases or inhibited phosphatases. The result is a metabolism typical of tumor cells, which gives them a selective advantage; stabilized by epigenetic changes. A proliferation process, in which the two daughter cells divide, increases the tumor mass at the detriment of the body. Inevitable mutations follow.

Maurice Israël, et al. Mol Cancer. 2011;10:70-70.
Transcriptomics and Regulatory Processes

What are lncRNAs?

It was traditionally thought that the transcriptome would be mostly comprised of mRNAs, however advances in high-throughput RNA sequencing technologies have revealed the complexity of our genome. Non-coding RNA is now known to make up the majority of transcribed RNAs and in addition to those that carry out well-known housekeeping functions (e.g. tRNA, rRNA etc), many different types of regulatory RNAs have been and continue to be discovered.

Long noncoding RNAs (lncRNAs) are a large and diverse class of transcribed RNA molecules with a length of more than 200 nucleotides that do not encode proteins. Their expression is developmentally regulated and lncRNAs can be tissue- and cell-type specific. A significant proportion of lncRNAs are located exclusively in the nucleus. They are comprised of many types of transcripts that can structurally resemble mRNAs, and are sometimes transcribed as whole or partial antisense transcripts to coding genes. LncRNAs are thought to carry out important regulatory functions, adding yet another layer of complexity to our understanding of genomic regulation.

lncRNA-s   A summary of the various functions described for lncRNA

 

The evolution of genome-scale models of cancer metabolism
The importance of metabolism in cancer is becoming increasingly apparent with the identification of metabolic enzyme mutations and the growing awareness of the influence of metabolism on signaling, epigenetic markers, and transcription. However, the complexity of these processes has challenged our ability to make sense of the metabolic changes in cancer. Fortunately, constraint-based modeling, a systems biology approach, now enables one to study the entirety of cancer metabolism and simulate basic phenotypes. With the newness of this field, there has been a rapid evolution of both the scope of these models and their applications. (NE Lewis and AM.Abdel-Haleem. frontiers physiol  2013;4(237): 1   http://dx.doi.org/10.3389/fphys.2013.00237)

Here we review the various constraint-based models built for cancer metabolism and how their predictions are shedding new light on basic cancer phenotypes, elucidating pathway differences between tumors, and discovering putative anti-cancer targets. As the field continues to evolve, the scope of these genome-scale cancer models must expand beyond central metabolism to address questions related to the diverse processes contributing to tumor development and metastasis.

“One of the goals of cancer research is to ascertain the mechanisms of cancer.”These words, penned by Dulbecco (1986), began a treatise on how a mechanistic understanding of cancer requires a sequenced human genome. Now with the abundance of sequence data, we are finding diverse genetic changes among different cancers (Vogelstein et al.,2013). While we are cataloging these mutations, the associated mechanisms leading to phenotypic changes are often unclear since mutations occur in the context of complex biological networks. For example, mutations to isocitrate dehydrogenase lead to oncometabolite synthesis, which alters DNA methylation and ultimately changes gene expression and the balance of normal cell processes (Sasakietal.,2012). Furthermore, many different combinations of mutations can lead to cancer. Since the genetic heterogeneity between tumors can be large, the biomolecular mechanisms underlying tumor physiology can vary substantially.

This is apparent in metabolism, where tumors can differ in serine metabolism  dependence (Possematoetal., 2011) or TCA cycle function (Frezzaetal., 2011b). In addition, diverse mutations can alter NADPH synthesis by differentially regulat ing  signaling pathways, such as the AMPK pathway (Cairnsetal., 2011; Jeonetal., 2012). The challenges regarding complexity and heterogeneity in cancer metabolism are beginning to be addressed with the COnstraint-Based Reconstruction and Analysis (COBRA) approach (Hernández Patiñoetal., 2012; Sharma and König,  2013), an emerging field in systems biology.Specifically, it accounts for the complexity of the perturbed biochemical processes by using genome-scale metabolic network reconstructions (Duarteetal., 2007; Maetal., 2007;Thieleetal., 2013).

In a reconstruction, the stoichiometric chemical reactions in a cell are carefully annotated and stitched together into a large network, often containing thousands of reactions. Genes and enzymes associated with each reaction are also delineated. The networks are converted into computational models and analyzed using many algorithms (Lewisetal., 2012). COBRA approaches are also beginning to address heterogeneity in cancer by integrating experimental data with the reconstructions (Blazier and Papin, 2012; Hydukeetal., 2013)  to tailor the models to the unique gene expression profiles of general cancer tissue, and even individual cell lines and tumors. Here we describe the recent conceptual evolution that has occurred for constraint-based cancer modeling.

Targeting of  gene expression

Tumor Suppressor Genes and its Implications in Human Cancer

Gain-of-function mutations in oncogenes and loss-of-function mutations in tumor suppressor genes (TSG) lead to cancer. In most human cancers, these mutations occur in somatic tissues. However, hereditary forms of cancer exist for which individuals are heterozygous for a germline mutation in a TSG locus at birth. The second allele is frequently inactivated by gene deletion, point mutation, or promoter methylation in classical TSGs that meet Knudson’s two-hit hypothesis. Conversely, the second allele remains as wild-type, even in tumors in which the gene is haplo-insufficient for tumor suppression. (K Inoue, EA Fry and Pj Taneja. Recent Progress in Mouse Models for Tumor Suppressor Genes and its Implications in Human Cancer. Clinical Medicine Insights: Oncology2013:7 103–122). This article highlights the importance of PTEN, APC, and other tumor suppressors for counteracting aberrant PI3K, β-catenin, and other oncogenic signaling pathways. We discuss the use of gene-engineered mouse models (GEMM) of human cancer focusing on Pten and Apc knockout mice that recapitulate key genetic events involved in initiation and progression of human neoplasia.

Targeting cancer metabolism – aiming at a tumour’s sweet-spot
Neil P. Jones and Almut Schulze
Drug Discovery Today   January 2012

Targeting cancer metabolism has emerged as a hot topic for drug discovery. Most cancers have a high demand for metabolic inputs (i.e. glucose/glutamine), which aid proliferation and survival. Interest in targeting cancer metabolism has been renewed in recent years with the discovery that many cancer related (e.g. oncogenic and tumor suppressor) pathways have a profound effect on metabolism and that many tumors become dependent on specific metabolic processes. Considering the recent increase in our understanding of cancer metabolism and the increasing knowledge of the enzymes and pathways involved, the question arises: could metabolism be cancer’s Achilles heel?
During recent years, interest into the possible therapeutic benefit of targeting metabolic pathways in cancer has increased dramatically with academic and pharmaceutical groups actively pursuing this aspect of tumor physiology. Therefore, what has fuelled this revived interest in targeting cancer metabolism and what are the major advances and potential challenges faced in the race to develop new therapeutics in this area? This review will attempt to answer these questions and illustrate why we, and others, believe that targeting metabolism in cancer presents such a promising therapeutic rationale.

Oncogenes and cancer metabolism
Glycolysis  TCA cycle  Pentose phosphate pathway

 FIGURE 1

Schematic representation of the regulation of cancer metabolism pathways. Metabolic enzymes are regulated by signaling pathways involving oncogenes and tumor suppressors. Complex regulatory mechanisms, key pathway interactions and enzymes are shown along with key metabolic endpoints (shown in purple) necessary for proliferation and survival (biosynthetic intermediates and NADPH). Key oncogenic pathways are shown in green and key tumor suppressor pathways are shown in red. Mutant IDH (mIDH) pathway is listed but is only functional in cancers containing mIDH.

FIGURE 2

Schematic representation of key components of the pentose phosphate pathway (PPP). Key enzymes are shown in blue boxes and key intermediates in purple text/box outline. DNA damage can activate ATM which in turn activates G6PDH to upregulate nucleotide synthesis for DNA repair and NAPDH to combat reactive oxygen species. PPP is also regulated by the tumour suppressor p53. The PPP can function as two separate branches (oxidative and non-oxidative) or be coupled into a recycling pathway – the pentose phosphate shunt – for maximum NADPH production.

Serine biosynthesis

Another branch diverting from glycolysis recently implicated in cancer is the serine biosynthesis pathway which converts the glycolytic intermediate 3-phosphoglycerate into serine (Fig. 3). Serine is an amino acid and an important neurotransmitter but can also provide fuel for the synthesis of other amino acids and nucleotides. The serine biosynthesis pathway also provides another key metabolic intermediate, a-KG, from glutamate breakdown via the action of phosphoserine aminotransferase (PSAT1). This pathway couples glycolysis (via 3-phosphoglycerate) with glutaminolysis (via glutamate), thereby linking two metabolic pathways known to be activated in many cancers.

FIGURE 3

Schematic representation of the serine biosynthesis pathway. Synthesis of serine involves integration of metabolites from glycolysis and  glutaminolysis pathways  and generates a-ketoglutarate, a key biosynthetic intermediate, and serine. Serine has many essential uses in the cell including amino acid, phospholipid and nucleotide synthesis.

 

Silencing of tumor suppressor genes by recruiting DNA methyltransferase 1 (DNMT1)

Ubiquitin-like containing PHD and Ring finger 1 (UHRF1) contributes to silencing of tumor suppressorgenes by recruiting DNA methyltransferase 1 (DNMT1) to their hemi-methylated promoters. Conversely,demethylation of these promoters has been ascribed to the natural anti-cancer drug, epigallocatechin-3-gallate (EGCG). The aim of the present study was to investigate whether the UHRF1/DNMT1 pair is an important target of EGCG action.  (Mayada Achour, et al. Epigallocatechin-3-gallate up-regulates tumor suppressor gene expression via a reactive oxygen species-dependent down-regulation of UHRF1.  Biochemical and Biophysical Research Communications 430 (2013) 208–212.    http://dx.doi.org/10.1016/j.bbrc.2012.11.087)

Here, we show that EGCG down-regulates UHRF1 and DNMT1 expression in Jurkat cells, with subsequent up-regulation of p73 and p16INK4A genes. The down-regulation of UHRF1 is dependent upon the generation of reactive oxygen species by EGCG. Up-regulation of p16INK4A  is strongly correlated with decreased promoter binding by UHRF1. UHRF1 over-expression counteracted EGCG-induced G1-arrested cells, apoptosis, and up-regulation of p16INK4A and p73. Mutants of the Set and Ring Associated (SRA) domain of UHRF1 were unable to down-regulate p16INK4A and p73, either in the presence or absence of EGCG. Our results show that down-regulation of UHRF1 is upstream to many cellular events, including G1 cell arrest, up-regulation of tumor suppressor genes and apoptosis.

Tumor Suppressor Activity of a Constitutively-Active ErbB4 Mutant

ErbB4 (HER4) is a member of the ErbB family of receptor tyrosine kinases, which includes the Epidermal Growth Factor Receptor (EGFR/ErbB1), ErbB2 (HER2/Neu), and ErbB3 (HER3). Mounting evidence indicates that ErbB4, unlike EGFR or ErbB2, functions as a tumor suppressor in many human malignancies. Previous analyses of the constitutively-dimerized and –active ErbB4 Q646C mutant indicate that ErbB4 kinase activity and phosphorylation of ErbB4 Tyr1056 are both required for the tumor suppressor activity of this mutant in human breast, prostate, and pancreatic cancer cell lines. However, the cytoplasmic region of ErbB4 possesses additional putative functional motifs, and the contributions of these functional motifs to ErbB4 tumor suppressor activity have been largely underexplored.  (Citation: Richard M. Gallo, et al. (2013) Multiple Functional Motifs Are Required for the Tumor Suppressor Activity of a Constitutively-Active ErbB4 Mutant. J Cancer Res Therap Oncol 1: 1-10)

Here we demonstrate that ErbB4 BH3 and LXXLL motifs, which are thought to mediate interactions with Bcl family proteins and steroid hormone receptors, respectively, are required for the tumor suppressor activity of the ErbB4 Q646C mutant. Furthermore, abrogation of the site of ErbB4 cleavage by gamma-secretase also disrupts the tumor suppressor activity of the ErbB4 Q646C mutant. This last result suggests that ErbB4 cleavage and subcellular trafficking of the ErbB4 cytoplasmic domain may be required for the tumor suppressor activity of the ErbB4 Q646C mutant. Indeed, here we demonstrate that mutants that disrupt ErbB4 kinase activity, ErbB4 phosphorylation at Tyr1056, or ErbB4 cleavage by gamma-secretase also disrupt ErbB4 trafficking away from the plasma membrane and to the cytoplasm. This supports a model for ErbB4 function in which ErbB4 tumor suppressor activity is dependent on ErbB4 trafficking away from the plasma membrane and to the cytoplasm, mitochondria, and/or the nucleus.

EGF Receptor

 Initiation of pancreatic ductal adenocarcinoma (PDA) is definitively linked to activating mutations in the KRAS oncogene. However, PDA mouse models show that mutant Kras expression early in development gives rise to a normal pancreas, with tumors forming only after a long latency or pancreatitis induction.

(CM Ardito,BM Gruner. ,EGF Receptor Is Required for KRAS-Induced Pancreatic Tumorigenesis.  http://dx.doi.org/10.1016/j.ccr.2012.07.024)

Here, we show that oncogenic KRAS upregulates endogenous EGFR expression and activation, the latter being dependent on the EGFR ligand sheddase, ADAM17. Genetic ablation or pharmacological inhibition of EGFR or ADAM17 effectively eliminates KRAS-driven tumorigenesis in vivo. Without EGFR activity, active RAS levels are not sufficient to induce robust MEK/ERK activity, a requirement for epithelial transformation

The almost universal lethality of PDA has led to the intense study of genetic mutations responsible for its formation and progression. The most common oncogenic mutations associated with all PDA stages are found in the KRAS gene, suggesting it as the primary initiator of pancreatic neoplasia. However, mutant Kras expression throughout the mouse pancreatic parenchyma shows that the oncogene remains largely indolent until secondary events, such as pancreatitis, unlock its transforming potential. We find KRAS requires an inside-outside-in signaling axis that involves ligand-dependent EGFR activation to initiate the signal transduction and cell biological changes that link PDA and pancreatitis. (Cancer Cell (2012); 22: 304–317).

HER4 (EGFR/ErbB, HER2/Neu, HER3)

 ErbB4 (HER4) is a member of the ErbB family of receptor tyrosine kinases, which includes the Epidermal Growth Factor Receptor (EGFR/ErbB1), ErbB2 (HER2/Neu), and ErbB3 (HER3). Mounting evidence indicates that ErbB4, unlike EGFR or ErbB2, functions as a tumor suppressor in many human malignancies. Previous analyses of the constitutively-dimerized and –active ErbB4 Q646C mutant indicate that ErbB4 kinase activity and phosphorylation of ErbB4 Tyr1056 are both required for the tumor suppressor activity of this mutant in human breast, prostate, and pancreatic cancer cell lines. However, the cytoplasmic region of ErbB4 possesses additional putative functional motifs, and the contributions of these functional motifs to ErbB4 tumor suppressor activity have been largely underexplored.

ErbB4 Possesses Multiple Functional Motifs and Mutations Have Been Engineered to Target These Motifs.

The organization of ErbB4 is as indicated in this schematic. The extracellular ligand-binding motifs reside in the amino-terminal region upstream of amino acid residue 651. The singlepass transmembrane domain consists of amino acid residues 652-675. The cytoplasmic tyrosine kinase domain consists of amino acid residues 713-989. The majority of cytoplasmic sites of tyrosine phosphorylation reside in amino acid residues 990-1308, most notably Tyr1056. Additional putative functional motifs include a TACE cleavage site, a gamma-secretase cleavage site, two LXXLL (steroid hormone receptor binding) motifs, a BH3 domain, three WW domain binding motifs, and a PDZ domain binding motif. Mutations that disrupt these motifs are noted. Finally, note the two locations of alternative transcriptional splicing, resulting in a total of four different splicing isoforms.

 

 

 

Here we demonstrate that ErbB4 BH3 and LXXLL motifs, which are thought to mediate interactions with Bcl family proteins and steroid hormone receptors, respectively, are required for the tumor suppressor activity of the ErbB4 Q646C mutant. Furthermore, abrogation of the site of ErbB4 cleavageby gamma-secretase also disrupts the tumor suppressor activity of the ErbB4 Q646C mutant. This last result suggests that ErbB4 cleavage and subcellular trafficking of the ErbB4 cytoplasmic domain may be required for the tumor suppressor activity of the ErbB4 Q646C mutant. Indeed, here we demonstrate that mutants that disrupt ErbB4 kinase activity, ErbB4 phosphorylation at Tyr1056, or ErbB4 cleavage by gamma-secretase also disrupt ErbB4 trafficking away from the plasma membrane and to the cytoplasm. This supports a model for ErbB4 function in which ErbB4 tumor suppressor activity is dependent on ErbB4 trafficking away from the plasma membrane and to the cytoplasm, mitochondria, and/or the nucleus.

(Richard M. Gallo, et al. (2013) Multiple Functional Motifs Are Required for the Tumor Suppressor Activity of a Constitutively-Active ErbB4 Mutant. J Cancer Res Therap Oncol 1: 1-10)

Resistance to Receptor Tyrosine Kinase Inhibition

Receptor tyrosine kinases (RTKs) are activated by somatic genetic alterations in a subset of cancers, and such cancers are often sensitive to specific inhibitors of the activated kinase. Two well-established examples of this paradigm include lung cancers with either EGFR mutations or ALK translocations. In these cancers, inhibition of the corresponding RTK leads to suppression of key downstream signaling pathways, such as the PI3K (phosphatidylinositol 3-kinase)/AKT and MEK (mitogen-activated protein kinase kinase)/ERK (extracellular signal–regulated kinase) pathways, resulting in cell growth arrest and death. Despite the initial clinical efficacy of ALK (anaplastic lymphoma kinase) and EGFR (epidermal growth factor receptor) inhibitors in these cancers, resistance invariably develops, typically within 1 to 2 years. (MJ Niederst and JA Engelman. Sci Signal, 24 Sep 2013; 6(294), p. re6 .  http://dx.doi.org/10.1126/scisignal.2004652)

Over the past several years, multiple molecular mechanisms of resistance have been identified, and some common themes have emerged. One is the development of resistance mutations in the drug target that prevent the drug from effectively inhibiting the respective RTK. A second is activation of alternative RTKs that maintain the signaling of key downstream pathways despite sustained inhibition of the original drug target. Indeed, several different RTKs have been implicated in promoting resistance to EGFR and ALK inhibitors in both laboratory studies and patient samples. In this mini-review, we summarize the concepts underlying RTK-mediated resistance, the specific examples known to date, and the challenges of applying this knowledge to develop improved therapeutic strategies to prevent or overcome resistance.

The TGF-β Pathway

Aberrations in the enzymes that modify ubiquitin moieties have been observed to cause a myriad of diseases, including cancer. Therefore a better understanding of these enzymes and their substrates will lead to the identification of prospective druggable targets. Here we discuss the role of ubiquitin modifying enzymes in the canonical TGF-β pathway highlighting the ubiquitin regulating enzymes, which may potentially be targeted by small molecule inhibitors. (Pieter Eichhorn. (DE) -Ubiquitination in The TGF-β Pathway. J Cancer Res Therap Oncol 2013; 1: 1-6).

TGF-β is a multifunctional cytokine that plays a key role in embryogenesis and adult tissue homoeostasis. TGF-β is secreted by a myriad of cell types triggering a varied array of cellular functions including apoptosis, proliferation, migration, endothelial and mesenchymal transition, and extracellular matrix production. Downstream TGFβ responses can also be modulated by other signalling pathways (i.e. PI3K, ERK, WNT, etc.) resulting in a complex web of TGF-β pathway activation or repression depending on the nature of the signal and cellular context. Apart from TGF-β mediated cell autonomous effects TGF-β can further play an important function in regulating tumour microenvironments effecting the interaction between stromal fibroblasts and tumour cells.
Due to the central role of TGF-β in cellular processes it is therefore unsurprising that loss of TGF-β pathway integrity is frequently observed in a variety of human diseases, including cancer. However, the TGF-β pathway plays a complex dual role in cancer. In normal epithelial cells and premalignant cells TGF-β acts a potent tumor suppressor eliciting a cytostatic response inhibiting tumor progression. Supporting this notion, inactivating mutations in members of the TGF-βpathway have been observed in a variety of cancers including pancreatic, colorectal, and head and neck cancer.

In contrast, during tumor progression the TGF-β antiproliferative function is lost, and in certain advanced cancers TGF-β becomes an oncogenic factor inducing cellular proliferation, invasion, angiogenesis, and immune suppression. As a consequence, the TGFβ pathway is currently considered a therapeutic target in advanced cancers and several anti- TGF-β agents in clinical trials have shown promising results. However, due to the complex dichotomous role of TGF-β in oncogenesis a detailed understanding of TGF-β biology is required in order to design successful therapeutic strategies to identify patient populations that will benefit most from these compounds.

G protein receptor

 G protein-coupled receptors (GPCRs) modulate a vast array of cellular processes. The current review gives an overview of the general characteristics of GPCRs and their role in physiological conditions. In addition, it describes the current knowledge of the physiological and pathophysiological functions of GPR55, an orphan GPCR, and how it can be exploited as a therapeutic target to combat various cancers.

(D Leyva-Illades, S DeMorrow . Orphan G protein receptor GPR55 as an emerging target in cancer therapy and management.  Cancer Management and Research 2013:5 147–155)

Signal transduction is essential for maintaining cellular homeostasis and to coordinate the activity of cells in all organisms. Proteins localized in the cell membrane serve as the interface between the outside and inside of the cell. G protein-coupled receptors (GPCRs) are the largest and most diverse group of membrane receptors in eukaryotes and are encoded by at least 800 genes in the human genome. GPCRs are also known as seven-transmembrane domain receptors, 7TM receptors, heptahelical receptors, serpentine receptors, and G protein-linked receptors. GPCRs can detect an expansive array of extracellular signals or ligands that include photons, ions, odors, pheromones, hormones, and neurotransmitters. Nonsensory GPCRs (excluding light, odor, and taste receptors) have been classified into four families: class A rhodopsin-like, class B secretin-like, class C metabotropic glutamate/pheromone, and frizzled receptors. They have a peculiar structure that has been highly conserved over the course of evolution and are made up of an amino acid chain, the N-terminal of which is localized outside of the cellular membrane and the C-terminal in the cytoplasm. The amino acid chain spans the cellular membrane seven times and has three intracellular and three extracellular loops.

GPCRs are called that because they exert their actions by associating with a family of heterotrimeric proteins (made up of α, β, and γ subunits) that are capable of binding and hydrolyzing guanosine triphosphate (GTP).To date, 16 different α subunits, five β subunits, and 11 γ subunits have been described in mammalian tissues. When activated, these receptors undergo conformational changes that are mechanically transduced to the G proteins, which then initiate a cycle of activation and inactivationassociated with the binding and hydrolysis of GTP. Activated G proteins can then positively or negatively modulate ion channels (mainly potassium and calcium) or the second messenger generating enzymes (ie, adenylate cyclase and phospholipase C [PLC]) that allow the signal to be propagated to the interior of the cell to ultimately affect cell function.

 Matrix Metalloproteinases

Degradation of extracellular matrix is crucial for malignant tumour growth, invasion, metastasis and angiogenesis. Matrix metalloproteinases (MMPs) are a family of zinc-dependent neutral endopeptidases collectively capable of degrading essentially all  components of the ECM. Elevated levels of distinct MMPs can be detected in tumour tissue or serumof patients with advanced cancer and their role as prognostic indicators in cancer is studied. In addition, therapeutic intervention of tumour growth and invasion based on inhibition of MMP activity is under intensive investigation and several MMP inhibitors are in clinical trials in cancer. In this review, we discuss the current view on the feasibility of MMPs as prognostic markers and as targets for therapeutic intervention in cancer.

(MATRIX METALLOPROTEINASES IN CANCER: PROGNOSTIC MARKERS AND THERAPEUTIC TARGETS.

Pia Vihinen and Veli-Matti Kahari.  Int. J. Cancer 2002;99: 157–166. http://dx.doi.org/10.1002/ijc.10329

Common properties of the MMPs include the requirement of zinc in their catalytic site for activity and their synthesis as inactive zymogens that generally need to be proteolytically cleaved to be active. Normally the MMPs are expressed only when and where needed for tissue remodeling accompanies various processes such as during embryonic development, wound healing, uterine and mammary involution, cartilage-to-bone transition during ossification, and trophoblast invasion into the endometrial stoma during placenta development. However, aberrant expression of various MMPs has been correlated with pathological conditions, such as periodontitis, rheumatoid arthritis, and tumor cell invasion and metastasis .

There are now over 20 members of the MMP family, and they can be subgrouped based on their structures. The minimal domain structure consists of a signal peptide, prodomain, and catalytic domain. The propeptide domain contains a conserved cysteine residue (the “cysteine switch”) that coordinates to the catalytic zinc to maintain inactivity. MMPs with only the minimal domain are referred to as matrilysins (MMP-7 and -26). The most common structures for secreted MMPs, including collagenases and stromelysins, have an additional hemopexin-like domain connected by a hinge region to the catalytic domain (MMP-1, -3, -8, -10, -12, -13, -19, and -20).

Terms: 1FN, fibronectin; 2M, 2-macroglobulin; 1PI, 1-proteinase inhibitor; COMP, cartilage oligomeric matrix protein; ND, not determined; TACE, TNF-converting enzyme; OP, osteopontin

FIGURE 1 – Structure of human matrix metalloproteinases

 

FIGURE 1 – Structure of human matrix metalloproteinases. The signal peptide directs the proenzyme for secretion. The propeptide contains a conserved sequence (PRCGxPD), in which the cysteine forms a covalent bond (cysteine switch), with the catalytic zinc (Zn2_) to maintain the latency of proMMPs. Catalytic domain contains the highly conserved zinc binding site (HExGHxxGxxHS) in which Zn2_is coordinated by 3 histidines. The proline-rich hinge region links the catalytic domain to the hemopexin domain, which determines the substrate specificity of specific MMPs. The hemopexin domain is absent in matrilysin (MMP-7) and matrilysin-2 (endometase, MMP-26). Gelatinases  A and B (MMP-2 and MMP-9, respectively) contain 3 repeats of the fibronectin-type II domain inserted in the catalytic domain. MT1-, MT2-, MT3- and MT5-MMP contain a transmembrane domain and MT4- and MT6-MMPs contain a glycosylphosphatidylinositol (GPI) anchor in the C-terminus of the molecule, which attach these MMPs to the cell surface. MT-MMPs, MMP-11, MMP-23 and MMP-28 contain a furin cleavage site (RxKR) between the propeptide and catalytic domain, making these proenzymes susceptible to activation by intracellular furin convertases. MMP-23 contains an N-terminal signal anchor, which anchors proMMP-23 to the Golgi complex and has a different C-terminal domain instead of hemopexin-like domain.

The physiologic expression of MMP-13 in vivo is limited to situations, such as fetal bone development and fetal wound repair, in which rapid remodeling of collagenous ECM is required. MMP-13 is expressed in pathologic conditions, such as arthritis, chronic dermal and intestinal ulcers, chronic periodontal inflammation and atherosclerotic plaques. The expression of MMP-13 is detected in vivo in invasive malignant tumours, breast carcinomas, squamous cell carcinomas (SCCs) of the head and neck and vulva, malignant melanomas, chondrosarcomas and urinary bladder carcinomas.

Table I. Human MMPS, their chromosomal localization, substrates, exogenous activators, and activating capacity1
Enzyme Chromosomal location Substrates Activated by Activator of
  • FN, fibronectin; 2M, 2-macroglobulin; 1PI, 1-proteinase inhibitor; COMP, cartilage oligomeric matrix protein; ND, not determined; TACE, TNF-converting enzyme; OP, osteopontin.

    …………..

Collagenases
 Collagenase-1 (MMP-1) 11q22.2-22.3 Collagen I, II, III, VII, VIII, X, aggregan, serpins, 2M MMP-3, -7, -10, plasmin kallikrein, chymase MMP-2
 Collagenase-2 (MMP-8) 11q22.2-22.3 Collagen I, II, III, aggregan, serpins, 2M MMP-3, -10, plasmin ND
 Collagenase-3 (MMP-13) 11q22.2-22.3 Collagen I, II, III, IV, IX, X, XIV, gelatin, FN, laminin, large tenascin aggrecan, fibrillin, osteonectin, serpins MMP-2, -3, -10, -14, -15, plasmin MMP-2, -9
Stromelysins
 Stromelysin-1 (MMP-3) 11q22.2-22.3 Collagen IV, V, IX, X, FN, elastin, gelatin, laminin, aggrecan, nidoge fibrillin*, osteonectin*, 1PI*, myelin basic protein*, OP, E-cadherin Plasmin, kallikrein, chymas tryptase MMP-1, -8, -9, -13
 Stromelysin-2 (MMP-10) 11q22.2-3 As MMP-3, except * Elastase, cathepsin G MMP-1, -7, -8, -9, -13
Stromelysin-like MMPs
 Stromelysin-3 (MMP-11) 22q11.2 Serine proteinase inhibitors, 1PI Furin ND
 Metalloelastase (MMP-12) 11q22.2-22.3 Collagen IV, gelatin, FN, laminin, vitronectin, elastin, fibrillin, 1-PI, myelin basic protein, apolipoprotein A ND ND
Matrilysins
 Matrilysin (MMP-7) 11q22.2-22.3 Elastin, FN, laminin, nidogen, collagen IV, tenascin, versican, 1PI, O E-cadherin, TNF- MMP-3, plasmin MMP-9
 Matrilysin-2 (MMP-26) 11q22.2 Gelatin, 1PI, synthetic MMP-substrates, TACE-substrate ND ND
Gelatinases
 Gelatinase A (MMP-2) 16q13 Gelatin, collagen I, IV, V, VII, X, FN, tenascin, fibrillin, osteonectin, Monocyte chemoattractant protein 3 MMP-1, -13, -14, -15, -16, -tryptase? MMP-9, -13
 Gelatinase B (MMP-9) 20q12-13 Gelatin, collagen IV, V, VII, XI, XIV, elastin, fibrillin, osteonectin 2 MMP-2, -3, 7, -13, plasmin, trypsin, chymotrypsin, cathepsin G ND
Membrane-type MMPs
 MT1-MMP (MMP-14) 14q12.2 Collagen I, II, III, gelatin, FN, laminin, vitronectin, aggrecan, tenasci nidogen, perlecan, fibrillin, 1PI, 2M, fibrin Plasmin, furin MMP-2, -13
 MT2-MMP (MMP-15) 16q12.2 FN, laminin, aggrecan, tenascin, nidogen, perlecan ND MMP-2, -13

 

MMP expression and activity are regulated at several levels. In most cases, MMPs are not synthesized until needed. Transcription can be induced by various signals including cytokines, growth factors, and mechanical stress. In certain cases, regulation of mRNA stability and translational efficiencyhave been reported. Because most MMPs are secreted as inactive zymogens, they need to be activated, usually by proteolytic cleavage of their NH2-terminal prodomains. Some MMPs are activated by other serine proteases such as plasmin and furin, whereas some of the MMPs can activate other members of their family. The most well characterized is the activation of pro-MMP-2 by MT1-MMP.

A number of MMPs have been strongly implicated in multiple stages of cancer progression including the acquisition of invasive and metastatic properties. Thus, efforts have been made for the past 20 years to develop MMPIs that can be used to halt the spread of cancer, which is what ultimately kills the person. However, initial clinical trials using first generation MMPIs proved to be disappointing . In the ensuing years, much has been learned about the roles of specific MMPs in the different processes of carcinogenesis and more specific MMPIs are being developed and brought to clinical trials.

However, the dosing and scheduling for optimal efficacy is not the same as required for conventional cytotoxic drugs because the MMPIs do not directly kill cancer cells, but instead target such processes as angiogenesis (the development of new blood vessels), invasion, and metastatic spread. (Matrix Metalloproteinases, Angiogenesis, and Cancer. Joyce E. Rundhaug.  Commentary re: A. C. Lockhart et al., Reduction of Wound Angiogenesis in Patients Treated with BMS-275291, a Broad Spectrum Matrix Metalloproteinase Inhibitor. Clin. Cancer Res., 2003; 9551–554).

 Role of p38 MAP Kinase Signal Transduction in Solid Tumors

HK Koul, M Pal, and S Koul. Genes & Cancer  2013 ; 4(9-10) 342–359.  http://dx.doi.org/10.1177/ 1947601913507951

Mitogen-activated protein kinases (MAPKs) mediate a wide variety of cellular behaviors in response to extracellular stimuli. One of the main subgroups, the p38 MAP kinases, has been implicated in a wide range of complex biologic processes, such as cell proliferation, cell differentiation, cell death, cell migration, and invasion. Dysregulation of p38 MAPK levels in patients are associated with advanced stages and short survival in cancer patients (e.g., prostate, breast, bladder, liver, and lung cancer). p38 MAPK plays a dual role as a regulator of cell death, and it can either mediate cell survival or cell death depending not only on the type of stimulus but also in a cell type specific manner. In addition to modulating cell survival, an essential role of p38 MAPK in modulation of cell migration and invasion offers a distinct opportunity to target this pathway with respect to tumor metastasis. The specific function of p38 MAPK appears to depend not only on the cell type but also on the stimuli and/or the isoform that is activated.

Mitogen-activated protein kinase (MAPK) signal transduction pathways are evolutionarily conserved among eukaryotes and have been implicated to play key roles in a number of biological processes, including cell growth, differentiation, apoptosis, inflammation, and responses to environmental stresses.

They are typically organized in 3-tiered architecture consisting of a MAPK, a MAPK activator (MAPK kinase), and a MAPKK activator (MAPKK kinase). The MAPK pathways can be regulated at multiple levels as well as via multiple mechanisms, of which the regulation of mitogen-activated protein kinase kinase kinase (MAPKKK/MAP3K) has been proved to be the most challenging due to the great diversity and versatility between different modules at this level. The complex array of growth factors and other ligands that can initiate intracellular cell signaling requires a very high level of coordination among the different proteins involved.

GTP cyclohydrolase (GCH1)

GTP cyclohydrolase (GCH1) is the key-enzyme to produce the essential enzyme cofactor, tetrahydrobiopterin. The byproduct, neopterin is increased in advanced human cancer and used as cancer-biomarker, suggesting that pathologically increased GCH1 activity may promote tumor growth.

(G Picker, Hee-Young Lim, et al. Inhibition of GTP cyclohydrolase attenuates tumor growth by reducing angiogenesis and M2-like polarization of tumor associated macrophages. Int. J. Cancer 2003; 132: 591–604 (2013)  http://dx.doi.org/10.1002/ijc.27706 )

We found that inhibition or silencing of GCH1 reduced tumor cell proliferation and survival and the tube formation of human umbilical vein endothelial cells, which upon hypoxia increased GCH1 and

endothelial NOS expression, the latter prevented by inhibition of GCH1. In nude mice xenografted with HT29-Luc colon cancer cells GCH1 inhibition reduced tumor growth and angiogenesis, determined by in vivo luciferase and near-infrared imaging of newly formed blood vessels. The treatment with the GCH1 inhibitor shifted the phenotype of tumor associated macrophages from the proangiogenic M2 towards M1, accompanied with a shift of plasma chemokine profiles towards tumor-attacking chemokines including CXCL10 and RANTES. GCH1 expression was increased in mouse AOM/DSS-induced colon tumors and in high grade human colon and skin cancer and oppositely, the growth of GCH1-deficient HT29-Luc tumor cells in mice was strongly reduced. The data suggest that GCH1 inhibition reduces tumor growth by (i) direct killing of tumor cells, (ii) by inhibiting angiogenesis, and (iii) by enhancing the antitumoral immune response.

The Role of Stroma in Tumour-Host Co-Existence

Molnár et al.,  The Role of Stroma in Tumour-Host Co-Existence: Some Perspectives in Stroma-Targeted Therapy of Cancer   Biochem Pharmacol 2013, 2:1    http://dx.doi.org/10.4172/2167-0501.1000107

 Cancer grows at the expense of the host as a parasite or superparasite following the second law of thermodynamics (conservation of energy). When the cancer cell progresses via replication to the special state called “spheroid”, a new phase begins with its intimate interaction and development of responses from the stroma which together assist in the formation of a full blown cancer. Among the processes involved are the development of blood vessels and lymphatic channels which are essential for maintenance and further growth of the cancer mass. In this way the condition of “parasitism” is completed with simultaneous suppression of the immune response of the host to the histo-incompatability of the tumor mass. Stroma/parenchyma promotes cancer invasion by feeding cancer cells and inducing immune tolerance. The dynamic changes in composition of stroma and biological consequences as feeder of cancer cells and immune tolerance can give a perspective for rational drug design in anti-stromal therapy. There are differences between normal and cancer cells at subcellular level such as compartmentalzation and structure of cytoskeleton and energy distribution (that is low generally, but locally high in normal cells). In cancer cannibalism of normal cells, the growing cancer mass is a factor for progression and invasion.

Cancer cells have been shown to kill normal cells and the products of cell death used for progression of growth of the cancer cell. Serum and growth factors produced by tumor stroma also provide the needed nutrients and conditions for further tumor growth. Cancer cannot feed off other cancer cells and therefore grow poorly. Probably, although not yet proven, the inability of cancer to “parasitise” other cancer cell types is probably due to some kind of competition or interference. The tumor is in charge of its own development due to its induction proteinases, lipid mobilization factors and angiogenetic factors as well as its ability to negate immune responses of the host response to what is in essence a foreign body.

In our review co-existence of normal and cancer cells in tumor with the growth promoting factors, and the immune tolerance mediating factors produced in the stromal and cancer cells/tissues will be discussed with perspective of stroma targeted therapy.

The clinical significance of cell cannibalism is well defined and described in a large number of publications. The direction of process of cancer development is defined as the tumor invades the normal tissue which never occurs in the reverse direction. This suggests that the cancer cell strives to achieve the lowest energy level possible. Therefore the first of the development of a full blown cancer can be considered as the 2nd Thermodynamic principle  that explains, describes and drives the invading cancer into normal surrounding tissue.

From the normal living state, under particular conditions such as hypoxia, where ATP synthesis is decreased resulting in a switch to glycolytic pathways, cancer cells are selected from a fraction of the population [4]. Energetically, in the presence of electron transfer, by using high energy from respiration, the proliferating state is more stable than resting cells where a higher degree of protein stabilization occurs such as that needed for maintainance of the cytoskeleton of the cell. It was proposed that tumor-promotion might be controlled or modulated by small electronic currents originating from reactive oxygen species and transported through the cytoskeletal microfilament network of the cancer cell.

Aerobic glycolysis is the main energy producing process in cancer cells. Among many other aspects, recently the mitochondria have also been regarded as potential targets in the therapy of cancer. Several small molecules have been tested to restore their dysfunctional functions either by direct or indirect effects. Because of poorly functioning mitochondria, the electron transfer component of the respiration cycle is inefficient; therefore, cancer cells have smaller Gibbs energy than healthy cells. This means, that these cancer cells exists in a metastable state and are not able maintain normal cell structure.

Therefore, the cytoskeleton system is collapsed and dielectric bilayers are formed as a lower grade of cellular structure with decreased electron conductivity. Consequently, to halt cancer growth, one has to evaluate the process of cancer cell development in situ, where the primary tumor is growing as well as that of the metastatic cell that is invading surrounding or distal tissues. This affords one to suggest that the stroma is formed first during long term repeated oxidative stress, a process that is initially accompanied with inflammation due to an active immune response to the histoincompatability antigens present on the surface of the cancer cell. If the cancer cell evades the activity of killer T cells (Treg cells) by either secreting agents that reduce the response of the Treg cells or the immune system for whatever reason is ineffective (immunosuppressed states such as HIV/AIDS, pregnancy, transplantation  therapy, etc.), the formed cancer cells have the opportunity to initiate tumor development. Because of the limited capacity of its electron transfer cycle, cancer cells are essentially starving cells that require glycolytically useful substrates. These substrates are obtained from the killing of normal cells by agents secreted by the cancer cell and the products yielded from dead normal cells “eaten” (phagocytosed) by the starving cancer cell which is digested by the cancer cells lysosomal system. This autophagic process of cannibalism keeps the cancer cell alive and thriving and is known as cytophagy, i.e., cannibalism of normal cells. This type of autophagocytosis  results in a parasitic co-existence of tumor cells with normal cells and will determine the main pathway of interaction between the growing cancer tissue (tumor) and normal tissue where the cancer tissue gradually destroys normal tissues. This process obeys the second law of thermodynamics-conservation of energy within a defined system.

Treatments for Cancer

 Bosutinib: a SRC–ABL tyrosine kinase inhibitor for treatment of chronic myeloid leukemia. 

FE Rassi, HJ Khoury. Pharmacogenomics and Personalized Medicine  2013:6 57–62.

Bosutinib is one of five tyrosine kinase inhibitors commercially available in the United States for the treatment of chronic myeloid leukemia. This review of bosutinib summarizes the mode of action, pharmacokinetics, efficacy and safety data, as well as the patient-focused perspective through quality-of-life data. Bosutinib has shown considerable and sustained efficacy in chronic myeloid leukemia, especially in the chronic phase, with resistance or intolerance to prior tyrosine kinase inhibitors. Bosutinib has distinct but manageable adverse events. In the absence of T315I and V299L mutations, there are no absolute contraindications for the use of bosutinib in this patient population

Chronic myeloid leukemia (CML) is a clonal myeloproliferative stem cell disorder characterized by the presence of a signature hybrid oncogene, the BCR–ABL. The Philadelphia chromosome (Ph+) results from a reciprocal translocation between chromosome 9 and chromosome 22 that juxtaposes the two genes BCR and ABL and drives the leukemogenesis in CML. The ABL gene encodes for a nonreceptor tyrosine kinase that becomes deregulated and constitutively active after the juxtaposition of BCR. BCR–ABL is central in controlling downstream pathways involved in cell proliferation, regulation of cellular adhesion, and apoptosis.The understanding of the importance of this kinase activity in the pathophysiology of CML led to the development of tyrosine kinase inhibitors (TKI) that specifically target BCR–ABL. These agents became the mainstay of modern therapy in CML. CML has a triphasic clinical course, and the majority of patients (∼80%) are diagnosed during the early phase or the chronic phase (CP). However, and without effective treatment, CML invariably progresses to the advanced phases of the disease – the accelerated phase (AP) and the blast phase (BP). BP CML is a lethal refractory secondary leukemia with a short predicted survival.

Comprehensive molecular portraits of human breast tumors

 The Cancer Genome Atlas Network

Nature. 2012 October 4; 490(7418): 61–70. http://dx.doi.org/10.1038/nature11412.

We analyzed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, mRNA arrays, microRNA sequencing and reverse phase protein arrays. Our ability to integrate information across platforms provided key insights into previously-defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity.

Somatic mutations in only three genes (TP53, PIK3CA and GATA3) occurred at  > 10% incidence across all breast cancers; however, there were numerous subtype-associated and novel gene mutations including the enrichment of specific mutations in GATA3, PIK3CA and MAP3K1 with the Luminal A subtype. We identified two novel protein expression-defined subgroups, possibly contributed by stromal/microenvironmental elements, and integrated analyses identified specific signaling pathways dominant in each molecular subtype including a HER2/p-HER2/HER1/p-HER1 signature within the HER2-Enriched expression subtype. Comparison of Basal-like breast tumors with high-grade Serous Ovarian tumors showed many molecular commonalities, suggesting a related etiology and similar therapeutic opportunities. The biologic finding of the four main breast cancer subtypes caused by different subsets of genetic and epigenetic abnormalities raises the hypothesis that much of the clinically observable plasticity and heterogeneity occurs within, and not across, these major biologic subtypes of breast cancer.

Most molecular studies of breast cancer have focused on just one or two high information content platforms, most frequently mRNA expression profiling or DNA copy number analysis, and more recently massively parallel sequencing. Supervised clustering of mRNA expression data has reproducibly established that breast cancers encompass several distinct disease entities, often referred to as the intrinsic subtypes of breast cancer. The recent development of additional high information content assays focused on abnormalities in DNA methylation, microRNA expression and protein expression, provide further opportunities to more completely characterize the molecular architecture of breast cancer.

Synbiology contribution and Nanotechnology

Synthetic RNAs Designed to Fight Cancer

Xiaowei Wang and his colleagues at  Washington University School of Medicine in St. Louis have designed synthetic molecules that combine the advantages of two experimental RNA therapies against cancer.  They have designed synthetic molecules that combine the advantages of two experimental RNA therapies against cancer.  RNA plays an important role in how genes are turned on and off in the body. Both siRNAs and microRNAs are snippets of RNA known to modulate a gene’s signal or shut it down entirely. Separately, siRNA and microRNA treatment strategies are in early clinical trials against cancer, but few groups have attempted to marry the two.

“We are trying to merge two largely separate fields of RNA research and harness the advantages of both,” said Xiaowei Wang, assistant professor of radiation oncology and a research member of the Siteman Cancer Center.  The study appears in the December issue of the journal RNA.

“We designed an artificial RNA that is a combination of siRNA and microRNA,” Wang said “our artificial RNA simultaneously inhibits both cell migration and proliferation.”  For therapeutic purposes, “small interfering” RNAs, or siRNAs, are designed and assembled in a lab and can be made to shut down– or interfere with– a single specific gene that drives cancer.  The siRNA molecules work extremely well at silencing a gene target because the siRNA sequence is made to perfectly complement the target sequence, thereby silencing a gene’s expression.

Though siRNAs are great at turning off the gene target, they also have potentially dangerous side effects: siRNAs inadvertently can shut down other genes that need to be expressed to carry out tasks that keep the body healthy.  The siRNAs interfere with off-target genesthat closely complement their “seed region,” a section of the siRNA  that governs binding to a gene target. “In the past, we tried to block the seed region in an attempt to reduce the side effects. Until now, we never tried to replace the seed region completely.”

Wang and his colleagues asked whether they could replace the siRNA’s seed region with the seed region from microRNA. Unlike siRNA, microRNA is a natural part of the body’s gene expression. And it can also shut down genes. As such, the microRNA seed region (with its natural targets) might reduce the toxic side effects caused by the artificial siRNA seed region. Plus, the microRNA seed region would add a new tool to shut down other genes that also may be driving cancer.

Wang’s group started with a bioinformatics approach, using a computer algorithm to design siRNA sequences against a common driver of cancer, a gene called AKT1 that encourages uncontrolled cell division. The program also selected siRNAs against AKT1 that had a seed region highly similar to the seed region of a microRNA known to inhibit a cell’s ability to move, thus potentially reducing the cancer’s ability to spread.

A Neutralizing RNA Aptamer

 Nucleic acid aptamers have been developed as high-affinity ligands that may act as antagonists of disease-associated proteins. Aptamers are non immunogenic and characterised by high specificity and low toxicity thus representing a valid alternative to antibodies or soluble ligand receptor traps/decoys to target specific cancer cell surface proteins in clinical diagnosis and therapy. The epidermal growth factor receptor (EGFR) has been implicated in the development of a wide range of human cancers including breast, glioma and lung. The observation that its inhibition can interfere with the growth of such tumors has led to the design of new drugs including monoclonal antibodies and tyrosine kinase inhibitors currently used in clinic. However, some of these molecules can result in toxicity and acquired resistance, hence the need to develop novel kinds of EGFR-targeting drugs with high specificity and low toxicity.

(CL Esposito, D Passaro, et al. A Neutralizing RNA Aptamer against EGFR Causes Selective Apoptotic Cell Death. PLoS ONE 6(9): e24071. http://dx.doi.org/10.1371/journal.pone.0024071)

Here we generated, by a cell-Systematic Evolution of  Ligands by EXponential enrichment (SELEX) approach, a nuclease resistant RNA-aptamer that specifically binds to EGFR with a binding constant of 10 nM. When applied to EGFR-expressing cancer cells the aptamer inhibits EGFR-mediated signal pathways causing selective cell death. Furthermore, at low doses it induces apoptosis even of cells that are resistant to the most frequently used EGFR-inhibitors, such as gefitinib and cetuximab, and inhibits tumor growth in a mouse xenograft model of human non-small-cell lung cancer (NSCLC). Interestingly, combined treatment with cetuximab and the aptamer shows clear synergy in inducing apoptosis in vitro and in vivo. In conclusion, we demonstrate that this neutralizing RNA aptamer is a promising bio-molecule that can be developed as a more effective alternative to the repertoire of already existing EGFR-inhibitors.

In-Silico Molecular Docking Analysis of Cancer Biomarkers

Currently, in the research scenario for cancer, the identification of anti-cancer drugs using immuno-modulatory proteins and other molecular agents to initiate apoptosis in cancer cells and to inhibit the signaling pathways of cancer biomarkers as a drug targeted therapy, for cancer cell proliferation assays by the researchers. In-Silico analysis is used to recognize anticancer compounds as a future prospective for In-Vitro and In-Vivo analysis. A large number of herbal remedies (e.g. garlic, mistletoe) are used by cancer patients for treating the cancer and/or reducing the toxicities of chemotherapeutic drugs. Some herbal medicines have shown potentially beneficial effects on cancer progression and may ameliorate chemotherapy-induced toxicities.  (K. Gowri Shankar et al., In-Silico Molecular Docking Analysis of Cancer Biomarkers with Bioactive Compounds of Tribulus terrestris. Intl J NOVEL TRENDS PHARMAL SCI. 2013; 3(4).

Tribulus terrestris is mentioned in ancient Indian Ayurvedic medical texts dating back thousands of years. Tribulus terrestris has been widely used in the Ayurvedic system of medicine for the treatment of sexualdysfunction and various urinary disorders. The aim of the present study is to evaluate the interactions of some bioactive compounds of Tribulus terrestris for In-Silico anticancer analysis with cancer biomarkers as targets. The targeted biomarkers for analysis include NSE-Lung cancer, Follistatin-Prostrate cancer, GGT Hepatocellular carcinoma, Human Prostasin-Ovarian cancer.

GC-MS analysis of Tribulus terrestris whole plant methanol extract revealed the existence of the major compound like 3,7,11,15-tetramethylhexadec-2-en-1-ol, 1,2-Benzenedicarboxylic acid, disooctyl ester, 9,12,15-Octadecatrienoic acid, (z,z,z)-, 9,12-Octadecadienoic acid (z,z)-, Hexadecadienoic acid, ethyl ester, n-Hexadecadienoic acid, Octadecanoic acid, Phytol, α-Amyrin are chosen as ligands. Hence, by analyzing the minimum binding energy of the ligand binding complex with the receptors by dockinganalysis using AutoDock tools will show effective nature of inhibition of these receptors by the unique ligands. Based on the results low minimum binding energy ligands are identified and used as a future studies can be done for specific receptors  docking.

Anti-Cancerous Effect of4,4′-Dihydroxychalcone ((2E,2′E)-3,3′-(1,4-Phenylene) Bis (1-(4-hydroxyphenyl) Prop-2-en-1-one)) on T47D Breast Cancer Cell Line

Narges Mahmoodi, T Besharati-Seidani, N Motamed, and NO Mahmoodi*
Annual Research & Review in Biology 2014; 4(12): 2045-2052
SCIENCEDOMAIN international    www.sciencedomain.org

Aims: The majority of human breast tumors are estrogen receptor α (ERα) positive. However, not all of the ERα+ breast cancers respond to anti-estrogens drugs for those women who do respond, initial positive responses can be of short duration. Thus, more effective drugs are needed to enhance the efficacy of anti-estrogens drugs or to be used separately in a period of time. In view of potential cytotoxicity associated with silybin as polyhydroxy compounds a synthetic 4-hydroxychalcones (bis-phenol) was considered to explore its anti-carcinogenic effects in comparison to silybin on ERα+ breast cancer cell line.

Methodology: We have studied the inhibitory effect of 4,4′-dihydroxychalcone on the T47D breast cancer cell line by MTT test and the IC50s were estimated using Pharm PCS.

Results: The 4,4′-dihydroxychalcone showed significant dose- and time-dependent cell growth inhibitory effects on T47D breast cancer cells. The IC50 of 4,4′-dihydroxychalcone on T47D cells after 24 and 48 hours was 160.88+/1 μM, 62.20+/1 μM and for silybin was 373.42+/-1 μM,176.98+/1 μM respectively.

Conclusion: Our results strongly suggests that this premade synthetic 4,4′-dihydroxychalcone can promote anti carcinogenic actions on T47D cell line. All 4,4′-dihydroxychalcone doses had a much larger inhibitory effect on cell viability than silybin doses in T47D cells. The ratio of the IC50 of 4,4′-dihydroxychalcone to silybin after 24 and 48 hours was 1: 2.3 and 1: 2.8 respectively.

Anticancer and multidrug resistance-reversal effects of solanidine analogs synthetized from pregnadienolone acetate.

István Zupkó, Judit Molnár, Borbála Réthy, Renáta Minorics, Eva Frank, et al.
Molecules (Impact Factor: 2.43). 01/2014; 19(2):2061-76.  http://dx.doi.org/10.3390/molecules19022061
Source: PubMed

ABSTRACT A set of solanidine analogs  with antiproliferative properties were recently synthetized from pregnadienolone acetate, which occurs in Nature. The aim of the present study was an in vitro characterization of their antiproliferative action and an investigation of their multidrug resistance-reversal activity on cancer cells. Six of the compounds elicited the accumulation of a hypodiploid population of HeLa cells, indicating their apoptosis-inducing character, and another one caused cell cycle arrest at the G2/M phase. The most effective agents inhibited the activity of topoisomerase I, as evidenced by plasmid supercoil relaxation assays. One of the most potent analogs down-regulated the expression of cell-cycle related genes at the mRNA level, including tumor necrosis factor alpha and S-phase kinase-associated protein 2, and induced growth arrest and DNA damage protein 45 alpha. Some of the investigated compounds inhibited the ABCB1 transporter and caused rhodamine-123 accumulation in murine lymphoma cells transfected by human MDR1 gene, expressing the efflux pump (L5178). One of the most active agents in this aspect potentiated the antiproliferative action of doxorubicin without substantial intrinsic cytostatic capacity. The current results indicate that the modified solanidine skeleton is a suitable substrate for the rational design and synthesis of further innovative drug candidates with anticancer activities.

Nutrition and Cancer

 Ascorbic Acid and Selenium Interaction: Its Relevance in Carcinogenesis

 Michael J. Gonzalez
Journal of Orthomolecular Medicine 1990; 5(2)

Ascorbic acid and selenium are two nutrients that seem to have a preventive potential in the process of carcinogenesis; because of a possible synergistic action that may produce an enhanced anticarcinogenic effect. Interaction between these nutrients have been reported. Results indicate that the protective effect of the inorganic form of selenium (Na Selenite) was nullified by ascorbic acid, whereas the chemopreventive action of the organic form (seleno-DL-methionine) was not affected.

A possibility exists that Selenite is reduced by ascorbic acid to elemental selenium and is therefore not available for tissue uptake. In experiments using Selenite; plasma and erythrocyte glutathione peroxidase enzyme activity was directly related to the level of ascorbic acid fed.

Complementary RNA and Protein Profiling Identifies Iron as a Key Regulator of Mitochondrial Biogenesis

J W. Rensvold, Shao-En On, A Jeevananthan, et al.
Cell Rep. 2013 January 31; 3(1): .   http://dx.doi.org/10.1016/j.celrep.2012.11.029

Mitochondria are centers of metabolism and signaling whose content and function must adapt to
changing cellular environments. The biological signals that initiate mitochondrial restructuring
and the cellular processes that drive this adaptive response are largely obscure. To better define
these systems, we performed matched quantitative genomic and proteomic analyses of mouse
muscle cells as they performed mitochondrial biogenesis. We find that proteins involved in
cellular iron homeostasis are highly coordinated with this process and that depletion of cellular
iron results in a rapid, dose-dependent decrease of select mitochondrial protein levels and
oxidative capacity. We further show that this process is universal across a broad range of cell
types and fully reversed when iron is reintroduced. Collectively, our work reveals that cellular iron
is a key regulator of mitochondrial biogenesis, and provides quantitative data sets that can be
leveraged to explore posttranscriptional and posttranslational processes that are essential for
mitochondrial adaptation.

Avemar outshines new cancer ‘breakthrough’ drug

by Michael Traub
Townsend Letter / Oct, 2010

Many of us in the cancer research community were happy to hear about progress against metastatic melanoma reported this June at the annual meeting of the American Society of Clinical
Oncology (ASCO). since there has not been an improvement in overall survival from chemotherapy in over three decades.
Data from a phase III clinical trial of the experimental monoclonal antibody ipilimumab (pronounced “ep-eh-lim-uemab”) showed that patients with melanoma survived longer if they were taking ipilimumab than if they were not, regardless of whether they also were taking the other drug in the study, an experimental cancer vaccine. (1)

A Closer Look: How Big an Improvement, at What Cost to Patients?

Overall Survival: the ‘Gold Standard’ for Judging Cancer Therapies

Overall survival (OS) is the length of time that a patient actuallysurvives a cancer after treatment. It can also be measured as the percentage of patients surviving a specific time. It is the gold
standard by which the usefulness of a cancer treatment should be determined. Many things can help a patient, but the most important goal of doctors and patients is for the cancer patient to live longer, with a decent quality of life (QOL).

Among patients taking ipilimumab with or without the experimental vaccine, median overall survival was about 10 months. That is compared with 6.4 months’ overall survival among patients receiving the vaccine by itself. About 45.6% of patients taking ipilimumab survived one year, an improvement of some 7% over the 38% seen in some earlier studies. This very modest improvement in survival comes at quite a price.

Severe Side Effects in More Than One in Four Ipilimumab Patients Ipilimumab has some side effects that can be “both severe and long-lasting,” according to the study report. Among patients taking ipilimumab by itself (without the vaccine), 19.1% had side effects requiring hospitalization or invasive intervention, 3.8% died from the effects of the drug, and another 33.8% had life-threatening or disabling side effects. All totaled, 26.7% of the patients taking ipilimumab by itself– more than 1 in 4-had side effects that were severe, very severe, or fatal. Severe side effects included diarrhea, nausea, constipation, vomiting, abdominal pain, fatigue, cough, and headache. Vernon Sondak, MD, of the H. Lee Moffitt Cancer and Research Institute, said that “using the drug requires the medical team to be on guard to manage toxicity at all times.” But even with its severe side effects, the researchers said that the drug should be welcomed because it can increase median survival from 6.4 months to 10.1 months. That is because any lengthening of lives is welcome in a disease that hasn’t seen a new drug that can do that in many years.

Fermented Wheat Germ (Avemar) Improves Melanoma Survival Without Harsh Side Effects

But what if there already were such a treatment available-not a drug, but a safe, natural substance shown in clinical trials to have a remarkably similar ability to lengthen the lives of melanoma patients, without the severe side effects of the new drug?
What if the other substance had no significant side effects at all?
What if, instead of causing severe and sometimes fatal side effects, that other substance actually helped prevent and reduce serious side effects caused by chemotherapy and radiotherapy?
In fact, there is just such a treatment available. It is known as fermented wheat germ extract (FWGE) and by its trade name Avemar. It has been approved as a medical nutriment for cancer
patients in Europe for years and is available in the US as a dietary supplement. It has been compared to dacarbazine (DTIC), standard melanoma therapy, in a clinical trial with longer
follow-up than the ipilimumab trial. And with better results.

In 2008, data were published in the research journal Cancer Biotherapy and Radiopharmaceuticals from seven years’ follow-up on a trial at the N. N. Blokhin Cancer Center in Moscow,
Russia, involving 52 patients who had taken or not taken Avemar while taking dacarbazine for the year following surgical removal of their stage III melanoma tumors. (2) Patients who got only dacarbazine survived 44.7 months. Those who got Avemar along with their dacarbazine survived 66.2 months. This is an improvement in overall survival time of over 48%. In the Russian study,
just as it has in other studies, Avemar reduced side effects of the chemotherapy. Among those taking only dacarbazine, 11 % experienced severe (grade 3 or grade 4) side effects that required hospitalization or invasive intervention. None of the Avemar patients had grade 3 or 4 side effects. Since it is difficult to compare length of survival between the recent ipilimumab study and the Avemar melanoma study, because the ipilimumab study tested mostly stage 4 melanoma patients and the Avemar study tested mostly stage 3 melanoma patients, it is most instructive to look at
the percentage improvement in overall survival from adding either treatment to the regimen. Ipilimumab and Avemar both produced very similar improvements in OS (56% vs. 48%, respectively),

Avemar Ameliorates Conventional Treatment Side Effects

The improvement of survival and the amelioration of chemotherapy side effects by Avemar seen in the Russian melanoma study is typical of Avemar’s effects when used in treating other cancers, including in combination with chemotherapy or radiotherapy. Among 170 colorectal cancer patients in a 2003 study published in the British journal of Cancer, Avemar improved overall survival
and reduced metastasis and recurrences after surgery, chemotherapy, and radiotherapy. (3) Taking Avemar for six months during and after those conventional treatments resulted in a 61.8% reduction in the death rate among those patients, compared with those who received only the conventional treatment. Those taking Avemar experienced lower rates of recurrences and metastases
as well, even though most patients in the Avemar group came into the study with more advanced disease, had more radiation earlier, and had been diagnosed longer. Side effects of Avemar, as in
other Avemar trials., were rare, mild, and transient, with no serious adverse events occurring.

In a 2004 study published in the journal of Pediatric Hematology and Oncology, childhood cancer patients taking Avemar during and after conventional therapies had a 42.8% reduction in the
low white blood cell counts and high fever known as febrile neutropenia, which can be a life-threatening consequence of chemotherapy and radiation. (4) This and similar results with
Avemar in other cancers are consistent with animal studies showing that Avemar helps the immune system recover a full white blood cell count after chemotherapy and radiation faster
than would otherwise happen. This study also demonstrated the safety of Avemar for children.

Why Avemar Works in Many Different Kinds of Cancer

Extensive studies in cells and animals have shown how Avemar works. Perhaps its most important action is to restrict cancer cells’ use of glucose. (5) Cancer cells use up to 50 times more glucose
than normal cells, a phenomenon known as the Warburg effect. (6) They use those enormous amounts of glucose to make ribose, the backbone sugar of DNA, much faster than normal cells can. To
do this, they must use a different series of biochemical reactions (“pathway”) than normal cells. Avemar makes this very difficult for cancer cells to do, because it inhibits the activity of the key enzyme in that pathway, transketolase (TK). (7) With the TK pathway blocked, cancer cells cannot use large amounts of glucose to make DNA fast enough to support the proliferation that makes them so dangerous.(8-10)

In experiments in the US and abroad, scientists have learned that Avemar has these additional effects. It:

* lowers the levels of a DNA repair enzyme known as poly (ADPribose) polymerase (PARP).” With this effect, cancer cells are forced to self-destruct, preventing them from proliferating and
producing a synergistic cancer-cell killing effect when given with chemotherapy, which also works to damage cancer cells’ DNA;
* reduces the number of molecules on cancer cells that identify them as originating within the body (MHC-1 molecules). (12) With cancer cells stripped of that protection, the immune system,
which recognizes the cancer cells as abnormal, no longer gives them the pass given to cells originating in the body. The cancer cells are attacked by the immune system’s natural killer (NK)
cells and destroyed;
* increases levels of molecules called intercellular adhesion molecule-1 (ICAM-1) on the blood vessels of cancer tumors. (13). The increase helps immune system cells pass through the walls of the blood vessels supplying the tumor blood flow, moving directly into the tumor to attack its cancer cells; increases the activity of the primary anticancer cytokine, tumor necrosis factor alpha (TNF-a), and produces a synergistic effect in interaction with other anticancer cytokines. (14) Cytokines are substances produced by cells to act directly on other cells. TNF-a helps force cancer cells into the programmed death known as apoptosis and inhibits tumorigenesis, the process through which new tumors are formed;
* inhibits the activity of ribonucleotide reductase (RR), a key enzyme that cells must have to make new DNA so that each cancer cell can divide to make two more like it. (15) With DNA
production slowed, increases in cancer cell growth and replication are inhibited.

Antimetastatic and Immune-Boosting Effects Are Key to Survival

Because the biochemical changes listed above have consistently been shown in both animal and human studies to be directly linked to reducing cancer’s ability to metastasize and to
improving the immune system’s ability to fight cancer, scientists count them as among the most likely main causes of improved survival seen in cancer patients when Avemar is used alone or,
more often, as an adjuvant in addition to standard-of-care therapies such as chemotherapy, radiotherapy, or the combination of the two. (16-23)

Extending Life: How Long, Exactly, and At What Cost in Quality of Life?

Any improvement in advanced melanoma survival, no matter how small, is certainly an achievement. But ipilimumab had severe side effects requiring hospitalization or invasive intervention in
over one-quarter of patients treated with it. And it increased median survival only by 3-plus months. On the other hand, Avemar added to dacarbazine improved survival very markedly, with no severe side effects. If actually improving overall survival substantially without significant side effects means that a drug should be considered as the new standard of care for first-line therapy, then there is no need to wait for further results. Avemar has already demonstrated very significant improvement in survival over chemotherapy alone and has a safety profile unmatched by
conventional therapies.

Michael Traub, ND, FABNO, is in private practice and serves as a member of Oncology Association of Naturopathic Physicians board of examiners.
Notes
(1.) Hodi FS, O’Day SJ, McDermott DF, et al. Improved survival with ipilimumab in patients with metastatic melanoma. N Engl J Med. 2010 Jun 14.
(2.) Demidov LV. Manziuk LV, Kharkevitch GY, Pirogova NA,  Artamonova EV. Adjuvant fermented wheat germ extract (Avemar) nutraceutical improves survival of high-risk skin
melanoma patients; a randomized, pilot, phase ll clinical study with a 7-year follow-up. Cancer Biother Radiopharm. 2008 Aug. 23(4):477-482. Erratum in: Cancer Biother Radiopharm. 2008
Oct;2315):669.
(3.) Jakab F, Shoenfeld Y, Balogh A. et al. A medical nutriment has supportive value in the treatment of colorectal cancer. Br J Cancer. 2001 Aug 4;89(3):465-9.
(4.) Garami M, Schuler D, Babosa M, et al. Fermented wheat germ extract reduces chemotherapy-induced febrile neutropenia in pediatric cancer patients, J Pediatr Hematol Oncol. 2004
Oct;26(10):631-635.
(5.) Boros I.G, Lapis K, Szende B, et al. Wheat germ extract decreases glucose uptake and RNA ribose formation but increases fatty acid synthesis in MIA pancreatic adenocarcinoma
cells. Pancreas. 2001 Aug:23(2):141-147.
(6.) Warburg, O. On the origin of cancer cells. Science. 1956 Feb 24; 123(31 91):309-314.
(7.) Boros LG, Lee VVN, Go VL., A metabolic hypothesis of cell growth and death in pancreatic cancer, Pancreas. 2002 Jan;
24:(1):26 33.
(8.) Boros LG, Lapis K, Szende B, et al. Op cit.
(9.) Comin-Anduix B, Boros LG, Marin S, et al. Fermented wheat germ extract inhibits glycolysis/pentose cycle enzymes and induces apoptosis through poly(ADP-ribose) polymerase
activation in Jurkat T-cell leukemia tumor cells. J Biol Chem. 2002 Nov 29;277 (48):46408-46414. Epub 2002 Sep 25.
(23.) Garami M, Schuler D, Babosa M, et al. Fermented wheat germ extract reduces chemotherapy-induced febrile neutropenia in pediatric cancer patients. J Pediatr Hematol Oncol. 2004 Oct;
26(10):631-635.

by Michael Traub, ND, FABNO
COPYRIGHT 2010 The Townsend Letter Group
COPYRIGHT 2010 Gale, Cengage Learning

Nanotechnology in Cancer Drug Delivery and Selective Targeting

Nanoparticles are rapidly being developed and trialed to overcome several limitations of traditional drug delivery systems and are coming up as a distinct therapeutics for cancer treatment. Conventional chemotherapeutics possess some serious side effects including damage of the immune system and other organs with rapidly proliferating cells due to nonspecific targeting, lack of solubility, and inability to enter the core of the tumors resulting in impaired treatment with reduced dose and with low survival rate.

Nanotechnology has provided the opportunity to get direct access of the cancerous cells selectively with increased drug localization and cellular uptake. Nanoparticles can be programmed for recognizing the cancerous cells and giving selective and accurate drug delivery avoiding interaction with the healthy cells. This review focuses on cell recognizing ability of nanoparticles by various strategies having unique identifying properties that distinguish them from previous anticancer therapies. It also discusses specific drug delivery by nanoparticles inside the cells illustrating many successful researches and how nanoparticles remove the side effects of conventional therapies with tailored cancer treatment.

(Kumar Bishwajit Sutradhar and Md. Lutful Amin. Hindawi Publ. Corp.  2014, Article ID 939378, 12 pages

http://dx.doi.org/10.1155/2014/939378)

Cancer, the uncontrolled proliferation of cells where apoptosis is greatly disappeared, requires very complex process of treatment. Because of complexity in genetic and phenotypic levels, it shows clinical diversity and therapeutic resistance. A variety of approaches are being practiced for the treatment of cancer each of which has some significant limitations and side effects. Cancer treatment includes surgical removal, chemotherapy, radiation, and hormone therapy. Chemotherapy, a  very common treatment, delivers anticancer drugs systemically to patients for quenching the uncontrolled proliferation of cancerous cells. Unfortunately, due to nonspecific targeting by anticancer agents, many side effects occur and poor drug delivery of those agents cannot bring out the desired outcome in most of the cases. Cancer drug development involves a very complex procedure which is associated with advanced polymer chemistry and electronic engineering.

The main challenge of cancer therapeutics is to differentiate the cancerous cells and the normal body cells. That is why the main objective becomes engineering the drug in such a way as it can identify the cancer cells to diminish their growth and proliferation. Conventional chemotherapy fails to target the cancerous cells selectively without interacting with the normal body cells. Thus they cause serious side effects including organ damage resulting in impaired  treatment with lower dose and ultimately low survival rates.

Nanotechnology is the science that usually deals with the size range from a few nanometers (nm) to several hundrednm, depending on their intended use. It has been the area of interest over the last decade for developing precise drug delivery systems as it offers numerous benefits to overcome the limitations of conventional formulations . It is very promising both in cancer diagnosis and treatment since it can enter the tissues at molecular level.

Cisplatin-incorporated nanoparticles of poly(acrylic acid-co-methyl methacrylate) copolymer

K Dong Lee, Young-Il Jeong,  DH Kim,  Gyun-Taek Lim,  Ki-Choon Choi.  Intl J Nanomedicine 2013:8 2835–2845.

Although cisplatin is extensively used in the clinical field, its intrinsic toxicity limits its clinical use. We investigated nanoparticle formations of poly(acrylic acid-co-methyl methacrylate) (PAA-MMA) incorporating cisplatin and their antitumor activity in vitro and in vivo.

Methods: Cisplatin-incorporated nanoparticles were prepared through the ion-complex for­mation between acrylic acid and cisplatin. The anticancer activity of cisplatin-incorporated nanoparticles was assessed with CT26 colorectal carcinoma cells.

Results: Cisplatin-incorporated nanoparticles have small particle sizes of less than 200 nm with spherical shapes. Drug content was increased according to the increase of the feeding amount of cisplatin and acrylic acid content in the copolymer. The higher acrylic acid content in the copolymer induced increase of particle size and decrease of zeta potential. Cisplatin-incorporated nanoparticles showed a similar growth-inhibitory effect against CT26 tumor cells in vitro. However, cisplatin-incorporated nanoparticles showed improved antitumor activity against an animal tumor xenograft model.

Conclusion: We suggest that PAA-MMA nanoparticles incorporating cisplatin are promising carriers for an antitumor drug-delivery system.

Researchers Say Molecule May Help Overcome Cancer Drug Resistance
By Estel Grace Masangkay

A group of researchers from the University of Delaware has discovered that a deubiquitinase (DUB) complex, USP1-UAF1, may present a key target in helping fight resistance to platinum-based anticancer drugs. The research team’s findings were published online in Nature Chemical Biology.

Zhihao Zhuang, associate professor in the Department of Chemistry and Biochemistry at UD, and his team studied a DNA damage tolerance mechanism called translesion synthesis (TLS). Enzymes known as TLS polymerases synthesize DNA over damaged nucleotide bases, followed by replication after lesion. The enzymes have been linked with building cancer cell resistance to certain cancer drugs including cisplatin. Cisplatin is used in treatment of ovarian, bladder, and testicular cancers which have spread.

“Cancer drugs like cisplatin work by damaging DNA and thereby preventing cancer cells from replicating the genomic DNA and dividing. However, cancer cells quickly develop resistance to cisplatin, and we and other researchers suspect that a polymerase known as Pol η is involved in overcoming cisplatin-induced lesions,” Professor Zhuang said.

The team found that USP1-UAF1 may play a crucial role in regulating DNA damage response. A new molecule ML323 can be used to inhibit processes such as translesion synthesis. Zhuang said, “Using ML323, we studied the cellular response to DNA damage and revealed new insights into the role of deubiquitination in both the TLS pathway and another one called the Fanconi anemia, or FA, pathway. We’re very encouraged by the fact that a single molecule is effective at inhibiting the USP1-UAF1 DUB complex and disrupting two essential DNA damage tolerance pathways.”

A novel small peptide as an epidermal growth factor receptor targeting ligand for nanodelivery in vitro

Cui-yan Han,  Li-ling Yue, Ling-yu Tai,  Li Zhou  et al.  Intl J Nanomedicine 2013:8 1541–1549

The discovery of suitable ligands that bind to cancer cells is important for drug delivery specifically targeted to tumors. Monoclonal antibodies and fragments that serve as ligands have specific targets. Natural ligands have strong mitogenic and neoangiogenic activities. Currently, small pep­tides are pursued as targeting moieties because of their small size, low immunogenicity, and their ability to be incorporated into certain delivery vectors.

The epidermal growth factor receptor (EGFR) serves an important function in the proliferation of tumors in humans and is an effective target for the treatment of cancer. The epidermal growth factor receptor (EGFR) is a transmembrane protein on the cell surface that is overexpressed in a wide variety of human cancers. EGFR is an effective tumor-specific target because of its significant functions in tumor cell growth, differentiation, and migration. EGFR-targeted small molecule peptides such as YHWYGYTPQNVI have been successfully identified using phage display library screening; by contrast, the peptide LARLLT has been generated using computer-assisted design (CAD).

These peptides can be conjugated to the surfaces of liposomes that are then delivered selectively to tumors by the specific and efficient binding of these peptides to cancer cells that express high levels of EGFR.

In this paper, we studied the targeting characteristics of small peptides (AEYLR, EYINQ, and PDYQQD) These small peptides were labeled with fluorescein isothiocyanate (FITC) and used the peptide LARLLT as a positive control, which bound to putative EGFR selected from a virtual peptide library by computer-aided design, and the independent peptide RALEL as a negative control.

Analyses with flow cytometry and an internalization assay using NCI-H1299 and K562 with high EGFR and no EGFR expression, respectively, indicated that FITC-AEYLR had high EGFR targeting activity. Biotin-AEYLR that was specifically bound to human EGFR proteins demonstrated a high affinity for human non-small-cell lung tumors.

We found that AEYLR peptide-conjugated, nanostructured lipid carriers enhanced specific cellular uptake in vitro during a process that was apparently mediated by tumor cells with high-expression EGFR. Analysis of the MTT assay indicated that the AEYLR peptide did not significantly stimulate or inhibit the growth activity of the cells. These findings suggest that, when mediated by EGFR, AEYLR may be a potentially safe and efficient delivery ligand for targeted chemotherapy, radiotherapy, and gene therapy.

Arginine-based cationic liposomes for efficient in vitro plasmid DNA delivery with low cytotoxicity

SR Sarker  Y Aoshima,   R Hokama  T Inoue  et al. Intl J Nanomedicine 2013:8 1361–1375.

Currently available gene delivery vehicles have many limitations such as low gene delivery efficiency and high cytotoxicity. To overcome these drawbacks, we designed and synthesized two cationic lipids comprised of n-tetradecyl alcohol as the hydrophobic moiety, 3-hydrocarbon chain as the spacer, and different counterions (eg, hydrogen chloride [HCl] salt or trifluoroacetic acid [TFA] salt) in the arginine head group.

 Cationic lipids were hydrated in 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffer to prepare cationic liposomes and characterized in terms of their size, zeta potential, phase transition temperature, and morphology. Lipoplexes were then prepared and characterized in terms of their size and zeta potential in the absence or presence of serum. The morphology of the lipoplexes was determined using transmission electron microscopy and atomic force microscopy. The gene delivery efficiency was evaluated in neuronal cells and HeLa cells and compared with that of lysine-based cationic assemblies and Lipofectamine™ 2000. The cytotoxicity level of the cationic lipids was investigated and compared with that of Lipofectamine™ 2000.

 We synthesized arginine-based cationic lipids having different counterions (ie, HCl-salt or TFA-salt) that formed cationic liposomes of around 100 nm in size. In the absence of serum, lipoplexes prepared from the arginine-based cationic liposomes and plasmid (p) DNA formed large aggregates and attained a positive zeta potential. However, in the presence of serum, the lipoplexes were smaller in size and negative in zeta potential. The morphology of the lipoplexes was vesicular.

Arginine-based cationic liposomes with HCl-salt showed the highest transfection efficiency in PC-12 cells. However, arginine-based cationic liposomes with TFA salt showed the highest transfection efficiency in HeLa cells, regardless of the presence of serum, with very low associated cytotoxicity.

The gene delivery efficiency of amino acid-based cationic assemblies is influ­enced by the amino acids (ie, arginine or lysine) present as the hydrophilic head group and their associated counterions.

Molecularly targeted approaches herald a new era of non-small-cell lung cancer treatment

H Kaneda, T Yoshida,  I Okamoto.   Cancer Management and Research 2013:5 91–101.

The discovery of activating mutations in the epidermal growth-factor receptor (EGFR) gene in 2004 opened a new era of personalized treatment for non-small-cell lung cancer (NSCLC). EGFR mutations are associated with a high sensitivity to EGFR tyrosine kinase inhibitors, such as gefitinib and erlotinib. Treatment with these agents in EGFR-mutant NSCLC patients results in dramatically high response rates and prolonged progression-free survival compared with conventional standard chemotherapy. Subsequently, echinoderm microtubule-associated protein-like 4 (EML4)–anaplastic lymphoma kinase (ALK), a novel driver oncogene, has been found in 2007. Crizotinib, the first clinically available ALK tyrosine kinase inhibitor, appeared more effective compared with standard chemotherapy in NSCLC patients harboring EML4-ALK. The identification of EGFR mutations and ALK rearrangement in NSCLC has further accelerated the shift to personalized treatmentbased on the appropriate patient selection according to detailed molecular genetic characterization. This review summarizes these genetic biomarker-based approaches to NSCLC, which allow the instigation of individualized therapy to provide the desired clinical outcome.

Non-small-cell lung cancer (NSCLC) has a poor prognosis and remains the leading cause of death related to cancer worldwide. For most individuals with advanced, metastatic NSCLC, cytotoxic chemotherapy is the mainstay of treatment on the basis of the associated moderate improvement in survival and quality of life. However, the outcome of chemotherapy in such patients has reached a plateau in terms of overall response rate (25%–35%) and overall survival (OS; 8–10 months). This poor outcome, even for patients with advanced NSCLC who respond to such chemotherapy, has motivated a search for new therapeutic approaches.

Recent years have seen rapid progress in the development of new treatment strat­egies for advanced NSCLC, in particular the introduction of molecularly targeted therapiesand appropriate patient selection. First, the most important change has been customization of treatment according to patient selection based on the genetic profile of the tumor. Small-molecule tyrosine kinase inhibitors (TKIs) that target the epidermal growth-factor receptor (EGFR), such as gefitinib and erlotinib, are especially effective in the treatment of NSCLC patients who harbor activating EGFR mutations.

Surgical Nanorobotics using nanorobots made from advanced DNA origami and Synthetic Biology

Ido Bachelet’s moonshot to use nanorobotics for surgery has the potential to change lives globally. But who is the man behind the moonshot?

Ido graduated from the Hebrew University of Jerusalem with a PhD in pharmacology and experimental therapeutics. Afterwards he did two postdocs; one in engineering at MIT and one in synthetic biology in the lab of George Church at the Wyss Institute at Harvard.

Now, his group at Bar-Ilan University designs and studies diverse technologies inspired by nature.

They will deliver enzymes that break down cells via programmable nanoparticles.

Delivering insulin to tell cells to grow and regenerate tissue at the desired location.

Surgery would be performed by putting the programmable nanoparticles into saline and injecting them into the body to seek out remove bad cells and grow new cells and perform other medical work.

 

http://2.bp.blogspot.com/-bnAE6hL2RIE/Uy0wFB8pYPI/AAAAAAAAubM/BeSpFC4vLu0/s1600/screenshot-by-nimbus+(3).png

 

Robots killing and suppressing cancer cells

 

http://1.bp.blogspot.com/-LGsE1msGIrw/Uy0vKGoaQ3I/AAAAAAAAubE/2E1_lcAspao/s1600/screenshot-by-nimbus+(2).png

 

Robots delivering payload

http://www.youtube.com/watch?feature=player_embedded&v=aA-H0L3eEo0

http://4.bp.blogspot.com/-kkfXlMyPRCI/Uy0wkYPMvBI/AAAAAAAAubU/0AQPpJpM5E4/s1600/screenshot-by-nimbus+(4).png

Molecular building blocks

 

http://www.youtube.com/watch?feature=player_embedded&v=aA-H0L3eEo0#t=236

http://www.youtube.com/watch?feature=player_embedded&v=aA-H0L3eEo0#t=283

http://www.youtube.com/watch?feature=player_embedded&v=aA-H0L3eEo0#t=287

http://www.youtube.com/watch?feature=player_embedded&v=aA-H0L3eEo0#t=292

http://www.youtube.com/watch?feature=player_embedded&v=aA-H0L3eEo0#t=333

http://www.youtube.com/watch?feature=player_embedded&v=aA-H0L3eEo0#t=397

http://2.bp.blogspot.com/-gCHiyZ2MBHg/Uy0ySRKw_II/AAAAAAAAubg/BeneEQ5bY-U/s1600/screenshot-by-nimbus+(5).png

 

Robot blocks neuron

http://4.bp.blogspot.com/-cbYNJnN_w7U/Uy0yrqyqebI/AAAAAAAAubo/b42r4WRMr8k/s1600/screenshot-by-nimbus+(6).png

 

automation of robotic surgery

 

http://www.youtube.com/watch?feature=player_embedded&v=aA-H0L3eEo0#t=470

Nanoparticles with computational logic has already been done

http://www.youtube.com/watch?feature=player_embedded&v=aA-H0L3eEo0#t=501

http://www.youtube.com/watch?feature=player_embedded&v=aA-H0L3eEo0#t=521

http://1.bp.blogspot.com/-rSyRzo7p50w/Uy0y5teQkDI/AAAAAAAAubw/8cxZ4t0WNHw/s1600/screenshot-by-nimbus+(7).png

 

 robotic algorithm

 

Load an ensemble of drugs into many particles for programmed release based on situation that is found in the body

http://1.bp.blogspot.com/-kc99CbOQYLs/Uy0zgUG13KI/AAAAAAAAub4/j6nM7hAVxUg/s1600/screenshot-by-nimbus+(8).png

http://www.youtube.com/watch?feature=player_embedded&v=aA-H0L3eEo0#t=572

http://www.youtube.com/watch?feature=player_embedded&v=aA-H0L3eEo0#t=577

 

robotic lung cancer Rx

 

chemotherapy regimen

 

Chemoprevention in Model Experiments

Effects of Two Disiloxanes ALIS-409 and ALIS-421 on Chemoprevention in Model Experiments

H TOKUDA,…. L AMARAL and J MOLNAR.ANTICANCER RESEARCH 33: 2021-2028 (2013).

ALIS

 

Figure 1. Chemical structures of ALIS-409 and ALIS-421.

Morpholino-disiloxane (ALIS-409) and piperazinodisiloxane (ALIS-421) compounds were developed as inhibitors of multidrug resistance of various types of cancer cells. In the present study, the effects of ALIS-409 and ALIS-421 compounds were investigated on cancer promotion and on co-existence of

tumor and normal cells. The two compounds were evaluated for their inhibitory effects on Epstein-Barr virus immediate early antigen (EBV-EA) expression induced by tetradecanoylphorbolacetate (TPA) in Raji cell cultures. The method is known as a primary screening test for antitumor effect, below the (IC50) concentration. ALIS-409 was more effective in inhibiting EBV-EA (100 μg/ml) and tumor promotion, than

ALIS-421, in the concentration range up to 1000 μg/ml. However, neither of the compounds were able to reduce tumor promotion significantly, expressed as inhibition of TPA-induced tumor antigen activation. Based on the in vitro results, the two disiloxanes were investigated in vivo for their effects on mouse skin tumors in a two-stage mouse skin carcinogenesis study.

 

 

 

 

 

 

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