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Archive for the ‘Liver & Digestive Diseases Research’ Category

Reporter: Aviva Lev-Ari, PhD, RN

 

Study Finds Dopamine Gene Variant Predictive of Placebo Response in IBS Patients

October 24, 2012
 

Researchers led by a group at Beth Israel Deaconess Medical Center have identified a genetic marker associated with the placebo effect in patients with irritable bowel syndrome.

According to the group, the finding is the first to show “genetic modulation of true placebo effects,” and supports the possibility of using genomic information to better design placebo-controlled clinical trials.

The researchers described their results in PLOS One this week. The project used genotyping to measure whether a polymorphism in the dopamine pathway‘s COMT gene was associated with differences in placebo response among 104 IBS patients enrolled in a three-arm trial of different placebo treatments.

After studying the distribution of the val158met polymorphism among the trial’s three arms — no treatment (a waitlist), treatment with placebo alone, and placebo treatment with an “augmented” physician-patient interaction involving more support — the group found that the strongest placebo response occurred in met/met homozygotes who received the augmented placebo treatment.

The researchers identified a weaker link between met/met and response in the placebo-only arm. And patients in the waitlist control arm showed no difference in response based on their genotype.

The study’s first author, Kathryn Hall, told PGx Reporter this week that having a genetic predictor of placebo response could allow researchers to stratify future placebo-controlled drug trials by potential responders and non-responders.

IBS is known to have a high placebo response rate. Hall said it’s likely that the use of genetic predictors for placebo response will be most relevant to trials of drugs for conditions that are similarly associated with high placebo response levels, such as depression, headache, allergies, and pain.

“In conditions where there tends to be a high placebo response, oftentimes a drug fails because it can’t prove efficacy above the placebo response. In those cases, the pharmaceutical companies are basically losing quite a bit of money and time and resources,” Hall said.

“So the question is – is this a possibility? Obviously, it hasn’t been done before and probably will need a lot more validation before anyone actually wants to do it,” she said. “But if it does hold true at least for some conditions and treatments, it would allow you to focus in on just the people who are [not going to respond to the placebo] – so it would build your power [and] reduce your cost, since you don’t have this set of people that are inflating the placebo response.”

Hall cited diseases like Parkinsons and schizophrenia, which involve dopamine metabolism, as examples where new treatments might see their efficacy estimation confounded by the placebo effect.

At a minimum, Hall suggested that drug developers might improve the success rates of their products by balancing the number of patients who are predisposed to respond and not respond to the placebo effect in both the treatment and placebo arms of a trial.

In the study, Hall and her colleagues evaluated a subset of patients from an earlier randomized controlled IBS trial.

In the previous trial, the group measured differences in response, based on patient-reported symptoms, after either placebo treatment alone, “augmented” placebo treatment in which patients were given extra physician interaction and support, or no treatment, and placement on a waiting list.

In the genetic follow-up, the researchers genotyped 104 patient samples to look for associations between val158met genotype and placebo-response, based on reported symptoms and quality of life.

The group coded each patient according to the presence of the COMT met allele and found that patients with the met/met genotype had the greatest level of improvement — based on their scores in a measure called the IBS-Symptom Severity Scale — while those with the val/val type had the least. Val/met patients fell in the middle.

While patients homozygous for the COMT val158met allele were the most responsive to placebo overall, the strongest signal was in the augmented treatment arm, with a smaller effect in the placebo-alone arm, and virtually no effect, or even a reverse effect, in the waitlist control arm.

Overall, the group concluded that the results “strongly suggest that COMT val158met, specifically the met/met genotype, is a potential marker for placebo response in IBS.”

The fact that the genotype is associated with a positive outcome only in groups given a placebo, and not in the control group, indicates that it is a true predictor of placebo effect, not just improvement in general, the group wrote.

While previous studies have looked for a genetic link to placebo response, they have not included this control arm, according to the Beth Israel team. Additional studies that hypothesize a COMT involvement and include a no-treatment arm “will be critical to confirm our findings,” the group added.

According to Hall, the field is likely still far away from using genomic information to influence the design of placebo-controlled trials. However, her group’s results suggest a path forward, she said.

The results may also have implications for more personalized treatment strategies, she said.

“On one hand, you could hypothesize that there are situations where people are placebo responders and taking a drug with a lot of side effects … Obviously giving people placebo pills is a long way off, but [perhaps you could] minimize someone’s drug intake if they are having more of a placebo response so they don’t have to have all the side effects,” she said.

At the same time, she said, the trial highlighted the influence of the “warm, caring doctor relationship.”

“Having a mechanistic understanding of what’s going on there, I think, will reinforce the need and the importance of this part of medicine,” she said, at least for some. The fact that val/val subjects, for example, showed the same lack of response in both the placebo-alone and augmented arms of the study may shed some light on why, “despite their best efforts, many a warm and caring physician has had patients that seemed to derive minimum benefit from their empathic attentions,” the study authors wrote.

      Molika Ashford is a GenomeWeb contributing editor and covers personalized medicine and molecular diagnostics. E-mail her here.

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Reporter: Aviva Lev-Ari, PhD, RN 

Mining the Unknown: A Systems Approach to Metabolite Identification Combining Genetic and Metabolic Information

Jan Krumsiek1, Karsten Suhre1,2, Anne M. Evans3, Matthew W. Mitchell3, Robert P. Mohney3, Michael V. Milburn3, Brigitte Wägele1,4, Werner Römisch-Margl1, Thomas Illig5,6, Jerzy Adamski7,8, Christian Gieger9, Fabian J. Theis1,10, Gabi Kastenmüller1*

 

1 Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany, 2 Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar, 3 Metabolon, Research Triangle Park, North Carolina, United States of America, 4 Department of Genome-Oriented Bioinformatics, Life and Food Science Center Weihenstephan, Technische Universität München, Freising, Germany, 5 Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany, 6 Biobank of the Hanover Medical School, Hanover Medical School, Hanover, Germany, 7 Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, Neuherberg, Germany, 8 Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany, 9 Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany, 10 Department of Mathematics, Technische Universität München, Garching, Germany

Abstract 

Recent genome-wide association studies (GWAS) with metabolomics data linked genetic variation in the human genome to differences in individual metabolite levels. A strong relevance of this metabolic individuality for biomedical and pharmaceutical research has been reported. However, a considerable amount of the molecules currently quantified by modern metabolomics techniques are chemically unidentified. The identification of these unknown metabolites is still a demanding and intricate task, limiting their usability as functional markers of metabolic processes. As a consequence, previous GWAS largely ignored unknown metabolites as metabolic traits for the analysis. Here we present a systems-level approach that combines genome-wide association analysis and Gaussian graphical modeling with metabolomics to predict the identity of the unknown metabolites. We apply our method to original data of 517 metabolic traits, of which 225 are unknowns, and genotyping information on 655,658 genetic variants, measured in 1,768 human blood samples. We report previously undescribed genotype–metabotype associations for six distinct gene loci (SLC22A2, COMT, CYP3A5, CYP2C18, GBA3, UGT3A1) and one locus not related to any known gene (rs12413935). Overlaying the inferred genetic associations, metabolic networks, and knowledge-based pathway information, we derive testable hypotheses on the biochemical identities of 106 unknown metabolites. As a proof of principle, we experimentally confirm nine concrete predictions. We demonstrate the benefit of our method for the functional interpretation of previous metabolomics biomarker studies on liver detoxification, hypertension, and insulin resistance. Our approach is generic in nature and can be directly transferred to metabolomics data from different experimental platforms.

Introduction 

Recently, genome-wide association studies (GWAS) on metabolic quantitative traits have proven valuable tools to uncover the genetically determined metabolic individuality in the general population [1][5]. Interestingly, a great portion of the genetic loci that were found to significantly associate with levels of specific metabolites are within or in close proximity to metabolic enzymes or transporters with known disease or pharmaceutical relevance. Moreover, compared to GWAS with clinical endpoints the effect sizes of the genotypes are exceptionally high.

The number and type of the metabolic features that went into these GWAS was mainly defined by the metabolomics techniques used: Gieger et al. [1] and Illig et al. [2] used a targeted mass spectrometry (MS)-based approach giving access to the concentrations of 363 and 163 metabolites, respectively. Suhre et al. [3] and Nicholson et al. [4] applied untargeted nuclear magnetic resonance (NMR) based metabolomics techniques, yielding 59 metabolites that had been identified in the spectra prior to the GWAS and 579 manually selected peaks from the spectra, respectively. In Suhre et al. [5], 276 metabolites from an untargeted MS-based approach were analyzed.

While these previous GWAS focused on metabolic features with known identity, untargeted metabolomics approaches additionally provide quantifications of so-called “unknown metabolites”. An unknown metabolite is a small molecule that can reproducibly be detected and quantified in a metabolomics experiment, but whose chemical identity has not been elucidated yet. In an experiment using liquid chromatography (LC) coupled to MS, such an unknown would be defined by a specific retention time, one or multiple masses (e.g. from adducts), and a characteristic fragmentation pattern of the primary ion(s). An unknown observed by NMR spectroscopy would correspond to a pattern in the chemical shifts. Unknowns may constitute previously undocumented small molecules, such as rare xenobiotics or secondary products of metabolism, or they may represent molecules from established pathways which could not be assigned using current libraries of MS fragmentation patterns [6], [7] or NMR reference spectra [8].

The impact of unknown metabolites for biomedical research has been shown in recent metabolomics-based discovery studies of novel biomarkers for diseases and various disease-causing conditions. This includes studies investigating altered metabolite levels in blood for insulin resistance [9], type 2 diabetes [10], and heart disorders [11]. A considerable number of high-ranking hits reported in these biomarker studies represent unknown metabolites. As long as their chemical identities are not clarified the usability of unknown metabolites as functional biomarkers for further investigations and clinical applications is rather limited.

In mass-spectrometry-based metabolomics approaches, the assignment of chemical identity usually involves the interpretation and comparison of experiment-specific parameters, such as accurate masses, isotope distributions, fragmentation patterns, and chromatography retention times [12][14]. Various computer-based methods have been developed to automate this process. For example, Rasche and colleagues [15] elucidated structural information of unknown metabolites in a mass-spectrometry setup using a graph-theoretical approach. Their approach attempts to reconstruct the underlying fragmentation tree based on mass-spectra at varying collision energies. Other authors excluded false candidates for a given unknown by comparing observed and predicted chromatography retention times [16], [17], or by the automatic determination of sum formulas from isotope distributions [18]. Furthermore, Gipson et al. [19] and Weber et al. [20] integrated public metabolic pathway information with correlating peak pairs in order to facilitate metabolite identification. However, these methods might not be applicable for high-throughput metabolomics datasets that have been produced in a fee-for-service manner, since the mass spectra as such might not be readily available.

Approaching the problem from a conceptually different perspective, we here present a novel functional metabolomics method to predict the identities of unknown metabolites using a systems biological framework. By combining high-throughput genotyping data, metabolomics data, and literature-derived metabolic pathway information, we generate testable hypotheses on the metabolite identities based solely on the obtained metabolite quantifications (Figure 1). No further experiment-specific data such as retention times, isotope patterns and fragmentation patterns are required for this analysis.

 

Figure 1. Data integration workflow for the systematic classification of unknown metabolites.

We combine high-throughput metabolomics and genotyping data in Gaussian graphical models (GGMs) [21] and in genome-wide association studies (GWAS) [5] in order to produce testable predictions of the unknown metabolites’ identities. These hypotheses are then subject to experimental verification by mass-spectrometry. Six such cases have been fully worked through and are presented in Table 3. doi:10.1371/journal.pgen.1003005.g001

 http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003005?imageURI=info:doi/10.1371/journal.pgen.1003005.g001#pgen-1003005-g001

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Discussion 

We developed and validated a novel integrative approach for the biochemical characterization of “unknown metabolites” from high-throughput metabolomics and genotyping datasets. Our method allows for the functional annotation of previously unidentified metabolites and, as a consequence, enhances the interpretability of metabolomics data in genome-wide association studies and biomarker discovery. For the first time, we systematically evaluated genetic associations of unknown metabolites, thereby discovering seven new loci of metabolic individuality. By classifying a series of unknown metabolites, we gained new insights into the functional interplay between genetic variation and the metabolome both for previously reported and new loci. Furthermore, several of the unknown compounds that we identified as well as their newly associated loci were independently reported in disease-related studies. In the following, we discuss three genetic loci and their associated phenotypes.

COMT and hepatic detoxification

The first example is a recent biomarker study, where Milburn et al. [34] reported an association of X-11593 with hepatic detoxification. In our GWAS, we find a strong association of X-11593 with the COMT locus, which encodes the catechol-O-methyltransferase enzyme. COMT is responsible for the inactivation of catecholamines such as L-dopa and various neuroactive drugs by O-methylation [35]. Following our identification approach, we experimentally confirmed the identity of X-11593 as O-methylascorbate. Notably, O-methylascorbate is a known product of ascorbate (vitamin C) O-methylation by COMT [36], [37]. Thus, our observations establish a link between O-methylascorbate blood levels, common genetic variation in the COMT locus and COMT-mediated liver detoxification processes.

ACE and hypertension

The second example relates to the ACE gene locus, which is a known risk locus for cardiovascular disease, hypertension and kidney failure. The protein encoded by the ACE locus, angiotensin-converting enzyme, is an exopeptidase which cleaves dipeptides from vasoactive oligopeptides, and plays a central role in the blood pressure-controlling renin-angiotensin system [38]. Moreover, the ACE protein is a target for various pharmaceuticals (ACE inhibitors), especially in the treatment of hypertension [39]. In our study, we identified three unknowns as dipeptides (X-14205, X-14208 and X-14478), two of which also associated with the ACE locus. These dipeptides could thus represent novel, interesting biomarkers for the activity of ACE. Moreover, Steffens et al. [11] reported a connection between heart failure and X-11805, which is in close proximity to angiontensin-related peptides in the GGM. This connection might be revisited after a successful identification of X-11805 in a future study.

UGT1A/ACADM and insulin resistance

The third example is an explorative study to detect biomarkers for insulin sensitivity. Gall et al. [9] reported several known metabolites (most prominently α-hydroxybutyrate) as biomarkers for insulin resistance. They also reported a series of unknown metabolites among their top hits. In the present study, we investigated three of these unknowns: X-11793 associates with UGT1A (UDP glucuronosyltransferase 1) and represents a bilirubin-related substance. Moreover, we experimentally validated X-11421 and X-13431, which display a strong association with ACADM (acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain), as acylcarnitines containing 10 and 9 carbon atoms, respectively. The identification of these latter two unknown metabolites as medium-chain length acylcarnitines is coherent with reports by Adams et al. [40]. The authors found elevated blood plasma acylcarnitine levels in women with type 2 diabetes. Functionally, they attributed this finding to incomplete β-oxidation. Thus, our identification of X-11421 and X-13431 now suggests incomplete β-oxidation as an explanation for the associations found by Gall et al. and implies that acylcarnitines containing 10 and 9 carbon atoms are potential biomarkers for insulin resistance.

Conclusion

In summary, we integrated high-throughput metabolomics and genotyping data from a large population cohort for elucidating the biochemical identities of unknown metabolites. To this end, we applied metabolomics genome-wide association studies and Gaussian graphical modeling in order to link these unknown metabolites with known metabolic classes and biological processes. For six specific scenarios, we went from systematic hypothesis generation over detailed investigation and identity prediction to direct experimental confirmation. Similar validations may now be undertaken for the remaining predictions that we report in Table S1. Finally, we demonstrated the benefit of our method by discussing several of these newly identified metabolites in the context of existing biomarker discovery studies on liver detoxification, hypertension and insulin resistance.

It is to be noted that our method does not specifically require genotyping data. Even metabolomics measurements alone, analyzed through the GGMs, may provide sufficient information for the classification and even precise identity prediction. The unknowns with GGM evidence but without GWAS hits in Figure 4 as well as the HETE scenario represent examples for this approach.

One limitation of our approach is the requirement for associations with functionally described loci or known metabolites. Certain metabolite groups might thus systematically not be identifiable. For instance, if the identity of a whole class of biochemically related molecules is unknown (which might be due to experimental reasons), then the GGM associations between those compounds will not aid in identity elucidation. The 118 unknown compounds for which we could not derive any classification might represent such cases. Thus, our functionally oriented method should be regarded as a complementary extension to the existing identity determination methods.

Accordingly, our approach can be extended in several directions. It can be combined with method-specific, automated techniques that further exclude sets of metabolites. Previously mentioned methods relying on mass-spectra [15] or chromatographic properties [17] are suitable candidates here. Moreover, the method can be directly transferred to other types of metabolomics datasets not specifically originating from MS experiments, such as NMR-based metabolomics.

Beyond the application to metabolite identification, our study demonstrates the general potential of functional metabolomics in the context of genome-wide association studies. The comprehensive metabolic picture provided by GGMs in combination with GWAS allows for the detailed analysis of metabolic functions, chemical classes, enzyme-metabolite relationships and metabolic pathways.

Author Contributions 

Conceived and designed the experiments: JK KS FJT GK. Performed the experiments: AME MWM RPM MVM. Analyzed the data: JK GK. Contributed reagents/materials/analysis tools: BW WR-M TI JA CG. Wrote the paper: JK KS FJT GK.

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Source:

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003005

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dimethyl arginineNitric Oxide and Sepsis

Nitric Oxide and Sepsis, Hemodynamic Collapse, and the Search for Therapeutic Options

Curator, Reporter, EAW: Larry H Bernstein, MD, FCAP

This document explores the current understanding of sepsis as a cascade of events that involves the microcirculation unevenly because of a differential effect on the large and contiguous intestinal epithelium, secondary effects on cardiopulmonary blood flows and cardiac output, and the role of Nitric Oxide in the emergence of beneficial and potentially deleterious effects. This leads to a substantial body of work on therapeutic targets, either aimed at total inhibition or selective inhibition of NO synthase, and the special role of iNOS. This is another of a series of discussions on the metabolic and regulatory role of NO in health and disease.

Introduction

Antioxidants are essential, and are involved in several important biological processes such as immunity, protection against tissue damage, reproduction, growth and development. Antioxidants preserve adequate function of cells against homeostatic disturbances such as those caused by septic shock, aging and, in general, processes involving oxidative stress. This review focuses on the involvement of reactive oxygen and nitrogen species.
The presence of free radicals in biological materials was discovered about 50 years ago. Today, there is a large body of evidence indicating that patients in hospital intensive care units (ICUs) are exposed to excessive free radicals from drugs and other substances that alter cellular reduction -oxidation (redox) balance, and disrupt normal biological functions. However, low levels of free radicals are also vital for many cell signaling events and are essential for proper cell function.
Excess free radicals can result from a variety of conditions such as tissue damage and hypoxia (limiting oxygen levels), overexposure to environmental factors (tobacco smoke, ultraviolet radiation, and pollutants), a lack of antioxidants, or destruction of free radical scavengers. When the production of damaging free radicals exceeds the capacity of the body’s antioxidant defenses to detoxify them, a condition known as oxidative stress occurs.

Free Radicals and Antioxidants: an Overview

A free radical can be described as any atom or a group of atoms or molecules in which there is at least one unpaired electron in the outermost shell . These free radicals are very reactive with adjacent molecules such as lipids, proteins, and carbohydrates and can cause cellular damage. Paradoxically, free radicals can also be produced by many cells as a protective mechanism, for example neutrophils produce free radicals to attack and destroy pathogens, while the liver uses free radicals for detoxification. However, the presence of free radicals within the body can also have a significant role in the development and progression of many disease processes for example heart disease, hypertension, cerebrovascular accidents, and diabetic complications. Any free radical involving O2 is referred to as a reactive oxygen species (ROS).
Normal cellular metabolism involves the production of ROS, and in humans, superoxide (O2 -) is the most commonly produced free radical. Phagocytic cells such as macrophages and neutrophils are prominent sources of O2 -. During an inflammatory response, these cells generate free radicals that attack invading pathogens such as bacteria and, because of this, the production of O2- by activated phagocytic cells in response to inflammation is one of the most studied free radical producing systems. The majority of the H2O2 is broken down to O2 and water by the antioxidant enzyme catalase. In addition to catalase, glutathione peroxidase can also break down H2O2 and also any peroxides that form on lipids within the body. When O2 – reacts with nitric oxide (NO), the toxic product peroxynitrite (ONOO-) is formed.
Cellular ROS originate from O2- generated as a by-product of oxidative phosphorylation (mitochondrial respiration), they differ in their mechanism of production, necessary cofactors, diffusion range, hydrophobicity, biological targets, detoxification pathways and breakdown products. O-2 damaging reactions largely involve disassembly of iron-sulphur clusters in proteins. H2O2 or O-2 alone lacked reactivity toward iron regulatory protein-1 (IRP-1), but a combined action of the two species induced reversible inactivation of IRP-1. Such an effect was attributed to direct interactions of O-2 and H2O2 with a preformed pool of IRP-1, resulting in reversible modifications of -SH residues; in fact, its action would be limited to removing only iron atoms, an effect sufficient to abolish enzyme activity.
The hydroxyl radical (.OH) is the most reactive of the free radical molecules. OH- damages cell membranes and lipoproteins by a process termed lipid peroxidation. In fact, lipid peroxidation can be defined as the process whereby free radicals “steal” electrons from the lipids in our cell membranes, resulting in cell damage and increased production of ROS. This process takes place in 3 stages:

  1. Initiation: In a peroxide-free lipid system, the initiation of a peroxidation sequence refers to the attack of an ROS (with sufficient reactivity) able to abstract a hydrogen (H) atom from a methylene group (- CH2-).
  2. Propagation: A peroxyl radical is able to abstract H from another lipid molecule (adjacent fatty acid), especially in the presence of metals such as copper or iron, thus causing an autocatalytic chain reaction. The peroxyl radical combines with H to give a lipid hydroperoxide (or peroxide).
  3. Termination: formation of a hydroperoxide. Lipid peroxidative damage to lipids in low-density lipoprotein (LDL) plays an important role in atherosclerosis [9]. To protect against oxidative damage, organisms have developed a variety of antioxidant defenses that include proteins, compounds such as vitamins, and specialized antioxidant enzymes.

Lipid-soluble antioxidants are located in the cellular membranes and lipoproteins, whereas the water-soluble antioxidants are present in the aqueous environments, such as fluids inside cells and in the blood. Preventative antioxidant enzymes inside the cell are an important defense against free radicals.
In humans, the highest levels of SOD are found in the liver, adrenal gland, kidney, and spleen. Catalase and glutathione peroxidase both work to detoxify O2-reactive radicals by catalyzing the formation of H2O2 derived from O2 -. The liver, kidney, and red blood cells possess high levels of catalase, which helps to detoxify chemicals in the body. The water-soluble tripeptide-thiol glutathione also plays an important role in a variety of detoxification processes. Glutathione is found in millimolar concentrations in the cell cytosol and other aqueous phases, and readily interacts with free radicals, especially the hydroxyl radical, by donating a hydrogen atom.

Sepsis and Signaling Pathways

Serious infections trigger systemic inflammatory response and can result in sepsis. It is believed that sepsis and therefore septic shock are due to the inappropriate increase in the innate immune response via circulating and tissue inflammatory cells, such as monocytes/macrophages and neutrophils. These cells normally exist in a nonactivated state but are rapidly activated in response to bacteria. Sepsis induces a dysfunction in immune cells that contributes to the development of injuries by producing mediators such as cytokines and ROS.

Lipopolysaccharide (Lps) Signaling

LPS of Gram-negative organisms induces macrophages to secrete cytokines, which in turn activate T, and B cells to upregulate the adaptive immune responses. Toll-like receptor 4 (TLR4) is the LPS receptor and its stimulation induces nuclear factor kB (NF-kB) activation. The activation of NF-kB involves phosphorylation and degradation of IkB, an inhibitor of NF-kB. The NF-kB/IkB system exerts transcriptional regulation on proinflammatory genes encoded for various adhesion molecules and cytokines. Activation of NF-kB leads to the induction of NF-kB binding elements in their promoter regions and also leads to the induction of NF-kB dependent effector genes, which produce modifications in blood flow, and aggregation of neutrophils, and platelets. This results in damaged endothelium and also coagulation abnormalities often seen in patients with sepsis and septic shock. Therefore, NF-kB is reported to be an O2 sensor in LPS-induced endotoxemia.

Free Radicals and Antioxidants In Sepsis

The sources of ROS during sepsis are:

  1. the mitochondrial respiratory chain.
  2. the metabolic cascade of arachidonic acid.
  3. the protease-mediated enzyme xanthine oxidase.
  4. granulocytes and other phagocytes activated by complement, bacteria, endotoxin, lysosomal enzymes, etc.
  5. Other oxidases mainly NADPH oxidase.

Under normal physiological conditions, the majority of ROS are formed during cellular respiration and by activated phagocytic cells, including neutrophils, involved in the inflammatory response. ROS have physiologically essential roles in mitochondrial respiration, prostaglandin production pathways and host defense . The electron reduction of O2 occurs in the mitochondrial electron transport system of all aerobically respiring cells. The enzyme catalyzing this transition metals iron and copper in its active site. These ions can be paramagnetic and contain stable unpaired electrons. By using the unpaired electrons in these transition metals to control the O2 reactions, mitochondria prevent the unwanted release of ROS.
In sepsis, there are several potential sources of ROS, including the mitochondrial respiratory electron transport chain, xanthine oxidase activation as a result of ischemia and reperfusion, the respiratory burst associated with immune cell activation, arachidonic acid metabolism and NADPH oxidase.

  • In fact, activated immune cells produce O2 – as a cytotoxic agent as part of the respiratory burst via the action of membrane-bound NADPH oxidase on O2.
  • The increase of ROS after LPS challenge has been demonstrated in different models of septic shock in peritoneal macrophages and lymphocytes.

This disturbance in the balance between pro-oxidants (ROS) and antioxidants in favor of the former is characteristic of oxidative stress in immune cells in response to endotoxin. In this context,

  • a typical behavior of these cells under an oxidative stress situation implies changes in different immune functions such as an increase in adherence and phagocytosis and a decrease in chemotaxis.
  • Neutrophils play a crucial role in the primary immune defense against infectious agents,which includes phagocytosis and the production of ROS.

Antioxidant Defenses

Antioxidants are central to the redox balance in the human body. They do not act in isolation, but synergistically with other classes of molecules. Primary antioxidants prevent oxygen radical formation, by either removing free radical precursors or by inhibiting catalysis, e.g. the enzymes glutathione peroxidase and catalase. Secondary antioxidants react with ROS which have already been formed, either to remove or inhibit them, e.g. vitamins C and E. Endogenous antioxidant defenses exist in a number of locations, namely intracellularly, on the cell membrane and extracellularly. The immune system is highly reliant on accurate cell-cell communication for optimal function, and any damage to the signaling systems involved will result in an impaired immune responsiveness.

  • Oxidant-mediated tissue injury is a particular hazard to the immune system, since phagocyte cells produce ROS as part of the defense against infection.
  • Therefore, adequate amounts of neutralizing antioxidants are required to prevent damage to the immune cells themselves.

The SOD enzymes are a family of metalloenzymes which rapidly promote the conversion of O2- to H2O2. Three forms of SOD are recognized to be important: copper-zinc SOD (cytoplasmic-located), manganese SOD (mitochondrial-located) and extracellular SOD (extracellular matrix-located). Catalase and glutathione peroxidase, a selenium containig enzyme which requires the presence of reduced GSH for its action, both catalyze the conversion of H2O2 to H 2O. GSH also has direct antioxidant activity, through donation of hydrogen ions, to repair damaged DNA. Oxidative stress and modulation on GSH/GSSG (GSSG=oxidized GSH) levels also up-regulate gene expression of several other antioxidant proteins, such as manganese SOD, glutathione peroxidase, thioredoxin (Trx) and metallothionein.

Effects of Nitric Oxide

NO is synthesized from L-arginine by different isoenzymes of (NOS), and is implicated in a wide range of disease processes, exerting both detrimental and beneficial effects at the cellular and vascular levels. To date, three main isoforms of NOS are known:

  • neuronal NOS (NOS-1 or nNOS),
  • inducible NOS (NOS-2 or iNOS), and
  • endothelial NOS (NOS-3 or eNOS).

NO has been shown to play a key role in the pathogenesis of septic shock

Hyperproduction of NO induces

  • excessive vasodilation,
  • changes in vascular permeability, and
  • inhibition of noradrenergic nerve transmission,

all characteristics of human septic shock.
The recogniton of NO production by activated macrophages as part of the inflammatory process was an important milestone for assesing both the biological production of NO and the phenomenon of induction of NOS activity. The observation has been extended to neutrophils, lymphocytes, and other cell types. The role of NO in the pathophysiology of endotoxic shock was advanced by Thiemermann and Vane, who observed that administration of the specific NOS inhibitor N-methyl-L-arginine (L-NMMA) decreased the severe hypotension produced by administration of LPS. Other groups simultaneously reported similar results indicating that endotoxin increases NO production and prompted the idea that pharmacological inhibition of NOS may be useful in the treatment of inflammation and septic shock. However, clinical trials using L-NMMA failed to show a beneficial effect in septic shock patient. The major limitation for the use of NOS inhibitors in clinical studies is the development of pulmonary hypertension as a side effect of NOS blockade, which can be alleviated by the use of inhaled NO.
However, several compounds which modulate NO synthesis have been patented in recent years, such as various inflammatory mediators that have been implicated in the induction and activation of iNOS, particularly IFNg, TNFa, IL-1b, and platelet-activating factor (PAF) alone or synergistically. In addition to the activation of iNOS, cytokines and endotoxin may increase NO release by increasing arginine availability through the opening of the specific y+ channels and the expression of the cationic amino acid transporter (CAT), or by increasing tetrahydrobiopterin levels, a key cofactor in NO synthesis. Several experimental studies have demonstrated a decrease in NOS activity resulting in an impairment in endothelial-dependent relaxation during endotoxemia and experimental sepsis, possibly as the result of a cytokine-or hypoxia-induced shortened half-life of NOS mRNA, or of altered calcium mobilization.
NO exerts in vitro toxic effects including nuclear damage, protein and membrane phospholipid alterations, and the inhibition of mitochondrial respiration in several cell types. Mitochondrial impairment could also be considered as an adaptive phenomenon, decreasing cellular metabolism when the energy supply is limited. The toxicity of NO itself may be enhanced by the formation of ONOO- from the reaction of NO with O-2. Therefore, the multiple organ failure syndrome (MOFS) that often accompanies severe sepsis may be related to the cellular effects of excess NO or ONOO-.

Involvement of Nitrogen Species

NO reacts rapidly with ferrous iron, and at physiological concentrations, NO also binds to soluble guanylate cyclase and to another hemoprotein, cytochrome c oxidase (Complex IV), the terminal enzyme of the mitochondrial respiratory chain. NO can therefore control cellular functions via the reversible inhibition of respiration. There are a number of reactive NO species, such as

  • N2O3 and
  • ONOO-

that can also alter critical cellular components.

During the first hours after injury, iNOS-mediated NO production is upregulated, producing a burst of NO that far exceeds basal levels. This overabundance of NO produces significant cellular injury via several mechanisms.
NO may

  • directly promote overwhelming peripheral vasodilation, resulting in vascular decomposition;
  •  NO may upregulate the transcription NF-kB initiating an inflammatory signaling pathway that, in turn,
  • triggers numerous inflammatory cytokines.

NO also interacts with the O-2 to yield ONOO-, a highly reactive compound that exacerbates the injury produced by either O-2 alone or NO alone.
The ONOO- generation which occurs during fluid resuscitation in the injured subject produces cellular death by enhancing DNA single strand breakage, activates the nuclear enzyme polyADP ribose synthetase (PARS), leading to cellular energy depletion and cellular necrosis. The detrimental effects of ONOO- in shock and resuscitation have been attributed to oxidation of sulfhydryl groups, the nitration of tyrosine, tryptophane, and guanine, as well as inhibition of the membrane sodium-potassium adenosine triphosphatase. PARS activation depletes NAD and thus alters electron transport, ATP synthesis, and glycolysis; and leads to DNA fragmentation and cellular apoptosis.
The activation of monocytes, macrophages and endothelial cells by LPS results in the expression of iNOS, and consequently increases the transformation of L-arginine to NO, which can combine with O2- to form ONOO-, causing tissue injury during shock, inflammation and ischemia reperfusion. NO stimulates H2O2 and O-2 production by mitochondria, increasing leakage of electrons from the respiratory chain. H2O2, in turn, participates in the upregulation of iNOS expression via NFkB activation. ONOO- has been shown to stimulate H2O2 production by isolated mitochondria. On the other hand, NO can decrease ROS-produced damage that occurs at physiological levels of NO. The high reactivity of NO with radicals might be beneficial in vivo by scavenging peroxyl radicals and inhibiting peroxidation. ONOO- may also be a signal transmitter and can mediate vasorelaxation, similarly to NO.
Local generation of RNS contributes to tissue injury. Recent studies have demonstrated that activation of the nuclear enzyme poly(ADP-ribose) polymerase-1 by RNS-mediated DNA damage is an important pathway of tissue injury in conditions associated with oxidative stress. Increased formation of RNS in response to endotoxin challenge is organ specific.
In sepsis, NO may exert direct and indirect effects on cardiac function. Sustained generation of NO occurs in systemic inflammatory reactions, such as septic shock with involvement in circulatory failure. In fact, myocardial iNOS activity has been reported in response to endotoxin and cytokines and inversely correlated with myocardial performance. Low-to-moderate doses of iNOS inhibitors restore myocardial contractility in hearts exposed to proinflammatory cytokines, whereas at higher doses, the effects are reversed. This finding may indicate that small amounts of NO produced by iNOS may be necessary to maintain contractility and can be cardio-protective in experimental sepsis.

Nitric oxide in Septic Shock

A list of effects of NO in sepsis is as follows.

  • Inhibition of nitric oxide synthesis causes myocardial ischemia in endotoxemic rats
  • Nitric oxide causes dysfunction of coronary autoregulation in endotoxemic rats
  • Prolonged inhibition of nitric oxide synthesis in severe septic shock
  • Effect of L-NAME, an inhibitor of nitric oxide synthesis, on cardiopulmonary function in human septic shock
  • Pulmonary hypertension and reduced cardiac output during inhibition of nitric oxide synthesis in human septic shock
  • Effect of L-NAME, an inhibitor of nitric oxide synthesis, on plasma levels of IL-6, IL-8, TNF-u and nitrite/nitrate in human septic shock
  • Endothelin-1 and blood pressure after inhibition of nitric oxide synthesis in human septic shock
  • Distribution and metabolism of NO-nitro-L-arginine methyl ester in patients with septic shock

The possible involvement of the L-arginine-NO pathway in both the vascular and cellular processes seen in sepsis has been supported by numerous in vitro and in vivo studies. iNOS appears to be expressed in a wide array of cell types during sepsis, including immune cells (such as macrophages, neutrophils, T lymphocytes), as well as cells outside the classical immune system (for example, hepatocytes, Kuppfer cells, vascular smooth muscle cells, endothelial cells, and fibroblasts). Expression of iNOS is regulated, both positively and negatively, by a number of mediators present during infection and inflammation. The main stimuli for iNOS induction indude lipopolysaccharide (LPS), interferon-y, interleukin (IL)-10, and tumor necrosis factor (TNF)-a; inhibitory cytokines, such as transforming growth factor-5, IL-4 and IL-10, as well as glucocorticoids, can prevent this induction. The expression of iNOS in response to these agents differs among cell types, but a maximal inducing effect is generally obtained by the combination of microbial products and cytokines acting synergistically.

iNOS activity is also regulated by substrate and cofactor availability. Tetrahydrobiopterin (BH4), an essential cofactor for the enzyme, is coinduced with iNOS in cytokine-stimulated vascular smooth muscle cells.
NO is a simple molecule, but its widespread production in sepsis, coupled with its effects on a variety of intracellular and extracellular target molecules, results in a complex array of biologic roles. Interaction of NO with the metalloproteins in a number of key enzymes can modulate their activity. Many of the signaling actions of ‘NO are mediated by soluble guanylate cyclase. By binding the iron on the heme component of soluble guanylate cyclase, NO is able to activate the enzyme leading to cyclic guanosine monophosphate (cGMP) formation.

Increased cGMP levels account for several of the important cellular actions of NO, including

  • smooth muscle relaxation,
  • platelet aggregation and adherence, as well as
  • neutrophil chemotaxis.

However, *NO can adversely affect cellular metabolism through its disruption of iron-sulfur clusters in essential energy-generating enzymes involved in mitochondrial electron transport, glycolysis, and the Krebs cycle. Further, high concentrations of induced macrophage produced NO can directly interfere with DNA in target cells, resulting in fragmentation.
Another critical reaction that ‘NO undergoes during inflammation is with the superoxide anion radical (02j, yielding peroxynitrite (OONO-). OONO- is a potent oxidant that can decay under acidic conditions to produce a powerful hydoxyl-like free radical. This reaction between *NO and O2 can have a protective or damaging consequence, depending on the individual sites and rates of production of the free radicals, and the redox status of both the generating cells as well as the target cells. OONO- formation can initiate adverse effects such as lipid peroxidation of membranes, and modification of structural proteins through nitration of tyrosine residues (14). Indeed, increased levels of 3-nitrotyrosine have been detected in the lungs of patients with sepsis and animals with acute lung injury. However, OONO- can also S-nitrosylate glutathione and other thiol-containing substances to form S-nitrosothiols, which have marked cardioprotective and cytoprotective effects.
The damaging effect of NOS inhibition may be, in part, mediated by oxygen radicals and platelet deposition, suggesting a cytoprotective role of NO in preventing microvascular thrombosis and as a free radical scavenger. In addition, ‘NO has a protective role in hepatic microcirculatory dysfunction during sepsis through its effect on leukocyte adherence to sinusoidal walls. ‘NO may also protect against circulatory vasoconstrictors during inflammation, as enhanced ‘NO synthesis counteracted phenylephrine-induced increases in intrahepatic resistance in endotoxin-treated rats. Finally, we have recently demonstrated that different types of NOS inhibitors resulted in detectable apoptosis in the liver following LPS injection. This increase in apoptosis was present even with L-N-iminoethyl-lysine (L-NIL), a rather specific inhibitor of iNOS, revealing another important protective role of NO as an antiapoptotic agent in sepsis.
Even though overproduction of *NO in the vasculature contributes to the vasodilatation seen in septic shock, iNOS expression during inflammation also represents a beneficial, adaptive response in some organ systems. Moreover, different tissues can react dissimilarly to the effects of ‘NO cytotoxicity. In this setting, global nonselective inhibition of NOS, including the potentially undesirable consequences of eNOS inhibition, would be harmful. If confirmed, this would suggest that use of isoform-specific inhibitors of NOS within the vascular bed would be more appropriate.

Pulmonary Hypertension and Reduced Cardiac Output

Pulmonary hypertension and reduced cardiac output can be major side effects of continuous NO synthase inhibition. Pulmonary vasoconstriction is undesirable because it may compromise pulmonary gas exchange and because it increases the workload on the right ventricle. In cases where strain already exists on the right ventricle (e.g. sepsis or PEEP ventilation) or in cases where right sided cardiac reserve is minimal, such increase in workload may lead to right ventricular failure, reduced cardiac output and compromised tissue perfusion.
Blood pressure and systemic vascular resistance increased during infusion of the NO synthase inhibitor L-NAME, and the dosage of catecholamines was reduced. The vasoconstrictive response to L-NAME most likely was the result of blocking the NO system . In addition to the systemic effects of L-NAME, severe pulmonary vasoconstriction was observed with L-NAME. Analogous to these findings, in patients with Adult Respiratory Distress Syndrome (ARDS), inhalation of NO is reported to be beneficial by causing local vasodilation in bronchial and pulmonary circulation which results in reduced pulmonary vascular resistance and improved oxygenation. This suggests that the pulmonary circulation is sensitive to the vasodilating effects of both endogenous and exogenous NO. Pulmonary vasoconstriction is not, therefore, unexpected with systemic inhibition of NO synthesis. With a continuous infusion of L-NAME, pulmonary vascular resistance increased five-fold, whereas systemic vascular resistance “only” doubled. pulmonary hypertension was reversible after stopping L-NAME infusion. In prior experiments with a lower dose of LNAME, pulmonary vasoconstriction was less pronounced and did not result in pulmonary hypertension.’ Thus, pulmonary hypertension is a dose-related effect of L-NAME that can probably be attributed to overdosing of the drug. Reduced cardiac output may have directly resulted from the extreme increase in pulmonary vascular resistance compromising venous return and left ventricular preload and/or a reflex reduction in heart rate by the increase in vascular resistance and blood pressure.
S-methyl-isothiourea, a relatively selective inhibitor of iNOS activity, decreased pulmonary leak and improved survival in endotoxemia. However, because of the tissue-protective and antiapoptotic effects of NO, even selective iNOS inhibitors may be detrimental in certain tissues during sepsis.Combining the salutary effects of site-specific local donors that exploit the cytoprotective actions of ‘NO with specific agents that combat the deleterious hypotensive and tissue-damaging effects of ‘NO overproduction may be needed to treat septic shock. In this regard, inhaled ‘NO gas has shown promise as a selective pulmonary vasodilator.

Role of Nitric Oxide in Inflammation and Tissue Injury

Since the discovery that nitric oxide (‘NO) accounts for the biologic activity of endothelial-derived relaxing factor, a torrent of research over the last decade has focused on its role, protective or detrimental, in myriad pathophysiologic conditions. Recently, increasing attention has focused on ‘NO as a possible mediator of the severe hypotension and impaired vasoreactivity characteristic of circulatory failure. Experimental and clinical studies have suggested NOS inhibition might have therapeutic potential in circulatory shock, and other studies have demonstrated the beneficial nature of iNOS expression in modulating tissue perfusion and mediating cytotoxicity. However, inhibition of ‘NO synthesis in experimental and clinical studies of shock has yielded mixed, sometimes contradictory, results. Overproduction of ‘NO in the vasculature may result in systemic vasodilatation, but still ‘NO synthesis has a beneficial role in regulating organ perfusion and mediating cytotoxicity.

Diminished *NO Production Occurs with Hemorrhage

These findings are consistent with those in trauma patients, where nitrite and nitrate levels were reduced for prolonged periods after injury. This impairment of ‘NO production in victims of hemorrhagic hypotension may be due to impairment of eNOS, and indeed, several investigators have demonstrated decreased vasodilatory activity in vascular rings taken from hemorrhaged animals in response to agonists that stimulate endothelial ‘NO production. In studies of hemorrhagic shock no iNOS expression could be detected until the very late irreversible phase of HS. The hemodynamic instability associated with decompensation occurred well before NOS induction.
Using either the selective inhibitor L-NIL or iNOS knockout mice, iNOS inhibition or deficiency not only prevented the upregulation of the inflammatory cytokines IL-6 and granulocyte colony-stimulating factor following resuscitation from HS but also produced a marked reduction in lung and liver injury. Furthermore, the activation of the proinflammatory transcriptional factors nuclear factor kappa B and signal transducer and activator of transcription 3 was also reduced, suggesting iNOS upregulation has a key role in proinflammatory signaling and the subsequent activation of inflammatory cascades. Recent studies have implicated a possible redox-sensitive mechanism. ‘NO activates the critical signaling enzyme p21ras through S-nitrosylation.
Vascular quenching of ‘NO using scavengers may again provide an alternative to NOS inhibition as a means to achieve the goal of reducing ‘NO levels. Use of ‘NO scavengers after HS and resuscitation may serve to supplement a possibly depleted antioxidant defense system and limit the harmful effects of free radicals such as OONO- and hydoxyl radicals. Removal of ‘NO by this method is complicated by the extreme rapidity of the reaction between ‘NO and 02’- .
iNOS upregulation also has a beneficial protective role in several organ systems. In conditions where excess NO production results in maladaptive damaging consequences with disruption of homeostasis, the therapeutic strategy should be to remove this surplus ‘NO without adversely affecting the cytoprotective actions of *NO. Interfering with the physiologic and microcirculatory role of eNOS through nonselective, global inhibition of NOS is undesirable in shock.

Effects of nitric oxide in endotoxemia and hemorrhagic shock and proposed therapeutic strategies for manipulation of nitric oxide production.

Endotoxemia Hemorrhagic shock
Effects of NO                         Beneficial                            Beneficial
by eNOS                      -maintains perfusion;    -maintains perfusion;
cytoprotective               cytoprotective
iNOS                             Beneficial and toxic-         Beneficial and toxic-

depending on site can induce tissue damage and  of production and promote inflammation with microenvironment sustained shock

Therapeutic strategy

Inhibition of eNOS                Avoid                                     Avoid
Inhibition of iNOS         Possibly desirable-       Probably desirable-
to reduce                          to limit exaggerated inflammatory
cytotoxicity and           response and development of
combat hypotension       MODS

NO scavengers   Probably desirable-quench    Probably desirable-quench
extracellular NO without        extracellular NO without
inhibition of eNOS or iNOS;    inhibition of eNOS or iNOS;
supplement antioxidant defenses       supplement antioxidant defenses
NO donors          Possibly desirable-site-            Possibly desirable-site-
specific donors without adverse     specific donors without adverse
systemic  side effects;                      systemic side effects;
limited availability                             limited availability

Therapeutic Outlook

LINCS: L-NAME (a NO synthase inhibitor)
Patients were randomized to supportive care alone (n=15, control group) or to supportive care in addition to L-NAME (1 mg/Kg bolus and 1 mg/Kg/h continuous IV drip for 5 h n=15). Death at one month was 27% in the L-NAME group vs. 67% in the control group (p=0.008). Time on IABP and time on mechanical ventilation were significantly shorter in the L-NAME group. The results of this study indicate that NO synthase inhibitors are beneficial in the treatment of patients with refractory cardiogenic shock.
Inducible Nitric Oxide Synthase Inhibitors
Inducible nitric oxide synthase (iNOS)-dependent production of nitric oxide (NO) plays an important role in inflammation. The effects of various naturally occurring furanocoumarins on NO production in lipopolysaccharide (LPS)-activated RAW 264.7 macrophage cells were evaluated in vitro. The results showed that angelicin, pimpinellin, sphondin, byakangelicol, oxypeucedanin, oxypeucedanin hydrate, xanthotoxin, and cnidilin are potential NO production inhibitors, and their IC50 values for inhibition of nitrite production were 19.5, 15.6, 9.8, 16.9, 16.8, 15.8, 16.6, and 17.7 mg/mL, respectively.

Distinct structure activity relationships were also revealed for the NO production inhibitory activities of these furanocoumarins. Activities of the angelicin type such as pimpinellin and sphondin were more potent than those of the psoralen type. Presence of a methoxy at the C6 position in the angelicin type seemed to be essential to augment the activity. Western blot analysis demonstrated that only sphondin dose-dependently inhibited the expression of the iNOS protein at 2.5±20 mg/mL. However, iNOS enzyme activity was stimulated with LPS for 12 h and sphondin was administered (20 mg/mL) for 24 h, which did not reasonably inhibit iNOS enzyme activity. l-NAME (100 mM), a known specific inhibitor of iNOS, was employed as a positive control with the same protocol and showed more than 50% inhibition activity. The results demonstrate that the NO production inhibitory activity of sphondin is due to the effect of iNOS expression, but not by direct inhibition of iNOS enzyme activity. Thus, sphondin may act as a potent inhibitor of NO production under tissue-damaging inflammatory conditions.
S-Methylisothiourea Sulfate, A Potent And Selective Inhibitor Of Inducible Nitric Oxide Synthase
Non-isoform-selective inhibition of NO formation, however, may lead to side effects by inhibiting the constitutive isoform of NOS and, thus, the various physiological actions of NO. S-Methylisothiourea sulfate (SMT) is at least 10- to 30-fold more potent as an inhibitor of inducible NOS (iNOS) in immuno-stimulated cultured macrophages (EC50, 6 ,AM) and vascular smooth muscle cells (EC50, 2 ,uM) than NG-methyl-L-arginine (MeArg) or any other NOS inhibitor yet known. The effect of SMT on iNOS activity can be reversed by excess L-arginine in a concentration-dependent manner.

Enhanced formation of NO following the induction of iNOS contributes importantly to the circulatory failure (hypotension and vascular hyporeactivity to vasoconstrictor agents) in circulatory shock of various etiologies.
SMT dose-dependently reverses (0.01-3 mg/kg) the hypotension and the vascular hyporeactivity to vasoconstrictor agents caused by endotoxin [bacterial lipopolysaccharide]
SMT, a potent and selective inhibitor of iNOS, may have considerable value in the therapy of circulatory shock of various etiologies and other pathophysiological conditions associated with induction of iNOS.
SMT, or other iNOS-selective inhibitors, are likely to have fewer side effects which are related to the inhibition of eNOS, such as excessive vasoconstriction and organ ischemia), increased platelet and neutrophil adhesion and accumulation, and microvascular leakage.

Iron Chelates Bind Nitric Oxide

Nitric oxide (NO), a short-lived potent vasodilator, was first described as the endothelium-derived relaxation factor (EDRF). The formation of NO from the guanidine nitrogen group of L-arginine is catalyzed by a group of enzymes termed constitutive (cNOs) and inducible (iNOs) NO synthases. The inducible form is not present constitutively in mammalian cells but is induced by proinflammatory stimuli such as bacterial lipopolysaccharide (LPS), Corynebacterium parvum, and the cytokines tumor necrosis factor-a, interleukin-1, or interferon-y, individually or in combination. Excess production of NO is reported to be associated with the development of hypotension associated with endotoxemia and sepsis.

Electrochemical studies show that FeIII-(DTPA)2- binds NO stoichiometrically upon reduction to iron(II) at biologically relevant potentials to form a stable NO adduct. In contrast, FeI”I(HDFB)+ is a stable and efficient electrocatalyst for the reduction of NO to N20 at biologically relevant potentials. These results suggest that the mechanism of protection against death by septic shock involves NO scavenging and that particularly effective drugs that operate a low dosages may be designed based on the principle of redox catalysis. These complexes constitute a new family of drugs that rely on the special ability of transition metals to activate small molecules.

Iron complexes could act as general NO scavengers and provide protection against septic shock. Iron complexes are capable of forming relatively stable NO adducts. Metal complexes, and in particular iron chelators, could act as “molecular sponges,” mopping up the excess NO produced during septic shock. Iron chelators can sequester and (as for 2) catalyze conversion of NO to benign products. Demonstration of mechanistic aspects of septic shock protection in vivo, including interaction with other free radicals, may be hampered by the detection limits of current analytical techniques. To detect the NO Fe-DETC complex formation in livers of LPS-treated mice by the electron paramagnetic resonance.

After screening a library of metal chelators and chelates [Fe(III)(H2DTPA)] and [Fe(III)(HDFB)]+ offered the highest mortality decrease in an experimental model of septic shock. The Fe(II) form of both complexes can bind NO, which appears to be related to their biological function.
Survival was greatly enhanced by the administration of 4 or 2 either 2 h before and at the time of or 30 min after LPS. In contrast, the Fe3+-free ligands of these compounds, 3 and 1, were less protective when administered before and at the time of LPS and virtually ineffective when administered after LPS. The clear advantage of 4 over 2 when administered after LPS was observed over a large number of experiments [76% survival with 4 (n = 102 mice) and 38% survival with 2 (n =64 mice)].

The hydroxamic acid siderophore ferrioxamine B [Fe”‘(HDFB)+] and the iron complex of diethylene-triamine-pentaacetic acid [FeI”(DTPA)2i] protected mice against death by septic shock induced by Corynebacterium parvum + lipopolysaccharide. Although Fem(DTPA)2- was somewhat more effective than FeI”(HDFB)+, the iron-free ligand H4DFB+ was significantly more effective than DTPA. The hydroxamic acid chelator has a much higher iron affinity than the amine carboxylate, allowing for more efficient formation of the FeI”(HDFB)+ complex upon administration of the iron-free ligand.

Efficacy of Treatment With the Iron (III) Complex of Diethylenetriamine Pentaacetic Acid

Bacteremia and septic shock also are associated with overproduction of free radicals such as hydroxyl, superoxide, and carbon- and oxygen-centered radicals. In addition, nitric oxide (NO) overproduction is at least partly responsible for the vasodilation that causes a reduction in mean systemic arterial pressure (MSAP) and organ perfusion pressure during septic shock. This overproduction of NO likely results from early activation of the endothelial constitutive form of NO synthase followed by induction of the inducible form of NO synthase via TNF and IL-1.
The simultaneous increase and further reaction of NO with superoxide, which yields the oxidant peroxynitrite anion, occurs in cellular systems in response to inflammatory mediators. In addition, in sepsis-associated adult respiratory distress syndrome (ARDS), the presence of nitrotyrosine residues (formed by reaction of peroxynitrite and the tyrosine residues of proteins) are apparent throughout the lung.

Administration of the iron (III) complex of diethylenetriamine pentaacetic acid (DTPA iron (III), prevented death in Corynebacterium parvum 1 LPS-treated mice. Using electrochemistry, the binding of NO to DTPA iron (II) is confirmed. The DTPA iron (II) form can be easily formed by common biological reductants, because the potential for the iron (III/II) couple is E = 0.22.
Treatment with DTPA iron (III) resulted in a significant decrease in mortality compared to the untreated controls. The efficacy of DTPA iron (III) increased when given to mice 2 h or more after infection. The best results were observed when DTPA iron (III) was given 5 h after infection.

The iron (III) complex of diethylenetriamine pentaacetic acid (DTPA iron [III]) protected mice and baboons from the lethal effects of an infusion with live LD 100 Escherichia coli. In mice, optimal results were obtained when DTPA iron (III) was administered two or more hours after infection. Prevention of death occurred in spite of the fact that the adverse effects of TNFa were well underway in the mouse model.
In septic baboons, survival was observed after administration of two doses of DTPA iron (III) at 2.125 mg/kg, the first one given before, or as late as 2 h after, severe hypotension. Administration of DTPA iron (III) did not alter mean systemic arterial pressure, but did protect baboons in the presence of high levels of TNFa and free radical overproduction. Furthermore, exaggerated production of nitric oxide was attenuated. Because of its ability to interact in vitro with free radicals, its poor cell permeability, and its short half-life, we postulate that DTPA iron (III) and/or its reduced form may have protected the mice and baboons by sequestration and subsequent elimination of free radicals (including nitric oxide) from their systems. (J. Clin. Invest.1996. 98:192–198.)
Inhibitor of Poly(Adenosine 5′-Diphosphate-Ribose) Synthetase
Poly(adenosine 5′-diphosphate [ADP]-ribose) synthetase (PARS) is a nuclear enzyme which, when activated by DNA singlestrand breaks, initiates an energy-consuming, inefficient metabolic cycle by transferring ADP-ribose units to nuclear proteins. The result of this process is a rapid depletion of intracellular oxidized nicotinamide adenine dinucleotide and adenosine 5′-triphosphate energetic pools, which slows the rate of glycolysis and mitochondrial respiration, leading to cellular dysfunction and death.
Reactive oxygen-centered radicals (superoxide, hydroxyl radicals, singlet oxygen, and hydrogen peroxide) and peroxynitrite (a reactive oxidant produced from the reaction of superoxide and nitric oxide) are powerful triggers of DNA single strand breakage, and they induce activation of a cell suicide cycle governed by PARS in various cell types in vitro.

Multiple reports implicated a role of PARS activation in the pathophysiology of endotoxic shock, hemorrhagic shock, and various forms of ischemia-reperfusion injury.
Twenty pigs were chronically instrumented with intracardiac transducers to measure left ventricular pressure, sonomicrometer crystals in the left ventricle to measure short axis diameter, an ultrasonic flow meter to measure cardiac output, and catheters in the pulmonary artery and aorta to measure blood pressures and collect samples. By using a randomized study design, either the novel potent PARS inhibitor PJ34 (10 mg/kg for 1 hr, 2 mg·kg 1·hr 1 for 96 hrs) or placebo to pigs immediately before intraperitoneal implantation of Escherichia coli 0111.B4 (2.3 0.1 1010 colony-forming units/kg)-laden fibrin clots to produce peritonitis and bacteremia.
PJ34 treatment significantly attenuated this cytokine response. The formation of peroxynitrite and the activation of PARS were confirmed in hearts and lungs of the septic pigs by the immunohistochemical detection of nitrotyrosine and poly(ADP-ribose), respectively. Inhibition of PARS with PJ34 abolished poly(ADP-ribose) formation in septic animals.

Cardiac inotropicity was evaluated by analysis of percentage of short axis diameter shortening (one-dimensional ejection fraction). Bacteremia induced a rapid and progressive loss of inotropy until death in vehicle-treated pigs. A similar decline was observed in the first 6 hrs in PJ34 pigs. This decline was reversed on all subsequent days. Control pigs exhibited rapid and significant increases in systemic vascular (SVR) and pulmonary vascular (PVR) resistances.
This experimental model mimics many aspects of the human sepsis syndrome. Therefore, the positive survival benefit of PARS inhibition suggests a potential utility of PARS inhibitors in human sepsis management. PARS activation is triggered by DNA single-strand breakage.

The current work, demonstrating increased poly(ADP-ribose) staining in the heart of septic pigs, may point toward the importance of a myocardial, PARS dependent cardiodepressive mechanism in the current model of shock. This hypothesis is supported by the following findings:

  • free radicals cause myocardial dysfunction and injury in a PARS dependent fashion in vitro;
  • in the current study, pharmacologic inhibition of PARS with PJ34 markedly improved myocardial function; and

in prior studies, pharmacologic inhibition of PARS markedly improved myocardial contractile function in hypoxic-reoxygenated hearts as well as in a porcine model of hemorrhagic shock.
Treatment with a potent PARS inhibitor improved survival and cardiovascular status and attenuated an important mediator component of the inflammatory response in a lethal porcine model of sepsis. (Crit Care Med 2002; 30:974 –980).

Decrease of the inflammatory response and induction of the Akt/protein kinase B pathway by poly-(ADP-ribose) polymerase 1 inhibitor

The lack of efficacy of anti-inflammatory drugs, anti-coagulants, anti-oxidants, etc. in critically ill patients has shifted interest towards developing alternative treatments. Since inhibitors of the nuclear enzyme poly-(ADP-ribose) polymerase (PARP) were found to be beneficial in many pathophysiological conditions associated with oxidative stress and PARP-1 knock-out mice proved to be resistant to bacterial lipopolysaccharide (LPS)-induced septic shock, PARP. The mechanism of the protective effect of a potent PARP-1 inhibitor, PJ34 was studied in LPS-induced (20 mg/kg, i.p.) septic shock in mice.

We demonstrated a significant inflammatory response by magnetic resonance imaging in the dorsal subcutaneous region, in the abdominal regions around the kidneys and in the inter-intestinal cavities. We have found necrotic and apoptotic histological changes as well as obstructed blood vessels in the liver and small intestine. Additionally, we have detected elevated tumor necrosis factor-a levels in the serum and nuclear factor kappa B activation in liver of LPS-treated mice.

Pre-treating the animals with PJ34 (10 mg/kg, i.p.), before the LPS challenge, besides rescuing the animals from LPS-induced death, attenuated all these changes presumably by activating the phosphatidylinositol 3-kinase–Akt/protein kinase B cytoprotective pathway.

PJ34, a novel, potent PARP-1 inhibitor was found to protect against LPS induced tissue damage. PARP inhibitors protected Langendorff-perfused hearts against ischemia-reperfusion induced damages by activating the PI3-kinase–Akt pathway. The importance of the PI3-kinase–Akt pathway in LPS induced inflammatory mechanisms has gained support, raising the question whether this pathway was involved in the effect of PJ34 on LPS-induced septic shock.
Among all the observed LPS-induced inflammatory responses, we found the most characteristic and most pronounced increases in the gastro-intestinal tract, but no signal increase could be observed inside the kidneys and in skeletal muscle, in the paravertebral or in the femoral muscle. All increases in signal intensities were significantly attenuated in mice treated with PJ34.

Effect of PJ34 on survival of LPS-treated mice

  • PARP-1 inhibitor significantly protected the animals against LPS-induced death, with 86 and 43% surviving mice, respectively.
  • PJ34 treatment itself did not induce death or any obvious damage.

Effect of PJ34 on LPS-induced NF-kB activation

LPS treatment in the lung caused a significant increase in NF-kB activation that was slightly but not statistically significantly attenuated by PJ34 pre-treatment.
in contrast to the lung, NF-kB activation in the liver was prevented by PJ34 pre-treatment
The other tissue with observable LPS-induced pathological changes was the small intestine. Atrophy of villi may reflect the diarrhea observed in the LPS-treated animals and is in agreement with the results of Abreu et al. who found a Fas-mediated apoptosis in intestinal epithelial cells that was sensitised by inhibitors of PI3-kinase and opposed by expressing constitutively active Akt.
Pre-treatment of the animals with a novel, potent PARP-1 inhibitor, PJ34, diminished the thoracic and abdominal inflammatory responses as revealed by T2 imaging, and abolished the above mentioned pathological changes.
The protective role of PARP inhibitors in septic shock is likely to be more complex than merely the regulation of NF-kB/Rel-dependent gene expression.
Activation of the PI3-kinase–Akt/protein kinase B cytoprotective pathway is likely to contribute to the protective effects of PARP inhibitors in shock and inflammation.

Carboxy-PTIO On Hemodynamic And Blood Gas Changes

Infusion of LPS caused a marked decrease in mean arterial pressure (MAP), metabolic acidosis, and hypoxia. These effects were reversed by co-administration of carboxy-PTIO, without affecting other hemodynamic parameters. In control animals, neither hemodynamic nor blood gas parameters changed with or without carboxy-PTIO.
These results indicate that carboxy-PTIO attenuates

  • LPS-induced hypotension,
  • metabolic acidosis, and
  • hypoxia

by scavenging excess NO from the circulation without affecting NO synthase (NOS) activity. An NO scavenger, carboxy-PTIO, may be preferable to non-selective NOS inhibitors for the treatment of human septic shock.

Asymmetrical Dimethyl Arginine Levels

Overwhelming infection with resultant multiple organ failure, which has been termed the ‘sepsis syndrome’ , is a devastating illness with an incidence of 3 per 1,000 population per annum. It has been characterised as a dysregulation of inflammation in response to infection attributable to a combination of

  • excessive inflammation,
  • disseminated coagulopathy and
  • disruption of the integrity of microvascular endothelium.

Asymmetrical dimethyl arginine (ADMA) is an endogenous non-selective inhibitor of nitric oxide synthase that may influence the severity of organ failure and the occurrence of shock secondary to an infectious insult. Levels may be genetically determined by a promoter polymorphism in a regulatory gene encoding dimethylarginine dimethylaminohydrolase II (DDAH II).

A prospective observational study was designed, and 47 intensive care unit (ICU) patients with severe sepsis and 10 healthy controls were enrolled. Serum ADMA and IL-6 were assayed on admission to the ICU and seven days later. Allelic variation for a polymorphism at position -449 in the DDAH II gene was assessed in each patient.
ADMA levels and Sequential Organ Failure Assessment scores were directly associated on day one (p = 0.0001) and day seven (p = 0.002). The degree of acidaemia and lactaemia was directly correlated with ADMA levels at both time points (p < 0.01). On day seven, IL-6 was directly correlated with ADMA levels (p = 0.006). The variant allele with G at position -449 in the DDAH II gene was associated with increased ADMA concentrations at both time points (p < 0.05).
Severity of organ failure, inflammation and presence of early shock in severe sepsis are associated with increased ADMA levels. ADMA concentrations may be influenced by a polymorphism in the DDAH II gene.

Several studies have added to the confusion surrounding the role of NO by demonstrating no effect of NO or NOS inhibition on the myocardium or on b-adrenergic responsiveness. Nevertheless, in most studies,

  • low-to-moderate doses of iNOS inhibitors restore myocardial contractility in hearts exposed to proinflammatory cytokines, whereas
  • at higher doses, the effects are reversed.

This finding may indicate that small amounts of NO produced by iNOS may be necessary to maintain contractility and can be cardio-protective in experimental sepsis.

English: Major cellular sources of ROS in livi...

Major cellular sources of ROS in living cells. Novo and Parola Fibrogenesis & Tissue Repair 2008 1:5 doi:10.1186/1755-1536-1-5 (Photo credit: Wikipedia)

References

  1. VM Victor, K J McCreath and M Rochaa. Recent Progress in Pharmacological Research of Antioxidants in Pathological Conditions: Cardiovascular Health. Recent Patents on Anti-Infective Drug Discovery, 2006, 1, 17-31 17.
  2. G Cottera, E Kaluskia, O Miloa, A Blatta, et al. LINCS: L-NAME (a NO synthase inhibitor) In the treatment of refractory Cardiogenic Shock. A prospective randomized study. The European Society of Cardiology. 2012. doi:10.1016/S0195-668X(03)00193-3 http://eurheartj.oxfordjournals.org/
  3. Ve Laubach, Eg Shesely, O Smithies, Pa Sherman. Mice lacking inducible nitric oxide synthase are not resistant to lipopolysaccharide-induced death. Proc. Natl. Acad. Sci. USA 1995; 92:10688-10692, Genetics
  4. NS Shah and TR Billiar. Role of Nitric Oxide in Inflammation and Tissue Injury during Endotoxemia and Hemorrhagic Shock. Environ Health Perspect 106(Suppl 5):1139-1143 (1998). http://ehpnetl.niehs.nih.gov/docs/1998/Suppl-5/1139-1 143shah/abstract.html
  5. CC Wang, JE Lai, LG Chen, KY Yen, et al. Inducible Nitric Oxide Synthase Inhibitors of Chinese Herbs. Part 2: Naturally Occurring Furanocoumarins’. Bioorganic & Medicinal Chemistry 2000; 8:2701-2707.
  6. MJ O’Dwyer, F Dempsey, V Crowley, DP Kelleher, R McManus, T Ryan. Septic shock is correlated with asymmetrical dimethyl arginine levels, which may be influenced by a polymorphism in the dimethylarginine dimethylaminohydrolase II gene: a prospective observational study. Critical Care 2006; 10:R139 (doi:10.1186/cc5053) http://ccforum.com/content/10/5/R139
  7. C Szab, Gj Southan, And C Thiemermann. Beneficial effects and improved survival in rodent models of septic shock with S-methylisothiourea sulfate, a potent and selective inhibitor of inducible nitric oxide synthase. Proc. Natl. Acad. Sci. USA 1994; 91:12472-12476. Pharmacology
  8. Wm Kazmierski, G Wolberg, Jgwilson, et al. Iron chelates bind nitric oxide and decrease mortality in an experimental model of septic shock. Proc. Natl. Acad. Sci. USA 1996;93:9138-9141.
  9. L Molina, S Studenberg, G Wolberg, W Kazmierski, et al. Efficacy of Treatment With the Iron (III) Complex of Diethylenetriamine Pentaacetic Acid in Mice and Primates Inoculated With Live Lethal Dose 100 Escherichia coli. J. Clin. Invest 1996; 98(1): 192-198. 0021-9738/96/07/192/07
  10. N Kayhan, B Funke, LO Conzelmann, H Winkler, et al. The adenosine deaminase inhibitor erythro-9-[2-hydroxyl-3-nonyl]-adenine decreases intestinal permeability and protects against experimental sepsis: a prospective, randomised laboratory investigation. Critical Care 2008, 12:R125 (doi:10.1186/cc7033) http://ccforum.com/content/12/5/R125
  11. RD Goldfarb, A Marton, É Szabó, L Virág, et al.. Protective effect of a novel, potent inhibitor of poly(adenosine 5′-diphosphate-ribose) synthetase in a porcine model of severe bacterial sepsis. Crit Care Med 2002; 30:974 –980.
  12. B Veres, F Gallyas Jr, G Varbiro, Z Berente, et al. Decrease of the inflammatory response and induction of the Akt/protein kinase B pathway by poly-(ADP-ribose) polymerase 1 inhibitor in endotoxin-induced septic shock. Biochemical Pharmacology 2003; 65: 1373–1382.
  13. C Martinez, C Abad, M Delgado, A Arranz, et al. Anti-inflammatory role in septic shock of pituitary adenylate cyclase-activating polypeptide receptor. PNAS 2002; 99(2):1053–1058. doi 10.1073 pnas.012367999
  • endogenously produced VIP and PACAP are participants of the natural anti-inflammatory machinery.
  • VIP and PACAP are two attractive candidates for the development of therapies against acute and chronic inflammatory diseases, septic shock, and autoimmune diseases

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Reporter: Aviva Lev-Ari, PhD, RN

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Word Cloud By Danielle Smolyar
GASTRIC CANCER

Methylation Subtypes and Large-Scale Epigenetic Alterations in Gastric Cancer

  1. Hermioni Zouridis1,*,,
  2. Niantao Deng1,2,*,
  3. Tatiana Ivanova1,
  4. Yansong Zhu1,
  5. Bernice Wong3,
  6. Dan Huang4,
  7. Yong Hui Wu1,5,
  8. Yingting Wu6,7,
  9. Iain Beehuat Tan2,8,
  10. Natalia Liem9,
  11. Veena Gopalakrishnan1,
  12. Qin Luo1,
  13. Jeanie Wu5,
  14. Minghui Lee5,
  15. Wei Peng Yong9,10,
  16. Liang Kee Goh1,
  17. Bin Tean Teh1,3,4,
  18. Steve Rozen6,11 and
  19. Patrick Tan1,5,9,12,

+Author Affiliations


  1. 1Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore.

  2. 2NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 119074, Singapore.

  3. 3National Cancer Centre Singapore–Van Andel Research Institute Translational Research Laboratory, Department of Medical Sciences, National Cancer Centre, 11 Hospital Drive, Singapore 169610, Singapore.

  4. 4Laboratory of Cancer Genetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.

  5. 5Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore.

  6. 6Neuroscience and Behavioural Disorders, Duke-NUS Graduate Medical School, Singapore 169857, Singapore.

  7. 7Singapore-MIT Alliance, National University of Singapore, Singapore 119074, Singapore.

  8. 8Division of Medical Oncology, National Cancer Centre, Singapore 169610, Singapore.

  9. 9Cancer Science Institute of Singapore, National University of Singapore, Singapore 119074, Singapore.

  10. 10National Cancer Institute Singapore, National University Hospital, Singapore 119228, Singapore.

  11. 11Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA.

  12. 12Genome Institute of Singapore, 60 Biopolis Street, Genome 02-01, Singapore 138672, Singapore.

+Author Notes

  • * These authors contributed equally to this work.

  • † Present address: LabConnect, LLC, 2910 First Avenue South, Suite 200, Seattle, WA 98134, USA.

  1. ‡To whom correspondence should be addressed. E-mail: gmstanp@duke-nus.edu.sg

ABSTRACT

Epigenetic alterations are fundamental hallmarks of cancer genomes. We surveyed the landscape of DNA methylation alterations in gastric cancer by analyzing genome-wide CG dinucleotide (CpG) methylation profiles of 240 gastric cancers (203 tumors and 37 cell lines) and 94 matched normal gastric tissues. Cancer-specific epigenetic alterations were observed in 44% of CpGs, comprising both tumor hyper- and hypomethylation. Twenty-five percent of the methylation alterations were significantly associated with changes in tumor gene expression. Whereas most methylation-expression correlations were negative, several positively correlated methylation-expression interactions were also observed, associated with CpG sites exhibiting atypical transcription start site distances and gene body localization. Methylation clustering of the tumors revealed a CpG island methylator phenotype (CIMP) subgroup associated with widespread hypermethylation, young patient age, and adverse patient outcome in a disease stage–independent manner. CIMP cell lines displayed sensitivity to 5-aza-2′-deoxycytidine, a clinically approved demethylating drug. We also identified long-range regions of epigenetic silencing (LRESs) in CIMP tumors. Combined analysis of the methylation, gene expression, and drug treatment data suggests that certain LRESs may silence specific genes within the region, rather than all genes. Finally, we discovered regions of long-range tumor hypomethylation, associated with increased chromosomal instability. Our results provide insights into the epigenetic impact of environmental and biological agents on gastric epithelial cells, which may contribute to cancer.

Sci Transl Med 17 October 2012: 
Vol. 4, Issue 156, p. 156ra140 
Sci. Transl. Med. DOI: 10.1126/scitranslmed.3004504
 

Methylation-based Stomach Cancer Subtypes

October 17, 2012

NEW YORK (GenomeWeb News) – A new study in Science Translational Medicine is highlighting the epigenetic subtypes that exist within stomach cancer.

“Our results strongly demonstrate that gastric cancer is not one disease but a conglomerate of multiple diseases, each with a different underlying biology and hallmark features,” senior author Patrick Tan, a cancer researcher with the Duke-National University of Singapore Graduate Medical School, said in a statement.

“If gastric cancer is the result of multiple interacting factors, including both environmental factors and host genetic factors, we need better ways to diagnosis and treat it,” added Tan, who is also affiliated with Singapore’s National Cancer Centre and the Genome Institute of Singapore.

Tan and colleagues based in Singapore and the US did array-based DNA methylation analyses on more than 200 gastric tumors and dozens of gastric cancer lines. Their subsequent analyses of these methylation profiles indicated that stomach cancers have many stretches of sequence with higher or lower levels of methylation compared with nearly 100 matched normal stomach samples.

Within the tumor and cell lines, the analysis revealed subsets of gastric cancer with distinct methylation profiles that appear to be prognostically important.

In particular, a group of tumors known as CIMP (CpG island methylator phenotype) tumors, which show excess methylation at some cytosine and guanine-rich regions of the genome, tended to turn up in younger gastric cancer patients and those with poor outcomes.

On the other hand, results of the study also hint that the pronounced methylation shifts in these CIMP gastric cancers could also render them more vulnerable to demethylating compounds.

“Gastric cancer is a heterogenous disease with individual patients often displaying markedly different responses to the same treatment,” Tan said. “Improving gastric cancer clinical outcomes will require molecular approaches capable of subdividing patients into biologically similar subgroups, and designing subtype-specific therapies for each group.”

Previous genomic studies have started to unravel the range of somatic mutations and other genetic alterations that can contribute to gastric adenocarcinoma, the researchers noted. Less is known about the epigenetic features of the often deadly disease, which is especially common in some Asian populations, though some studies have identified specific genes with unusual epigenetic profiles in gastric cancer.

In an effort to more fully understand the epigenetic features of stomach cancer, Tan and his colleagues used Illumina Infinium arrays to profile cytosine methylation patterns in tumor samples from 203 individuals with gastric cancer, along with matched normal stomach tissue samples for 94 of the patients.

Using a similar strategy, the group also measured genome-wide methylation patterns in 37 stomach cancer cell lines.

When they compared methylation profiles across the samples, the researchers saw that some 44 percent of the CpG sites tested had higher- or lower-than-usual cytosine methylation levels that were specific to the stomach cancer. Around a quarter of these seemed to coincide with either jumps or — more frequently — dips in gene expression in the tumors, they reported.

A subset of the tumors had especially high levels of CpG island methylation, the team found. Follow-up analyses indicated that these tumors — which comprise an apparent CIMP sub-group of the stomach cancer — were more commonly found in young patients and/or those with poor survival outcomes.

Over-represented amongst the genes in highly methylated regions of CIMP tumors were genes implicated in stem cell-related processes, researchers noted, as were sites recognized by the histone regulating Polycomb repressive complex.

“Taken collectively,” they wrote, “these results suggest that CIMP tumors may represent a clinically and biologically distinct sub-group of gastric cancers.”

Moreover, in one of its follow-up experiments the team found that it was possible to curb the proliferation of seven gastric cancer-derived cell lines in the CIMP sub-group using a demethylating drug called 5-aza-2′-deoxycytidine, or 5-Aza-dC — an effect they did not see in 10 non-CIMP cell lines treated with the drug.

Based on findings from their methylation and gene expression profiling in gastric cancer so far, the study authors argued that an improved appreciation of the methylome-based sub-types present in the disease might aid future efforts to improve stomach cancer diagnosis and treatment options.

“[A]dditional work will focus on developing simple diagnostic tests to detect gastric cancer at earlier stages, plus drugs and drug targets that might exhibit high potency against different molecular subtypes of disease,” Tan said in a statement.

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Is the Warburg Effect the Cause or the Effect of Cancer: A 21st Century View?

Author: Larry H. Bernstein, MD, FCAP  

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word cloud by Danielle Smolyar

A Critical Review

What is the Warburg effect?

“Warburg Effect” describes the preference of glycolysis and lactate fermentation rather than oxidative phosphorylation for energy production in cancer cells. Mitochondrial metabolism is an important and necessary component in the functioning and maintenance of the organelle, and accumulating evidence suggests that dysfunction of mitochondrial metabolism plays a role in cancer. Progress has demonstrated the mechanisms of the mitochondrial metabolism-to-glycolysis switch in cancer development and how to target this metabolic switch.
In vertebrates, food is digested and supplied to cells mainly in the form of glucose. Glucose is broken down further to make Adenosine Triphosphate (ATP) by two pathways. One is via anaerobic metabolism occurring in the cytoplasm, also known as glycolysis. The major physiological significance of glycolysis lies in making ATP quickly, but in a minuscule amount. The breakdown process continues in the mitochondria via the Krebs’s cycle coupled with oxidative phosphorylation, which is more efficient for ATP production. Cancer cells seem to be well-adjust to glycolysis. In the 1920s, Otto Warburg first proposed that cancer cells show increased levels of glucose consumption and lactate fermentation even in the presence of ample oxygen (known as “Warburg Effect”). Based on this theory, oxidative phosphorylation switches to glycolysis which promotes the proliferation of cancer cells. Many studies have demonstrated glycolysis as the main metabolic pathway in cancer cells.
Why cancer cells prefer glycolysis, an inefficient metabolic pathway?

It is now accepted that glycolysis provides cancer cells with the most abundant extracellular nutrient, glucose, to make ample ATP metabolic intermediates, such as ribose sugars, glycerol and citrate, nonessential amino acids, and the oxidative pentose phosphate pathway, which serve as building blocks for cancer cells.
Since, cancer cells have increased rates of aerobic glycolysis, investigators argue over the function of mitochondria in cancer cells. Mitochondrion, a one of the smaller organelles, produces most of the energy in the form of ATP to supply the body. In Warburg’s theory, the function of cellular mitochondrial respiration is dampened and mitochondria are not fully functional. There are many studies backing this theory. A recent review on hypoxia nicely summarizes some current studies and speculates that the “Warburg Effect” provides a benefit to the tumor not by increasing glycolysis but by decreasing mitochondrial activity.
Glycolysis
Glycolysis is enhanced and beneficial to cancer cells. The mammalian target of rapamycin (mTOR) has been well discussed in its role to promote glycolysis; recent literature has revealed some new mechanisms of how glycolysis is promoted during skin cancer development.
On the other hand, Akt is not only involved in the regulation of mitochondrial metabolism in skin cancer but also of glycolysis. Activation of Akt has been found to phosphorylate FoxO3a, a downstream transcription factor of Akt, which promotes glycolysis by inhibiting apoptosis in melanoma. In addition, activated Akt is also associated with stabilized c-Myc and activation of mTOR, which both increase glycolysis for cancer cells.
Nevertheless, ras mutational activation prevails in skin cancer. Oncogenic ras induces glycolysis. In human squamous cell carcinoma, the c-Jun NH(2)-terminal Kinase (JNK) is activated as a mediator of ras signaling, and is essential for ras-induced glycolysis, since pharmacological inhibitors if JNK suppress glycolysis. CD147/basigin, a member of the immunoglobulin superfamily, is high expressed in melanoma and other cancers.
Glyoxalase I (GLO1) is a ubiquitous cellular defense enzyme involved in the detoxification of methylglyoxal, a cytotoxic byproduct of glycolysis. In human melanoma tissue, GLO1 is upregulated at both the mRNA and protein levels.
Knockdown of GLO1 sensitizes A375 and G361 human metastatic melanoma cells to apoptosis.
The transcription factor HIF-1 upregulates a number of genes in low oxygen conditions including glycolytic enzymes, which promotes ATP synthesis in an oxygen independent manner. Studies have demonstrated that hypoxia induces HIF-1 overexpression and its transcriptional activity increases in parallel with the progression of many tumor types. A recent study demonstrated that in malignant melanoma cells, HIF-1 is upregulated, leading to elevated expression of Pyruvate Dehydrogenase Kinase 1 (PDK1), and downregulated mitochondrial oxygen consumption.
The M2 isoform of Pyruvate Kinase (PKM2), which is required for catalyzing the final step of aerobic glycolysis, is highly expressed in cancer cells; whereas the M1 isoform (PKM1) is expressed in normal cells. Studies using the skin cell promotion model (JB6 cells) demonstrated that PKM2 is activated whereas PKM1 is inactivated upon tumor promoter treatment. Acute increases in ROS inhibited PKM2 through oxidation of Cys358 in human lung cancer cells. The levels of ROS and stage of tumor development may be pivotal for the role of PKM2.

Mitochondrial metabolism and glycolysis targeting for cancer drug delivery
In cancer cells including skin cancer cells, the metabolic shift is composed of increased glycolysis, activation of anabolic pathways including amino acid and pentose phosphate production, and increased fatty acid biosynthesis. More and more studies have converged on particular glycolytic and mitochondrial metabolic targets for cancer drug discovery.
A marker for increased glycolysis in melanoma is the elevated levels of Lactate Dehydrogenase (LDH) in the blood of patients with melanoma, which has proven to be an accurate predictor of prognosis and response to treatments. LDH converts pyruvate, the final product of glycolysis, to lactate when oxygen is absent. High concentrations of lactate, in turn, negatively regulate LDH. Therefore, targeting acid excretion may provide a feasible and effective therapeutic approach for melanoma. For instance, JugloSne, a main active component in walnut, has been used in traditional medicines. Studies have shown that Juglone causes cell membrane damage and increased LDH levels in a concentration-dependent manner in cultured melanoma cells. As one of the rate-limiting enzyme of glycolysis, 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase isozyme 3 (PFKFB3) is activated in neoplastic cells. Studies have confirmed that an inhibitor of PFKFB3, 3-(3-pyridinyl)-1-(4-pyridinyl)-2-propen-1-one (3PO), suppresses glycolysis in neoplastic cells. In melanoma cell lines, the concentrations of Fru-2, 6-BP, lactate, ATP, NAD+, and NADH are diminished by 3PO. Therefore, targeting PFKFB3 using 3PO and other PFKFB3 specific inhibitors could be effective in melanoma chemotherapy.
A new NO (nitric oxide) donating compound [(S,R)-3-phenyl-4,5-dihydro-5-isoxazole acetic acid–nitric oxide (GIT-27NO)] has been tested in treating melanoma cells. The results suggest that GIT-27/NO causes a dose-dependent reduction of mitochondrial respiration in treated A375 human melanoma cells.

At least two mitochondrial enzymes are affected by angiostatin which include malate dehydrogenase, a member of the Kreb’s cycle enzymes; and adenosine triphosphate synthase. Both are identified potential angiostatin-binding partners. Treated with angiostatin, the ATP concentrations of A2058 cells were decreased. Meanwhile, using siRNA of these two enzymes also inhibited the ATP production. PKM2 is up regulated in the early stage of skin carcinogenesis, therefore, targeting PKM2 could serve as a new approach for skin cancer prevention and therapy.
The signaling pathways critical for this glycolytic activation could serve as preventive and therapeutic targets for human skin cancer.

The Historical Challenge posed by the Warburg Hypothesis.

Impaired cellular energy metabolism is the defining characteristic of nearly all cancers regardless of cellular or tissue origin. In contrast to normal cells, which derive most of their usable energy from oxidative phosphorylation, most cancer cells become heavily dependent on substrate level phosphorylation to meet energy demands. Evidence is reviewed supporting a general hypothesis that genomic instability and essentially all hallmarks of cancer, including aerobic glycolysis (Warburg effect), can be linked to impaired mitochondrial function and energy metabolism.
In a landmark review, six essential alterations in cell physiology could underlie malignant cell growth. These six alterations were described as the hallmarks of nearly all cancers and included,

  • self-sufficiency in growth signals,
  • insensitivity to growth inhibitory (antigrowth) signals,
  • evasion of programmed cell death (apoptosis),
  • limitless replicative potential,
  • sustained vascularity (angiogenesis), and
  • tissue invasion and metastasis.

Genome instability, leading to increased mutability, was considered the essential enabling characteristic for manifesting the six hallmarks. The loss of genomic “caretakers” or “guardians”, involved in sensing and repairing DNA damage, was proposed to explain the increased mutability of tumor cells. The loss of these caretaker systems would allow genomic instability thus enabling pre-malignant cells to reach the six essential hallmarks of cancer.
In addition to the six recognized hallmarks of cancer, aerobic glycolysis or the Warburg effect is also a robust metabolic hallmark of most tumors. Aerobic glycolysis in cancer cells involves elevated glucose uptake with lactic acid production in the presence of oxygen. This metabolic phenotype is the basis for tumor imaging using labeled glucose analogues and has become an important diagnostic tool for cancer detection and management. Genes for glycolysis are overexpressed in the majority of cancers examined.
Although aerobic glycolysis and anaerobic glycolysis are similar in that lactic acid is produced under both situations, aerobic glycolysis can arise in tumor cells from damaged respiration whereas anaerobic glycolysis arises from the absence of oxygen. As oxygen will reduce anaerobic glycolysis and lactic acid production in most normal cells (Pasteur effect), the continued production of lactic acid in the presence of oxygen can represent an abnormal Pasteur effect. This is the situation in most tumor cells.
Warburg proposed with considerable certainty and insight that irreversible damage to respiration was the prime cause of cancer. Warburg’s biographer, Hans Krebs, mentioned that Warburg’s idea on the primary cause of cancer, i.e., the replacement of respiration by fermentation (glycolysis), was only a symptom of cancer and not the cause. While there is renewed interest in the energy metabolism of cancer cells, it is widely thought that the Warburg effect and the metabolic defects expressed in cancer cells arise primarily from genomic mutability selected during tumor progression. Emerging evidence, however, questions the genetic origin of cancer and suggests that cancer is primarily a metabolic disease.
Genomic mutability and essentially all hallmarks of cancer, including the Warburg effect, can be linked to impaired respiration and energy metabolism. In brief, damage to cellular respiration precedes and underlies the genome instability that accompanies tumor development. Once established, genome instability contributes to further respiratory impairment, genome mutability, and tumor progression. In other words, effects become causes. This hypothesis is based on evidence that nuclear genome integrity is largely dependent on mitochondrial energy homeostasis and that all cells require a constant level of useable energy to maintain viability. While Warburg recognized the centrality of impaired respiration in the origin of cancer, he did not link this phenomenon to what are now recognize as the hallmarks of cancer.
Abnormal metabolism of tumors, a selective advantage
The initial observation of Warburg 1916 on tumor glycolysis with lactate production is still a crucial observation. Two fundamental findings complete the metabolic picture:

  • the discovery of the M2 pyruvate kinase (PK) typical of tumors
  • and the implication of tyrosine kinase signals and subsequent phosphorylations in the M2 PK blockade.

A typical feature of tumor cells is a glycolysis associated to an inhibition of apoptosis. Tumors overexpress 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. 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. 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 bisphosphate; 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 phospho-enolpyruvate (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.
PK and a PDH of tumors are 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.
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 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. It is as 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!
The 21st Century Genomic Challenge?
According to the modern understanding of cancer, it is a disease caused by genetic and epigenetic alterations. Although this is now widely accepted, perhaps more emphasis has been given to the fact that cancer is a genetic disease. Numerous studies, including our earlier works, have supported the notion that carcinogenesis involves the activation of tumor-promoting oncogenes and the inactivation of growth-inhibiting tumor suppressor genes. It should be noted that in the post-genome sequencing project period of the 21st century, an in depth investigation of the factors associated with tumorigenesis is required for achieving it. Extensive research is warranted in two areas, namely, tumor bioenergetics and the cancer stem cell (CSC) hypothesis, neither of which received the required attention after the success of the genome sequencing project. An investigation of these two concepts would give rise to a new era in the study of cancer biology. Indeed, recent studies have indicated that the two apparently distinct fields might be related to each other and can converge more rapidly than previously recognized.
Warburg Effect Revisited
Cancer cells rarely depend on mitochondria for respiration and obtain almost half of their ATP by directly metabolizing glucose to lactic acid, even in the presence of oxygen. However, with the discovery that tumors do not show any shift to glycolysis, Warburg’s cancer theory (high lactate production and low mitochondrial respiration in tumor under normal oxygen pressure) was gradually discredited. Otto Warburg 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. The increasing number of recent reports on the Warburg effect has reestablished the significance of this effect in tumorigenesis, indicating that bioenergetics may play a critical role in malignant transformation. Furthermore, it has been reported that TP53, which is one of the most commonly mutated genes in cancer, can trigger the Warburg effect. Glycolytic conversion is initiated in the early stages in cells that are genetically engineered to become cancerous, and the conversion was enhanced as the cells became more malignant. Therefore, 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. This effect may also produce a metabolic shift to enhanced glycolysis and play a role in the early stages of multistep tumorigenesis in vivo.

Cancer Stem Cells (CSC) and Embryonic Stem Cells (ESC)
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.

Embryonic stem (ES) cells and immortalized primary and cancerous cells show a common concerted metabolic shift, including:

  • enhanced glycolysis,
  • decreased apoptosis, and
  • reduced mitochondrial respiration.

This finding reinforces the use of somatic stem cells or metastatic tumor cells in hypoxic niches. Hypoxia appears to regulate the functions of hematopoietic stem cells in the bone marrow and metastatic tumor cells by preserving important stem cell functions, such as:

  • cell cycle control,
  • survival,
  • metabolism, and
  • protection against oxidative stress.

Several companies and laboratories are now attempting to evaluate the bioenergetics associated with tumorigenesis by testing and challenging the available anticancer drugs.

A small population of cancer-initiating cells plays a very important role in current investigations. These CSCs may cause resistance to chemotherapy or radiation therapy or lead to post-therapy recurrence even when most of the cancer cells appear to be dead. In addition to their genetic alterations, CSCs are believed to mimic normal adult stem cells with regard to properties like self-renewal and undifferentiated status, which eventually leads to the formation of differentiated cells. Unlike well-differentiated daughter cells, small populations of CSCs are believed to be more resistant to toxic injuries and chemoradiotherapy. Indeed, the conventional cancer therapies have always been targeted toward proliferating cells. The control of CSCs, which is often exercised in the dormant phase of the cell cycle, can now be applied to achieve complete tumor regression.
Identification of cancer-specific markers
Due to their potential use in clinical applications, the surface markers of CSCs have been studied and identified. Adult stem cells and their malignant counterparts share similar intrinsic and extrinsic factors that regulate the

  • self renewal,
  • differentiation, and
  • proliferation pathways.

The following are the examples of candidate markers: musashi-1 (Msi-1), hairy and enhancer of split homolog-1 (Hes-1), CD133 (prominin-1, Prom1), epithelial cellular adhesion molecule (EpCam), claudin-7,29 CD44 variant isoforms, Lgr5,30Hedgehog (Hh), bone morphogenic protein (Bmp), Notch, and Wnt.
Is cancer a metabolic disease and genomic instability a secondary effect?
Bioenergetics of Cancer Stem Cells
The bioenergetics associated with the adaptation of CSCs to their micro-environment still requires extensive research. Although numerous studied suggested the association between Warburg effect and reduced oxidative stress in cancer, the relevant molecular mechanism was not known until very recently when Ruckenstuhl, et al. reported their findings in a yeast model.

How cancer cells achieve one of the most common phenotypes, namely, the “Warburg effect,” i.e., elevated glycolysis in the presence of oxygen, is still a topic of hypothesis, unless the involvement of glycolysis genes is considered.
The Warburg effect has been observed in differentiating cancer cells (e.g., cells that undergo epithelial-to-mesenchymal and mesenchymal-to-amoeboid transition), cells resistant to anoikis, and cells which interact with the stromal components of the metastatic niche. The epithelial-to-mesenchymal transition is involved in the resistance to chemotherapy in gastrointestinal cancer cells.

Cancer metastasis can be regarded as an integrated “escape program” triggered by redox changes. These alterations might be associated with avoiding oxidative stress in the niche of the tumor cells, or presumably with the response to treatments aimed at genetic targets, such as chemotherapy and radiation.
The introduction of induced pluripotent stem (iPS) cell genes was necessary for inducing the expression of immature status-related proteins in gastrointestinal cancer cells, and that the induced pluripotent cancer (iPC) cells were distinct from natural cancer cells with regard to their sensitivity to differentiation inducing treatment. For the complete eradication of cancer, however, future efforts should be directed toward improving translational research.
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 b-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, ATP citrate 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”.

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 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.

Warburg effect and the prognostic value of stromal caveolin-1 as a marker of a lethal tumor microenvironment
Cancer cells show a broad spectrum of bioenergetic states, with some cells using aerobic glycolysis while others rely on oxidative phosphorylation as their main source of energy. In addition, there is mounting evidence that metabolic coupling occurs in aggressive tumors, between epithelial cancer cells and the stromal compartment, and between well-oxygenated and hypoxic compartments. We recently showed that oxidative stress in the tumor stroma, due to aerobic glycolysis and mitochondrial dysfunction, is important for cancer cell mutagenesis and tumor progression. More specifically, increased autophagy/mitophagy in the tumor stroma drives a form of parasitic epithelial-stromal metabolic coupling. These findings explain why it is effective to treat tumors with either inducers or inhibitors of autophagy, as both would disrupt this energetic coupling. We also discuss evidence that glutamine addiction in cancer cells produces ammonia via oxidative mitochondrial metabolism.

Ammonia production in cancer cells, in turn, could then help maintain autophagy in the tumor stromal compartment. In this vicious cycle, the initial glutamine provided to cancer cells would be produced by autophagy in the tumor stroma. Thus, we believe that parasitic epithelial-stromal metabolic coupling has important implications for cancer diagnosis and therapy, for example, in designing novel metabolic imaging techniques and establishing new targeted therapies. In direct support of this notion, we identified a loss of stromal caveolin-1 as a marker of oxidative stress, hypoxia, and autophagy in the tumor microenvironment, explaining its powerful predictive value. Loss of stromal caveolin-1 in breast cancers is associated with early tumor recurrence, metastasis, and drug resistance, leading to poor clinical outcome.
The conventional ‘Warburg effect’ versus oxidative mitochondrial metabolism
Warburg’s original work indicated that while glucose uptake and lactate production are greatly elevated, a cancer cell’s rate of mitochondrial respiration is similar to that of normal cells. He, however, described it as a ‘respiratory impairment’ due to the fact that, in cancer cells, mitochondrial respiration is smaller, relative to their glycolytic power, but not smaller relative to normal cells. He recognized that oxygen consumption is not diminished in tumor cells, but that respiration is disturbed because glycolysis persists in the presence of oxygen. Unfortunately, the perception of his original findings was simplified over the years, and most subsequent papers validated that cancer cells undergo aerobic glycolysis and produce lactate, but did not measure mitochondrial respiration, and just presumed decreased tricarboxylic acid (TCA) cycle activity and reduced oxidative phosphorylation [1,2]. It is indeed well documented that, as a consequence of intra-tumoral hypoxia, the hypoxia-inducible factor (HIF)1α pathway is activated in many tumors cells, resulting in the direct up-regulation of lactate dehydrogenase (LDH) and increased glucose consumption.
It is now clear that cancer cells utilize both glycolysis and oxidative phosphorylation to satisfy their metabolic needs. Experimental assessments of ATP production in cancer cells have demonstrated that oxidative pathways play a signifi cant role in energy generation, and may be responsible for about 50 to 80% of the ATP generated. several studies now clearly indicate that mitochondrial activity and oxidative phosphorylation support tumor growth. Loss-of-function mutations in the TCA cycle gene IDH1 (isocitrate dehydrogenase 1) are found in about 70% of gliomas, but, interestingly, correlate with a better prognosis and improved survival, suggesting that severely decreased activity in one of the TCA cycle enzymes does not favor tumor aggressiveness. The mitochondrial protein p32 was shown to maintain high levels of oxidative phosphorylation in human cancer cells and to sustain tumorigenicity in vivo. In addition, STAT3 is known to enhance tumor growth and to predict poor prognosis in human cancers. Interestingly, a pool of STAT3 localizes to the mitochondria, to sustain high levels of mitochondrial respiration and to augment transformation by oncogenic Ras. Similarly, the mitochondrial transcription factor A (TFAM), which is required for mitochondrial DNA replication and oxidative phosphorylation, is also required for K-Ras induced lung tumorigenesis.
There is also evidence that pro-oncogenic molecules regulate mitochondrial function. Cyclin D1 inhibits mitochondrial function in breast cancer cells. Overexpression of cyclin D1 is observed in about 50% of invasive breast cancers and is associated with a good clinical outcome, indicating that inhibition of mitochondrial activity correlates with favorable prognosis. Importantly, it was shown that the oncogene c-Myc stimulates mitochondrial biogenesis, and enhances glutamine metabolism by regulating the expression of mitochondrial glutaminase, the first enzyme in the glutamine utilization pathway. Glutamine is an essential metabolic fuel that is converted to alpha-ketoglutarate and serves as a substrate for the TCA cycle or for glutathione synthesis, to promote energy production and cellular biosynthesis, and to protect against oxidative stress. Interestingly, pharmacological targeting of mitochondrial glutaminase inhibits cancer cell transforming activity, suggesting that glutamine metabolism and its role in fueling and replenishing the TCA cycle are required for neoplastic transformation.
Reverse Warburg Effect.
It is increasingly apparent that the tumor microenvironment regulates neoplastic growth and progression. Activation of the stroma is a critical step required for tumor formation. Among the stromal players, cancer associated fi broblasts (CAFs) have recently taken center stage [25]. CAFs are activated, contractile        fibroblasts that display features of myo-fibroblasts, express muscle specific actin, and show an increased ability to secrete and remodel the extracellular matrix. They are not just neutral spectators, but actively support malignant transformation and metastasis, as compared to normal resting fibroblasts.

Importantly, the tumor stroma dictates clinical outcome and constitutes a source of potential biomarkers. Expression profiling has identified a cancer-associated stromal signature that predicts good and poor clinical prognosis in breast cancer patients, independently of other factors.

A loss of caveolin-1 (Cav-1) in the stromal compartment is a novel biomarker for predicting poor clinical outcome in all of the most common subtypes of human breast cancer, including the more lethal triple negative subtype. A loss of stromal Cav-1 predicts early tumor recurrence, lymph node metastasis, tamoxifen-resistance, and poor survival.

Overall, breast cancer patients with a loss of stromal Cav-1show a 20% 5-year survival rate, compared to the 80% 5-year survival of patients with high stromal Cav-1 expression. In triple negative patients, the 5-year survival rate is 75.5% for high stromal Cav-1 versus 9.4% for absent stromal Cav-1. A loss of stromal Cav-1 also predicts progression to invasive disease in ductal carcinoma in situ patients, suggesting that a loss of Cav-1 regulates tumor progression. Similarly, a loss of stromal Cav-1 is associated with advanced disease and metastasis, as well as a high Gleason score, in prostate cancer patients.

The autophagic tumor stroma model of cancer metabolism.
Cancer cells induce oxidative stress in adjacent cancer-associated fibroblasts (CAFs). This activates reactive oxygen species (ROS) production and autophagy. ROS production in CAFs, via the bystander eff ect, serves to induce random mutagenesis in epithelial cancer cells, leading to double-strand DNA breaks and aneuploidy. Cancer cells mount an anti-oxidant defense and upregulate molecules that protect them against ROS and autophagy, preventing them from undergoing apoptosis. So, stromal fibroblasts conveniently feed and mutagenize cancer cells, while protecting them against death. See the text for more details. A+, autophagy positive; A-, autophagy negative; AR, autophagy resistant.

1. Recycled Nutrients
2. Random Mutagenesis
3. Protection Against Apoptosis
The clinical use of PET is well established in Hodgkin’s lymphomas which are composed of less than 10% tumor cells, the rest being stromal and inflammatory cells. Yet, Hodgkin’s lymphomas are very PET avid tumors, suggesting that 2-deoxy-glucose uptake may be associated with the tumor stroma. That the fibrotic component may be glucose avid is further supported by the notion that PET is clinically used to assess the therapeutic response in gastrointestinal stromal tumors (GIST), which are a subset of tumors of mesenchymal origin.
The reverse Warburg effect can be described as ‘metabolic coupling’ between supporting glycolytic stromal cells and oxidative tumor cells. Metabolic cooperativity between adjacent cell-compartments is observed in several normal physiological settings.
The reverse Warburg effect.
Via oxidative stress, cancer cells activate two major transcription factors in adjacent stromal fibroblasts (hypoxia-inducible factor (HIF)1α and NFκB).
This leads to the onset of both autophagy and mitophagy, as well as aerobic glycolysis, which then produces recycled nutrients (such as lactate, ketones, and glutamine).
These high-energy chemical building blocks can then be transferred and used as fuel in the tricarboxylic acid cycle (TCA) in adjacent cancer cells.
The outcome is high ATP production in cancer cells, and protection against cell death. ROS, reactive oxygen species.
The methylation hypothesis and the role of PP2A phosphatase
Diethanolamine decreased choline derivatives and methyl donors in the liver, like seen in 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. 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 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. the catalytic C subunit of PP2A is associated to a structural subunit A. When C receives a methyl, the dimer recruits a regulatory subunit B. The trimer then targets specific proteins that are dephosphorylated. 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. 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. The targeting of PP2A towards proteins of the signaling pathway depends of the assembly of the different holoenzymes.

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. Moreover, PK, and PDH would become active after the phosphatase action. One would also gain to inhibit their kinases as recently done with dichloroacetate for PDH kinase. The nuclear or cytosolic targeting of PP2A isoforms is a hypothesis also inspired by several works.
Hypoxic adaptations in the presence of oxygen
Through different biochemical and biophysical pathways, which are characteristic to cancer cells, tumor cells adopt this phenotype, i.e., high glycolysis and decreased respiration, in the presence of oxygen. It has been shown that although the induction of hypoxia and cellular proliferation engage entirely different cellular pathways, they often coexist during tumor growth. The ability of cells to grow during hypoxia results, in part, from the crosstalk between hypoxia-inducible factors (Hifs) and the proto-oncogene c-Myc. These genes partially regulate the development of complex adaptations of tumor cells growing in low O2, and contribute to fine tuning the adaptive responses of cells to hypoxic environments.

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 eacetylase (HDAC) inhibition or of histone acetyltransferase (HAT) activation, and represents the main switch

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 b 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. Since citrate synthase activity is elevated in tumors, ketone bodies do not form. This result silences several genes like PETEN, P53, or methylase inhibitory genes. It is probable that the IGFBP gene gets silent as well.

Uncoupling Proteins in Cancer
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.

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.
Briefly, oxidation of reduced nutrient molecules, such as carbohydrates, lipids, and proteins, through cellular metabolism yields electrons in the form of reduced hydrogen carriers NADH+ and FADH2. These reduced cofactors donate electrons to a series of protein complexes embedded in the inner mitochondrial membrane known as the electron transport chain (ETC). These complexes use the energy released from electron transport for active pumping of protons across the inner membrane, generating an electrochemical gradient. Mitochondria orchestrate conversions between different forms of energy, coupling aerobic respiration to phosphorylation.
Conversion of metabolic fuel into ATP is not a fully efficient process. Some of the energy of the electrochemical gradient is not coupled to ATP production due to a phenomenon known as proton leak, which consists of the return of protons to the mitochondrial matrix through alternative pathways that bypass ATP synthase. Although this apparently futile cycle of protons is physiologically important, accounting for 20-25% of basal metabolic rate, its function is still a subject of debate. Several different functions have been suggested for proton leak, including thermogenesis, regulation of energy metabolism, and control of body weight and attenuation of reactive oxygen species (ROS) production. Although a part of the proton leak may be attributed to biophysical properties of the inner membrane, such as protein/lipid interfaces, the bulk of the proton conductance is linked to the action of a family of mitochondrial proteins termed uncoupling proteins.

Mitochondria are the major sources of reactive oxygen species (ROS). Aerobic respiration involves the complete reduction of oxygen to water, which is catalysed by complex IV (or cytochrome c oxidase). Nevertheless, during the transfer of electrons along the electron transport complexes, single electrons sometimes escape and result in a single electron reduction of molecular oxygen to form a superoxide anion, which, in turn is the precursor of other ROS.

One of the most interesting functions attributed to UCPs is their ability to decrease the formation of mitochondrial ROS. Mitochondria are the main source of ROS in cells. Superoxide formation is strongly activated under resting (state 4) conditions when the membrane potential is high and the rate of electron transport is limited by lack of ADP and Pi. Thus, there is a well established strong positive correlation between membrane potential and ROS production.
A small increase in membrane potential gives rise to a large stimulation of ROS production, whereas a small decrease in membrane potential (10 mV) is able to inhibit ROS production by 70% . Therefore, mild uncoupling, i.e., a small decrease in membrane potential, has been suggested to have a natural antioxidant effect.

Consistent with such a proposal, the inhibition of UCPs by GDP in mitochondria has been shown to increase membrane potential and mitochondrial ROS production. The loss of UCP2 or UCP3 in knockouts yielded increased ROS production concurrent with elevated membrane potential specifically in those tissues normally expressing the missing protein.
The hypothesis of UCPs as an antioxidant defense has been strongly supported by the fact that these proteins have been shown to be activated by ROS or by-products of lipid peroxidation, showing that UCPs would form part of a negative feed-back mechanism aimed to mitigate excessive ROS production and oxidative damage.
ROS and Cancer
ROS are thought to play multiple roles in tumor initiation, progression and maintenance, eliciting cellular responses that range from proliferation to cell death. In normal cells, ROS play crucial roles in several biological mechanisms including phagocytosis, proliferation, apoptosis, detoxification and other biochemical reactions. Low levels of ROS regulate cellular signaling and play an important role in normal cell proliferation. During initiation of cancer, ROS may cause DNA damage and mutagenesis, while ROS acting as second messengers stimulate proliferation and inhibit apoptosis, conferring growth advantage to established cancer cells. Cancer cells have been found to have increased ROS levels.

One of the functional roles of these elevated ROS levels during tumor progression is constant activation of transcription factors such as NF-kappaB and AP-1 which induce genes that promote proliferation and inhibit apoptosis. In addition, oxidative stress can induce DNA damage which leads to genomic instability and the acquisition of new mutations, which may contribute to cancer progression.

Role of ROS in control of proliferation and apoptosis
ROS are also essential mediators of apoptosis which eliminates cancer and other cells that threaten our health [81–86]. Many chemotherapeutic drugs and radiotherapy are aimed at increasing ROS levels to promote apoptosis by stimulating pro-apoptotic singaling molecules such as ASK1, JNK and p38. Because of the pivotal role of ROS in triggering apoptosis, antioxidants can inhibit this protective mechanism by depleting ROS. Thus, antioxidant mechanisms are thought to interfere with the therapeutic activity of anticancer drugs that kill advanced stage cancer cells by apoptosis.

Effect of uncoupling proteins on proliferation and apoptosis in relation to ROS levels

Uncoupling-to-survive hypothesis (proposed by Brand)

  • the ability of UCP2 to increase lifespan is mediated by decreased ROS production and oxidative stress.
  • the ability of mild uncoupling to avoid ROS formation, gives a reasonable argument to hypothesize about a role for UCPs in cancer prevention

Consistently, Derdák et al. showed that Ucp2−/− mice treated with the carcinogen azoxymethane were found to develop more aberrant crypt foci and colon tumours than Ucp2+/+ in relation with increased oxidative stress and enhanced NF-kappaB activation.

Roles of UCPs in Cancer Progression
The growth of a tumor from a single genetically altered cell is a stepwise progression requiring the alterations of several genes which contribute to the acquisition of a malignant phenotype. Such genetic alterations are positively selected when in the tumor, they confer a proliferative, survival or treatment resistance advantage for the host cell. In addition, several mutations, such as those silencing tumour suppressor genes, trigger the probability of accumulating new mutations, so the process of malignant transformation is progressively self-accelerated.

Considering the ability of UCPs to modulate mutagenic ROS, as well as mitochondrial bioenergetics and membrane potential, both involved in regulation of cell survival, an interesting question is whether UCPs can be involved in the progression of cancer.

Increased uncoupled respiration may be a mechanism to lower cellular oxygen concentration and, thus, alter molecular pathways of oxygen sensing such as those regulated by hypoxia-inducible factor (HIF). In normoxia, the alpha subunit of HIF-1 is a target for prolyl hydroxylase, which makes HIF-1alpha a target for degradation by the proteasome. During hypoxia, prolyl hydroxylase is inhibited since it requires oxygen as a cosubstrate. Thus, hypoxia allows HIF to accumulate and translocate into the nucleus for induction of target genes regulating glycolysis, angiogenesis and hematopoiesis. By this mechanism, UCPs activity may contribute to increase the expression of genes related to the formation of blood vessels, and thus promote tumor growth.

Roles of UCPs in Cancer Energy Metabolism
Lynen and colleagues proposed that the root of the Warburg effect is not in the inability of mitochondria to carry out respiration, but rather would rely on their incapacity to synthesize ATP in response to membrane potential.

The ability of UCPs to uncouple ATP synthesis from respiration and the fact that UCP2 is overexpressed in several chemoresistant cancer cell lines and primary human colon cancers have lead to speculate about the existence of a link between UCPs and the Warburg effect. As mentioned above, uncoupling induced by overexpression of UCP2 has been shown to prevent ROS formation, and, in turn, increase apoptotic threshold in cancer cells, providing a pro-survival advantage and a resistance mechanism to cope with ROS-inducing chemo-therapeutic agents.

Mitochondrial Krebs cycle is one of the sources for these anabolic precursors. The export of these metabolites to cytoplasm for anabolic purposes involves the replenishment of the cycle intermediates by anaplerotic substrates such as pyruvate and glutamate. Thus, glycolysis-derived pyruvate, as well as alpha-ketoglutarate derived from glutaminolysis, may be necessary to sustain anaplerotic reactions. At the same time, to keep Krebs cycle functional, the reduced cofactors NADH and FADH2 would have to be re-oxidized, a function which relies on the mitochondrial respiratory chain. Once again, uncoupling may be crucial for cancer cell mitochondrial metabolism, allowing Krebs cycle to be kept functional to meet the vigorous biosynthetic demand of cancer cells.

Several cancer cells resistant to chemotherapeutics and radiation often exhibit higher rates of fatty acid oxidation and it has been observed that inhibition of fatty acid oxidation potentiates apoptotic death induced by chemotherapeutic agents. These findings are in agreement with the proposed need of fatty acid for the activity of UCPs, suggesting that the lack of these potential substrates or activators would decrease uncoupling activity, subsequently increasing membrane potential, ROS production and therefore lowering apoptotic threshold.

Roles of UCPs in Cancer Cachexia
Cachexia is a wasting syndrome characterized by weakness, weight and fat loss, and muscle atrophy which is often seen in patients with advanced cancer or AIDS. Cachexia has been suggested to be responsible for at least 20 % of cancer deaths and also plays an important part in the compromised immunity leading to death from infection. The imbalance between energy intake and energy expenditure underlying cachexia cannot be reversed nutritionally.

Alterations leading to high energy expenditure, such as excessive proton leak or mitochondrial uncoupling, are likely mechanisms underlying cachexia. In fact, increased expression of UCP1 in BAT and UCP2 and UCP3 in skeletal muscle have been shown in several murine models of cancer cachexia

Roles of UCPs in Chemoresistance

Cancer cells acquire drug resistance as a result of selection pressure dictated by unfavorable microenvironments. Although mild uncoupling may clearly be useful under normal conditions or under severe or chronic metabolic stress such as hypoxia or anoxia, it may be a mechanism to elude oxidative stress-induced apoptosis in advanced cancer cells. Several anti-cancer treatments are based on promotion of ROS formation, to induce cell growth arrest and apoptosis. Thus, increased UCP levels in cancer cells, rather than a marker of oxidative stress, may be a mechanisms conferring anti-apoptotic advantages to the malignant cell, increasing their ability to survive in adverse microenvironments, radiotherapy and chemotherapy. UCPs appear to play a permissive role in tumor cell survival and growth.

Expression of UCPs promote bioenergetics adaptation and cell survival. UCPs appear to be critical to determine the sensitivity of cancer cells to several chemotherapeutic agents and radiotherapy, interfering with the activation of mitochondria driven apoptosis.

From a therapeutic viewpoint, inhibition of glycolysis in UCP2 expressing tumours or specific inhibition of UCP2 are, respectively, attractive strategies to target the specific metabolic signature of cancer cells.

Hypoxia-inducible factor-1 in tumour angiogenesis
HIF-b subunits, is a heterodimeric transcriptional activator. In response to
hypoxia,

  • stimulation of growth factors, and
  • activation of oncogenes as well as carcinogens,

HIF-1a is overexpressed and/or activated and targets those genes which are required for angiogenesis, metabolic adaptation to low oxygen and promotes survival.

Several dozens of putative direct HIF-1 target genes have been identified on the basis of one or more cis-acting hypoxia-response elements that contain an HIF-1 binding site. Activation of HIF-1 in combination with activated signaling pathways and regulators is implicated in tumour progression and prognosis.
In order for a macroscopic tumour to grow, adequate oxygen delivery must be effected via tumor angiogenesis that results from an increased synthesis of angiogenic factors and a decreased synthesis of anti-angiogenic factors. The metabolic adaptation of tumor cells to reduced oxygen availability by increasing glucose transport and glycolysis to promote survival are important consequences in response to hypoxia.

Hypoxia and HIF-1
Hypoxia is one of the major drivers to tumour progression as hypoxic areas form in human tumours when the growth of tumour cells in a given area outstrips local neovascularization, thereby creating areas of inadequate perfusion. Although several transcriptional factors have been reported to be involved
in the response to hypoxic stress such as AP-1, NF-kB and HIF-1, HIF-1 is the most potent inducer of the expression of genes such as those encoding for glycolytic enzymes, VEGF and erythropoietin.

HIF-a subunit exists as at least three isoforms, HIF-1a, HIF-2a and HIF-3a. HIF-1a and HIF-2a can form heterodimers with HIF-b. Although HIF-b subunits are constitutive nuclear proteins, both HIF-1a andHIF-2a subunits are strongly induced by hypoxia in a similar manner. HIF-1a is up-regulated in hypoxic tumour cells and activates the transcription of target genes by binding to cis-acting enhancers, hypoxic responsive element (HRE) close to the promoters of these genes with a result of tumour cellular adaptation to hypoxia and tumour angiogenesis, and promotion of further growth of the primary tumour. Studies have shown HIF-1a to be over-expressed by both tumour cells and such stromal cells as macrophages in many forms of human malignancy.

Regulation of HIF-1
The first regulator of HIF-1 is oxygen. HIF-1α appears to be the HIF-1 subunit regulated by hypoxia. The oxygen sensors in the HIF-1α pathway are two kinds of oxygen dependent hydroxylases. One is prolyl hydroxylase which could hydroxylize the proline residues 402 and 564 at the oxygen dependent domain (ODD) of HIF-1 in the presence of oxygen and iron with a result of HIF-α degradation. The other is hydroxylation of Asn803 at the C-terminal transactivation domain (TAD-C) by FIH-1, which could inhibit the interaction of HIF-1α with co-activator p300 with a subsequent inhibition of HIF-1α transactivity. The hydroxylation of proline 564 at ODD of HIF-1α under normoxia was shown using a novel hydroxylation-specific antibody to detect hydroxylized HIF-1α.

Oncogene comes as the second regulator. Many oncogenes have effects on HIF-1α. Among them, some function in regulation of HIF-1α protein stability or degradation, others play roles in several activated signaling pathways. Tumor suppressor genes as p53 and von Hippel-Lindau (VHL) influence the levels and functions of HIF-1. The wild type (wt) form of p53 protein was involved in inhibiting HIF-1 activity by targeting the HIF-1a subunit for Mdm2-mediated ubiquitination and proteasomal degradation, and in inducing inhibitors of angiogenesis such as thrombospondin-1, while loss of wt p53 (by gene deletion or mutation) could enhance HIF-1α accumulation in hypoxia.

The third regulator is a battery of growth factors and cytokines from stromal and parenchymal cells such as

  • EGF,
  • transforming growth factor-α,
  • insulin-like growth factors 1 and 2,
  • heregulin, and interleukin-1b

via autocrine and paracrine pathways. These regulators not only induce the expression of HIF-1α protein, HIF-1 DNA binding activity and transactivity, but also make HIF-1 target gene expression under normoxia or hypoxia.
The fourth one is a group of reactive oxygen species (ROS) resulting from carcinogens such as Vanadate and Cr (VI) or stimulation of cytokines such as angiotensin and TNFa. However, it seems controversial when it comes to the production of ROS under hypoxia and their individual role in regulation of HIF-1a. It is well known that ROS plays an important role in carcinogenesis induced by a variety of carcinogens.

Signaling Pathways Involved in Regulation of HIF-1α
HIF-1 is a phosphorylated protein and its phosphorylation is involved in HIF-1a subunit expression and/or stabilization as well as in the regulation of HIF-1 transcriptional activity. Three signaling pathways involved in the regulation of HIF-1α have been reported to date.

  • The PI-3k pathway has been mainly and frequently implicated in regulation of HIF-1α protein expression and stability.
  • Akt is also activated by hypoxia. Activated Akt initiates two different pathways in regulation of HIF-1α. The function of these two pathways appears to show consistent impact on HIF-1α activation.
  • Signal transduction pathway in HIF-1α regulation.Oncogenes, growth factors and hypoxia have been documented to regulate HIF-1α protein and increase its transactivity. GSK and mTOR were two target events of Akt and could contribute to decreasing HIF-1α degradation and increasing HIF-1α protein synthesis. Activated ERK1/2 could mainly up-regulate.

HIF-1a, Angiogenesis and Tumour Prognosis
Hypoxia, oncogenes and a variety of growth factors and cytokines increase HIF-1α stability and/or synthesis and transactivation to initiate tumour angiogenesis, metabolic adaptation to hypoxic situation and promote cell survival or anti-apoptosis resulting from a consequence of more than sixty putative direct HIF-1 target gene expressions.

The crucial role of HIF-1 in tumour angiogenesis has sparked scientists and clinical researchers to try their best to understand the whole diagram of HIF-1 so as to find out novel approaches to inhibit HIF-1 overexpression. Indeed, the combination of anti-angiogenic agent and inhibitor of HIF-1 might be particularly efficacious, as the angiogenesis inhibitor would cut off the tumour’s blood supply and HIF-1 inhibitor would reduce the ability of tumour adaptation to hypoxia and suppress the proliferation and promote apoptosis. Screens for small-molecule inhibitors of HIF-1 are underway and several agents that inhibit HIF-1, angiogenesis and xenograft growth have been identified.

Hypoxia, autophagy, and mitophagy in the tumor stroma
Metabolomic profiling reveals that Cav-1(-/-) null mammary fat pads display a highly catabolic metabolism, with the increased release of several metabolites, such as amino acids, ribose and nucleotides, and a shift towards gluconeogenesis, as well as mitochondrial dysfunction. These changes are consistent with increased autophagy, mitophagy and aerobic glycolysis, all processes that are induced by oxidative stress. Autophagy or ‘self-eating’ is the process by which cells degrade their own cellular components to survive during starvation or to eliminate damaged organelles after oxidative stress. Mitophagy, or mitochondrial-autophagy, is particularly important to remove damaged ROS-generating mitochondria.

An autophagy/mitophagy program is also triggered by hypoxia. Hypoxia is a common feature of solid tumors, and promotes cancer progression, invasion and metastasis. Interestingly, via induction of autophagy, hypoxia is sufficient to induce a dramatic loss of Cav-1 in fibroblasts. The hypoxia-induced loss of Cav-1 can be inhibited by the autophagy inhibitor chloroquine, or by pharmacological inhibition of HIF1α. Conversely, small interfering RNA-mediated Cav-1 knock-down is sufficient to induce pseudo-hypoxia, with HIF1α and NFκB activation, and to promote autophagy/mitophagy, as well as a loss of mitochondrial membrane potential in stromal cells. These results indicate that a loss of stromal Cav-1 is a marker of hypoxia and oxidative stress.

In a co-culture model, autophagy in cancer-associated fibroblasts was shown to promote tumor cell survival via the induction of the pro-autophagic HIF1α and NFκB pathways in the tumor stromal microenvironment. Finally, the mitophagy marker Bnip3L is selectively upregulated in the stroma of human breast cancers lacking Cav-1, but is notably absent from the adjacent breast cancer epithelial cells.

Metabolome profiling of several types of human cancer tissues versus corresponding normal tissues have consistently shown that cancer tissues are highly catabolic, with the significant accumulation of many amino acids and TCA cycle metabolites. The levels of reduced glutathione were decreased in primary and metastatic prostate cancers compared to benign adjacent prostate tissue, suggesting that aggressive disease is associated with increased oxidative stress. Also, these data show that the tumor microenvironment has increased oxidative-stress-induced autophagy and increased catabolism.

Taken together, all these findings suggest an integrated model whereby
A loss of stromal Cav-1 induces autophagy/mitophagy in the tumor stroma, via oxidative stress.

This creates a catabolic micro-environment with the local accumulation of chemical building blocks and recycled nutrients (such as amino acids and nucleotides), directly feeding cancer cells to sustain their survival and growth.
This novel idea is termed the ‘autophagic tumor stroma model of cancer’ .
This new paradigm may explain the ‘autophagy paradox’, which is based on the fact that both the systemic inhibition and systemic stimulation of autophagy prevent tumor formation.

What is presented suggests that vectorial energy transfer from the tumor stroma to cancer cells directly sustains tumor growth, and that interruption of such metabolic coupling will block tumor growth. Autophagy inhibitors (such as chloroquine) functionally block the catabolic transfer of metabolites from the stroma to the tumor, inducing cancer cell starvation and death. Conversely, autophagy inducers (such as rapamycin) promote autophagy in tumor cells and induce cell death. Thus, both inhibitors and inducers of autophagy will have a similar effect by severing the metabolic coupling of the stroma and tumor cells, resulting in tumor growth inhibition (cutting ‘off ’ the fuel supply).

This model may also explain why enthusiasm for antiangiogenic therapy has been dampened. In most cases, the clinical benefits are short term, and more importantly, new data suggest an unexpected link between anti-angiogenic treatments and metastasis. In pre-clinical models, anti-vascular endothelial growth factor (anti-VEGF) drugs (sunitinib and anti-VEGFR2 blocking antibodies) were shown to inhibit localized tumor formation, but potently induced relapse and metastasis. Thus, by inducing hypoxia in the tumor microenvironment, antiangiogenic drugs may create a more favorable metastatic niche.
Glutamine, glutaminolysis.
In direct support that cancer cells use mitochondrial oxidative metabolism, many investigators have shown that cancer cells are ‘addicted’ to glutamine. Glutamine is a non-essential amino acid that is metabolized to glutamate and enters the TCA cycle as α-ketoglutarate, resulting in high ATP generation via oxidative phosphorylation. Recent studies also show that ammonia is a by-product of glutaminolysis. In addition, ammonia can act as a diffusible inducer of autophagy. Given these observations, glutamine addiction in cancer cells provides another mechanism for driving and maintaining autophagy in the tumor micro-environment .

In support of this idea, a loss of Cav-1 in the stroma is sufficient to drive autophagy, resulting in increased glutamine production in the tumor micro-environment. Thus, this concept defines a new vicious cycle in which autophagy in the tumor stroma transfers glutamine to cancer cells, and the by-product of this metabolism, ammonia, maintains autophagic glutamine production. This model fits well with the ‘autophagic tumor stroma model of cancer metabolism’, in which energy rich recycled nutrients (lactate, ketones, and glutamine) fuel oxidative mitochondrial metabolism in cancer cells.

Glutamine utilization in cancer cells and the tumor stroma. Oxidative mitochondrial metabolism of glutamine in cancer cells produces ammonia. Ammonia production is sufficient to induce autophagy. Thus, autophagy in cancer-associated fibroblasts provides cancer cells with an abundant source of glutamine. In turn, the ammonia produced maintains the autophagic phenotype of the adjacent stromal fibroblasts.

Lessons from other paradigms

an infectious parasitic cancer cell that metastasizes and captures mitochondrial DNA from host cells
Cancer cells behave like ‘parasites’, by inducing oxidative stress in normal host fibroblasts, resulting in the production of recycled nutrients via autophagy.

This is exactly the same mechanism by which infectious parasites (such as malaria) obtain nutrients and are propagated by inducing oxidative stress and autophagy in host cells. In this regard, malaria is an ‘intracellular’ parasite, while cancer cells may be thought of as ‘extracellular’ parasites. This explains why chloroquine is both an effective antimalarial drug and an effective anti-tumor agent, as it functions as an autophagy inhibitor, cutting off the ‘fuel supply’ in both disease states.

Human cancer cells can ‘steal’ live mitochondria or mitochondrial DNA from adjacent mesenchymal stem cells in culture, which then rescues aerobic glycolysis in these cancer cells. This is known as mitochondrial transfer. Interestingly, metastatic breast cancer cells show the up-regulation of numerous mitochondrial proteins, specifically associated with oxidative phosphorylation, as seen by unbiased proteomic analysis.

Thus, increased mitochondrial oxidative metabolism may be a key driver of tumor cell metastasis. In further support of this argument, treatment of MCF7 cancer cells with lactate is indeed sufficient to induce mitochondrial biogenesis in these cells.

To determine if these findings may be clinically relevant, a lactate-induced gene signature was recently generated using MCF7 cells. This gene signature shows that lactate induces ‘stemness’ in cancer cells, and this lactate induced gene signature predicts poor clinical outcome (including tumor recurrence and metastasis) in breast cancer patients.

REFERENCES

Li W and Zhao Y. “Warburg Effect” and Mitochondrial Metabolism in Skin Cancer. Epidermal Pigmentation, Nucleotide Excision Repair and Risk of Skin Cancer. J Carcinogene Mutagene 2012; S4:002 doi:10.4172/2157-2518.
Seyfried TN, Shelton LM. Cancer as a metabolic disease. Nutrition & Metabolism 2010; 7:7(22 pg). doi:10.1186/1743-7075-7-7
Israël M, Schwartz L. The metabolic advantage of tumor cells. Molecular Cancer 2011, 10:70-82. http://www.molecular-cancer.com/content/10/1/70
Valle A, Oliver J, Roca P. Role of Uncoupling Proteins in Cancer. Cancers 2010, 2, 567-591; doi:10.3390/cancers2020567
Ishii H, Doki Y, Mori M. Perspective beyond Cancer Genomics: Bioenergetics of Cancer Stem Cells. Yonsei Med J 2010; 51(5):617-621. DOI 10.3349/ymj. 2010.51.5.617 pISSN: 0513-5796, eISSN: 1976-2437
Sotgia F, Martinez-Outschoorn, Pavlides S,Howell A . Understanding the Warburg effect and the prognostic value of stromal caveolin-1 as a marker of a lethal tumor microenvironment. Breast Cancer Research 2011, 13:213-26. http://breast-cancer-research.com/content/13/4/213
Yong-Hong Shi, Wei-Gang Fang. Hypoxia-inducible factor-1 in tumour angiogenesis. World J Gastroenterol 2004; 10(8): 1082-1087. http:// wjgnet.com /1007-9327/10/1082.asp

English: Glycolysis pathway overview.

English: Glycolysis pathway overview. (Photo credit: Wikipedia)

Adenosine triphosphate

 

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Warburg Effect, glycolysis, pyruvate kinase, PKM2, PIM2, mtDNA, complex I, NSCLC

Ribeirão Preto Area, Brazil|Government Relations
Current- University, USP-FMRP Physiology – Biochemistry
Previous- Imperial Cancer Research Fund Lab, Instituto de Investigaciones Bioquimicas, Luta armada e CIA
Education – FMRP-USP
While exile interrupted ny graduation in Medicine, started a port grade at Leloir´s Instituto Investigaciones bioquímicas Buenos Aires Argentina Jan 1970 – jan 1972. PhD from 1972- jan 1976 FMRP-USP . Post Doc ICRF London England 1979 -1980

“Those…..whose acquitance with scientific research is derived chiefly from its practical results easily develop a completely false notion of the { scientific } mentality.”

My goal and previous experience besides laboratory work was dedicated to solve this apparent conflict.

When Pasteur did his work studying the chemistry outside yeast-cells, he was able to perceive that in anaerobiosis yeast cells were able to convert sugar at a great velocity to its end products. While the same yeast cells, therefore with the same genome did it at a very slow speed in aerobiosis. Warburg tested tumor cells for the same and found that while normal cells from the organ in which he has found tumors presented a similar metabolic regulatory response to anaerobic/aerobic transition tumor cells did not. Tumos cells continued to display strong acidification (producing great amounts of lactate in the culture media) in aerobiosis.

Tumor cells displayed a failure in this regulatory mechanism that, he O. Warburg, named Pasteur effect. He also noticed that this defect continues from old cancer cells to newer ones. Therefore, for him, it is a genetic defect. Furthermore, as mitochondria generates newer mitochondria in the cells, the genetic component is in the mitochondria that were the site of core metabolism in aerobiosis.

Larry Bernstein
Part of what you describe is in Warburg biography by Hans Krebs (out of print). He also refers to a Meyerhof Quotient to express the degree of metabolic anaerobiosis. I don’t recall a reference to a mitochondrial “genetic” defect. That is farsighted. He did conclude that once the cancer cells were truly anaplastic, metastatic behavior was irreversible. It was only later that another Nobelist who described fatty acid synthesis, I think, concluded that the synthetic process tied up the same aerobic pathway so that anaerobic glycolysis became essential for the cells energetics. You can correct me if I’m in error. Where does the substrate come from? Lean body mass breaks down to provide gluconeogenic precursors. Points of concern are – deamination of branch chain AAs, the splitting of a 6 carbon sugar into 2 3-carbon chains, and the conversion of pyruvate to lactate with the reverse reaction blocked. There is also evidence that there is an impairment in the TCA cycle at the point of fumarase. Then there is never any consideration of the flow of substrates back and forth across the mitochondrial membrane (malate, aspartate), and the redox potentials.

Jose: For reasons independent of my will, the copy of Science,123(3191):309-14,1956 translation of O Warburg original article is not in my hands. Some that do not find any alternative form to respond to my critics concerning molecular biology distortion of biochemistry left on purpose, almost all of my older reprints on the rain. Anyway, O. Warburg refers to mitochondria using the expression of “grana” or “grains” if my recollections are correct. The original work of O Warburg is one of 1924 – Biochemisch ZeiTschrift.,152:51-60.1924. “Weberssert method zur messing der atmung un glycolyse, drese zeitschr.” Other aspects of your interesting comment I will try to comment latter.

By Jose Eduardo de Salles Roselino
Larry Bernstein, not as a correction but , following my line of reasoning about carbono fluxes…It is almost impossible to figure out what was really inside the mind-set of a scientific researcher at the time he has performed his work. Anyway, by the knowledge available at his time, we may conjecture about, even when we acknowledge that, what he may have had in mind at the start could be quite different from what he have latter published from his results.
In case, we try to present the ideas behind Warburg´s works we may take into account the following pre-existing knowledge: Lavoisier (done by 1779-1784) measured very carefully the amount of heat released by respiration and chemical oxidative processes. Reached the conclusion that respiration was slower but essentially similar to carbon combustion by chemical oxidative processes. By early XIX caloric values for gram of sugar, lipids and proteins where made clear. T Schwann recognized that yeast cells convert sugar in ethanol plus a volatile acid (carbon dioxide). Pasteur-effect was seen just as a change in the velocity of product production from a same sugar and/or a decrease in sugar concentration in the growth medium. This is a change in carbon flux velocity in the oxidative process calorimetrically measured by Lavoisier.
In Germany, however, the preponderance of organic chemical point of view has great scientists as Berzelius, Liebig etc. to consider that yeast where similar to inorganic catalysts. The oxidative process was caused by oxygen only. You may amuse yourself reading, how they attack T. Schwann proposal in Annalen, 29: 100 (1839). When O Warburg paid tribute to L. Pasteur, we can see clearly on which side he was. Furthermore, his apparatus, in which I was introduced to this line of research, a rather modern version at that time (1960s) that look like a very futuristic robotic version of the original with a pair of blinking red and green round lights as two eyes on a metallic head, offers a very important clue about the change in carbon flow.
Inside a Warburg glass flask, kept at very finely controlled temperature to avoid changes in pressure derived from changes in the temperature, you would certainly find a central well in which the volatile acid must be trapped in order to determine a pressure reduction only due to the decrease in oxygen pressure. Inside this central well, you could determine one product (carbon dioxide) and in the outside of it where tissues or cells where in the media you could also determine the other end product of the oxidative combustion of sugar (lactate). This has provide him with the result that indicate not only a change in the velocity as originally found by Pasteur in yeast cells but in the organic flow of sugar carbons.

comment –  E-mail: vbungau11@yahoo.com

-About carcinogenesis- Electronegativity is a nucleus of an atom’s ability to attract and maintain a cloud of electrons. Copper atom electronegativity is higher than the Iron atom electronegativity. Atom with lower electronegativity (Iron),remove the atom with higher electronegativity (Copper) of combinations. This means that,in conditions of acidosis, we have cytochrome oxidase with iron (red, neoplastic), instead of cytochrome oxidase with copper (green, normal).I think this is the key to carcinogenesis. Siincerely, Dr. Viorel Bungau

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Personalized Pancreatic Cancer Treatment Option

Reporter: Aviva Lev-Ari, PhD, RN

Clovis on Track to Unveil Data on New Personalized Pancreatic Cancer Treatment Option by Year End

October 10, 2012
 

Drug developer Clovis Oncology is planning to report data from a clinical trial later this year that may yield a new treatment option for pancreatic cancer patients who are poor responders to gemcitabine.

Clovis is conducting a study, called LEAP, of 360 chemotherapy-naïve metastatic pancreatic cancer patients who are randomized to receive the current standard of care gemcitabine, or the investigational CO-101, a gemcitabine-lipid conjugate. The study investigators are hypothesizing that unlike gemcitabine, CO-101 won’t depend on the expression levels of the protein cellular transporter hENT1 to enter and destroy tumor cells.

Gemcitabine, currently the first-line standard chemotherapy treatment for metastatic pancreatic cancer patients, requires a transport mechanism to help it enter tumor cells. Previously published data suggest that patients with high hENT1 expression respond well to gemcitabine, while those with low expression — about two-thirds of pancreatic cancer patients — respond poorly to the chemotherapeutic.

LEAP researchers have prospectively collected biopsy samples and have enrolled both high- and low-hENT1 expressers. Study investigators will be blind to the hENT1 expression status of patients until the end of the trial. Clovis is working with Roche subsidiary Ventana Medical Systems to simultaneously develop and validate a companion diagnostic that can gauge low and high hENT1 expression. The primary outcome that study investigators are measuring in LEAP is overall survival in the hENT1-low population.

“The question really is whether the lipid, which facilitates entry into the cell through passive diffusion, is going to be able to deliver gemcitabine as efficiently as when a nucleoside transporter is present,” Clovis CEO Patrick Mahaffy told PGx Reporter. “The answer is we don’t know, but we’ll find out in the study.”

The study may reveal that since CO-101 doesn’t depend on hENT1 to enter tumor cells, all metastatic pancreatic cancer patients, regardless of low or high expression of this protein, derive a level of benefit from the new treatment. Still, Clovis is using a companion test to stratify patients after factoring in reimbursement and cost-effectiveness considerations, which currently are perhaps the biggest barriers to the adoption of personalized treatments.

“Nothing we know suggests that we would be better than gemcitabine … in the hENT1 high population. Given the evolving reimbursement environment and the fact that gemcitabine is generic and is priced as such, pending a successful outcome we anticipate that [CO-101] would be used primarily, if not solely, in the hENT1 low population where we anticipate poor outcomes for gemcitabine,” Mahaffy said. “We anticipate that gemcitabine would continue to be the favored product on price alone even if we were to show equivalence to CO-101 in the hENT1 high population.”

Clovis Oncology will commercialize CO-101 globally. The company is currently setting up commercialization infrastructure in the US for the drug, anticipating a launch as early as next year. Clovis won’t necessarily co-promote CO-101 and the companion test with Ventana. The test developer will be in charge of commercializing the test, and Clovis will market the drug with its sales representatives, who will also be educating oncologists about the need for a companion test.

Ventana will submit its premarket approval application for the hENT1 expression test at the same time that Clovis submits its new drug application for CO-101. The test will be marketed as not just a companion diagnostic to assess whether pancreatic cancer patients have low levels of hENT1 and would therefore respond to CO-101, but Ventana will also be able to market the diagnostic as a tool to determine which high-hENT1 expressing patients should be given gemcitabine.

“The [LEAP] trial will clinically validate the diagnostic both for determining response to both gemcitabine and CO-101,” Mahaffy said.

There are around 120,000 cases of pancreatic cancer each year in the US, EU, and Japan, and around 24 percent of patients survive for one year. Around 80 percent of pancreatic cancer patients receive gemcitabine as monotherapy or in combination with other cytotoxic agents. Based on the low incidence of metastatic pancreatic cancer, Clovis has garnered Orphan Drug status for CO-101 from US and European regulatory authorities.

Although a number of retrospective trials have demonstrated that hENT1 expression levels impact outcomes in pancreatic cancer patients in the metastatic and adjuvant setting, LEAP will be the first prospective validation of this observation. “That’s why this trial is so important to the pancreatic cancer community,” Mahaffy said. “Because not only are we going to learn about CO-101, but we’re going to learn prospectively about the role hENT1 plays in determining the outcome for patients’ treatment with gemcitabine alone.”

Testing for hENT1 expression status is not widely conducted by doctors in the care of pancreatic patients. “In fact, it’s not even widely known in the broader community setting,” noted Mahaffy, adding that academic oncologists are increasingly aware of the association between hENT1 expression and gemcitabine efficacy. After LEAP concludes and if the trial is successful, Clovis plans to initiate discussions with treatment guideline-setting bodies.

In addition to looking at CO-101 as a first-line metastatic pancreatic cancer treatment in hENT1-low patients, Clovis is also studying the drug-conjugate as a second-line treatment in metastatic pancreatic cancer (Phase II), as well as in non-small cell lung cancer (Phase I).

Personalized NSCLC Drug

In addition to CO-101, Clovis has a number of investigational agents in its pipeline that it is developing in molecularly defined patient subsets. For example, CO-1686 is a selective covalent inhibitor of EGFR mutations that the firm is exploring in patients with NSCLC. Currently Clovis is conducting a dose-finding Phase I/II trial involving CO-1686 in NSCLC patients with T790M mutations. Patients with these “gatekeeper” mutations become resistant to treatment to widely prescribed EGFR-inhibiting NSCLC drugs, Roche/Genentech’s Tarceva and AstraZeneca’s Iressa.

CO-1686 “is a very potent inhibitor of T790M … [mutations in] which occur in 50 percent of lung cancer patients, after treatment with Tarceva,” Mahaffy said. After the dose-finding portion of the Phase I/II trial, Clovis plans to initiate an expansion cohort looking at T790M mutation-positive patients who are resistant to Tarceva. “If we see the kind of results we hope to in that expansion cohort, we would initiate a registration study beginning in 2014 in Tarceva-failed patients with T790M mutations,” he said.

While CO-1686 is an inhibitor of T790M mutations and other activating mutations of EGFR, the drug doesn’t inhibit wild-type EGFR like Tarceva and Iressa do, which can make NSCLC patients prone to serious side effects. “What is interesting about [CO-1686] is it is a very potent inhibitor of activating mutations of EGFR, the same targets that Tarceva or Iressa address, but unlike those drugs, [CO-1686] does not inhibit wild-type EGFR,” Mahaffy said. With CO-1686, “we should see very limited rash and diarrhea side effects associated with Tarceva and Iressa.”

First, Clovis will study CO-1686 as a second-line treatment in NSCLC patients with T790M mutations. Eventually, Clovis plans to study the drug head-to-head against Tarceva in the first-line setting. “Given the activity of our drug in animal models so far, we think we may have the ability to demonstrate superiority in terms of efficacy and from the side effects of Tarceva,” Mahaffy said. “We would hope to demonstrate in addition to a cleaner safety profile, a longer duration of benefit, because we would prevent that primary resistance mechanism in T790M from emerging.”

Roche Molecular Systems has partnered with Clovis to develop a companion diagnostic for CO-1686.

Meanwhile, last year, the European Commission approved the use of Roche/Genentech’s Tarceva as a first-line treatment for NSCLC in patients with EGFR mutations (PGx Reporter 9/7/2012). Last month, UK’s National Institute for Health and Clinical Excellence issued a draft guidance recommending that the country’s National Health Service pay for Tarceva as an option for this patient population. The company is in discussions with the US Food and Drug Administration about launching Tarceva in this population (PGx Reporter 06/08/2011).

Additionally, Boehringer Ingelheim is developing afatinib, a drug intended for advanced NSCLC patients with EGFR mutation-positive tumors (PGx Reporter 6/6/2012). Boehringer is working with Qiagen to advance a companion test for its drug.

An NGS-Based Companion Dx?

Another drug in Clovis’ pipeline is an inhibitor of PARP 1 and PARP 2, called rucaparib, which the company licensed from Pfizer. Rucaparib is currently undergoing Phase I/II trials in breast and ovarian cancer. The company is investigating the efficacy and safety of the drug in patients who lack the ability to repair damaged DNA that cancer cells need to thrive.

Mahaffy highlighted that Clovis is currently continuing a dose-finding Phase I study initiated by Pfizer combining rucaparib with carboplatin, and is conducting a Phase I trial investigating the drug as a monotherapy. This latter study will include an extension cohort of ovarian cancer patients with germline BRCA mutations.

Clovis is among a handful of drug developers, including Abbott and AstraZeneca, that are advancing PARP inhibitors with a personalized medicine strategy, betting that patients with BRCA 1/2 mutations will respond better to this class of drugs than those without these mutations. Previous studies have demonstrated that the PARP 1 enzyme and the BRCA gene work in concert to repair DNA damage, enabling survival of cancer tumors. Patients with BRCA mutations can’t repair DNA damage in this way, so then PARP inhibitors can be more effective in stopping cancer growth.

Abbott and AstraZeneca are using a companion test developed by Myriad Genetics to study their PARP inhibitors in BRCA-mutated patients with these diseases. Myriad markets BRACAnalysis, a test that gauges germline BRCA mutations associated with hereditary breast and ovarian cancer. However, gene alternations other than germline BRCA 1/2 mutations are linked to faulty DNA repair and PARP inhibitor response. For example, Clovis estimates that around 15 percent of women with ovarian cancer harbor germline BRCA 1/2 mutations, but another 8 percent of patients have somatic mutations in BRCA. Meanwhile, germline BRCA 1/2 mutations comprise only 5 percent of breast cancers.

When Pfizer was developing rucaparib, it was working with MDxHealth to explore methylation-specific markers associated with DNA damage repair and response to PARP inhibiters (PGx Reporter 2/2/2011). According to MDxHealth both methylation and mutation testing can characterize BRCA gene activity. The company previously estimated that BRCA methylation appears in about 40 percent to 50 percent of triple-negative breast cancer patients, and in about 10 percent to 30 percent in sporadic breast cancers.

Clovis has an open contract with MDxHealth looking at methylation profiles in breast and ovarian cancer, and will continue to explore this approach, specifically for methylated BRCA in triple-negative breast cancer. Additionally, Clovis is “considering the opportunity to look at both germline and somatic mutations of BRCA, based on a tissue-based assay,” Mahaffy said.

Beyond this, in August, Clovis and Foundation Medicine announced they are working together to investigate other genetic defects related to DNA repair deficiency.

“We went with Foundation Medicine … because it will allow us to reach a broader population,” Mahaffy said. For example, in ovarian cancer, Foundation Medicine’s next-generation sequencing platform could identify other mechanisms of DNA repair deficiencies that could potentially increase the intent-to-treat population for rucaparib from 15 percent of ovarian cancer patients with germline BRCA mutations to as much as 50 percent of the population that has somatic mutations in 28 additional genes that have been described as conferring “BRCA-ness” or as having a BRCA-like effect on DNA repair.

Clovis plans to develop a companion test for rucaparib on Foundation Medicine’s Foundation One targeted NGS platform. However, one challenge for Clovis is that the FDA hasn’t yet elucidated how it plans to regulate NGS-based tests. “Clearly, there is a seismic shift underway, and we may be one of the first to have plans to go forward on a premarket approval path with next-gen sequencing,” Mahaffy said. “But clearly the FDA and everyone else knows this tidal wave is coming.”

Clovis hopes to initiate a registration trial in the second half of next year looking at rucaparib as a maintenance therapy in ovarian cancer patients sensitive to platinum-based chemotherapy who have alterations in BRCA and deficiencies in other DNA repair genes. Foundation Medicine and Clovis have separately initiated discussions with the FDA about getting taking NGS-based tests through regulatory approval, Mahaffy said.

      Turna Ray is the editor of GenomeWeb’s Pharmacogenomics Reporter. She covers pharmacogenomics, personalized medicine, and companion diagnostics. E-mail her here or follow her GenomeWeb Twitter account at @PGxReporter.

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Reporter: Aviva Lev-Ari, PhD, RN

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Word Cloud By Danielle Smolyar

PTEN Mutations as a Cause of Constitutive Insulin Sensitivity and Obesity

Aparna Pal, M.R.C.P., Thomas M. Barber, D.Phil., M.R.C.P., Martijn Van de Bunt, M.D., Simon A. Rudge, Ph.D., Qifeng Zhang, Ph.D., Katherine L. Lachlan, M.R.C.P.C.H., Nicola S. Cooper, M.R.C.P., Helen Linden, M.R.C.P., Jonathan C. Levy, M.D., F.R.C.P., Michael J.O. Wakelam, Ph.D., Lisa Walker, D.Phil., M.R.C.P.C.H., Fredrik Karpe, Ph.D., F.R.C.P., and Anna L. Gloyn, D.Phil.

N Engl J Med 2012; 367:1002-1011  September 13, 2012DOI: 10.1056/NEJMoa1113966

BACKGROUND

Epidemiologic and genetic evidence links type 2 diabetes, obesity, and cancer. The tumor-suppressor phosphatase and tensin homologue (PTEN) has roles in both cellular growth and metabolic signaling. Germline PTEN mutations cause a cancer-predisposition syndrome, providing an opportunity to study the effect of PTENhaploinsufficiency in humans.

METHODS

We measured insulin sensitivity and beta-cell function in 15 PTENmutation carriers and 15 matched controls. Insulin signaling was measured in muscle and adipose-tissue biopsy specimens from 5 mutation carriers and 5 well-matched controls. We also assessed the effect of PTEN haploinsufficiency on obesity by comparing anthropometric indexes between the 15 patients and 2097 controls from a population-based study of healthy adults. Body composition was evaluated by means of dual-emission x-ray absorptiometry and skinfold thickness.

RESULTS

Measures of insulin resistance were lower in the patients with aPTEN mutation than in controls (e.g., mean fasting plasma insulin level, 29 pmol per liter [range, 9 to 99] vs. 74 pmol per liter [range, 22 to 185]; P=0.001). This finding was confirmed with the use of hyperinsulinemic euglycemic clamping, showing a glucose infusion rate among carriers 2 times that among controls (P=0.009). The patients’ insulin sensitivity could be explained by the presence of enhanced insulin signaling through the PI3K-AKT pathway, as evidenced by increased AKT phosphorylation. The PTEN mutation carriers were obese as compared with population-based controls (mean body-mass index [the weight in kilograms divided by the square of the height in meters], 32 [range, 23 to 42] vs. 26 [range, 15 to 48]; P<0.001). This increased body mass in the patients was due to augmented adiposity without corresponding changes in fat distribution.

CONCLUSIONS

PTEN haploinsufficiency is a monogenic cause of profound constitutive insulin sensitization that is apparently obesogenic. We demonstrate an apparently divergent effect of PTEN mutations: increased risks of obesity and cancer but a decreased risk of type 2 diabetes owing to enhanced insulin sensitivity. (Funded by the Wellcome Trust and others.)

Supported by grants from the Wellcome Trust (095101/Z/10Z, to Dr. Gloyn), the Medical Research Council (G0700222, to Dr. Gloyn; and G0800467, to Drs. Pal and Gloyn), the National Institute for Health Research Oxford Biomedical Research Centre (to Drs. Pal, Karpe, and Gloyn), the Biotechnology and Biological Sciences Research Council (to Drs. Rudge, Zhang, and Wakelam), and the European Union Seventh Framework Program LipodomicNet (202272, for adipocyte signaling work, to Drs. Wakelam and Karpe).

Disclosure forms provided by the authors are available with the full text of this article at NEJM.org.

We thank the clinicians Trevor R.P. Cole, Louise Izatt, Carole McKeown, Eamonn R. Maher, and Mary Porteous for referring patients for this study; the research nurses Beryl Barrow and Jane Cheeseman for assistance with collecting clinical data; Amy Barrett for analysis of PTEN expression; Sandy Humphries for analysis of apolipoprotein B; Tim James and colleagues at the John Radcliffe Hospital, Oxford, for analysis of glucose and insulin; the NIHR Cambridge Biomedical Research Centre Core Biochemical Assay Laboratory for analysis of leptin and adiponectin; Leanne Hodson and Barbara Fielding for access to control dual-emission x-ray absorptiometry scans and phenotypic data on postmenopausal controls; and Jonathan Clark and Izabella Niewczas for providing lipid standards for the mass-spectrometry analysis.

SOURCE INFORMATION

From the Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford (A.P., T.M.B., M.V.B., J.C.L., F.K., A.L.G.); the Oxford National Institute for Health Research Biomedical Research Centre (A.P., J.C.L., F.K., A.L.G.) and the Oxford Regional Genetics Centre (H.L., L.W.), Churchill Hospital, Oxford; the Inositide Laboratory, the Babraham Institute, Babraham, Cambridge (S.A.R., Q.Z., M.J.O.W.); Wessex Clinical Genetics Service, University Hospital Southampton, Southampton (K.L.L.); the Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton (K.L.L.); and West Midlands Regional Clinical Genetics Service, Birmingham Women’s Hospital, Birmingham (N.S.C.) — all in the United Kingdom.

Address reprint requests to Dr. Gloyn at the Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LE, United Kingdom, or atanna.gloyn@drl.ox.ac.uk.

 Source:

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Author: Margaret Baker, PhD, Registered Patent Agent

The Encyclopedia of DNA Elements (ENCODE) Project was launched in September of 2003. In 2007 the ENCODE project was expanded to study the entire human genome, Genome-wide association studies or GWAS, and published a Nature paper entitled “An integrated encyclopedia of DNA elements in the human genome,” this month also all data are available at http://genome.ucsc.edu/ENCODE/.  Novel functional roles have been discovered for both transcribed and non-transcribed portions of DNA.  See several articles and commentary in Science 7 September 2012: Vol. 337 no. 6099 including Maurano et al. pp. 1190-1195  DOI: 10.1126/science.1222794b

For the first time, the 3-dimensional connections that cross the genome have been mapped as long-range looping interactions between functional elements and the genes controlled. These regions of the genome, formerly referred to as “junk DNA”, have the potential to be involved in disease initiation, pathophysiology, and complications. Further, epigenetic factors may be seen to play a more direct role in the expression or silencing of protein coding genes as DNase I hot spots, nucleosomal anchor points, and DNA methylation sites are added to the map.

Non-coding transcribed DNA includes a large percentage of sequences coding for RNA. In fact, RNA encoding genes number nearly equal to the protein encoding genes- 18,400 v 20,687 – and previously unknown non-coding RNA (ncRNA) have also been characterized.

Some of the known elements that were cataloged include:

  • cis elements – promoters, transcription factor binding sites;
  • gene contiguous non-coding stretches such as introns, polyA, and UTR, splice variants;
  • pseudogenes (11,224);
  • long range gene associated elements – enhancers, insulators, suppressors, and predicted promoter flanking regions;
  • ribosomal RNA genes; and
  • sequences for 7,052 small RNAs of which 85% are small nuclear(sn)RNA, small nucleolar(sno)RNA), transfer(t)RNA, and micro(mi)RNA.

What has been found is that distinct non-coding regions, including ncRNA, can be associated with distinct disease traits. miRNA are among the non-gene encoding sequences in the genome which have already been shown to play a major post-transcriptional role in expression of multiple genes..

Most miRNA genes are intergenic or oriented antisense to neighboring genes and therefore assumed to be controlled by independent promoter units. However, in some cases a microRNA gene is transcribed together with its target gene implying coupled regulation of miRNA and protein-coding gene. About one third of miRNA genes reside in polycistronic clusters. miRNA genes can occupy the introns of protein, non-protein coding genes, or nonprotein-coding transcripts. The promoters have been shown to have some similarities in their motifs to promoters of other genes transcribed by RNA polymerase II such as protein coding genes. The ENCODE project also noted that miRNA promoters were in chromatin regions of high promiscuity. There may be up to 1000 miRNA genes in the human genome. In addition, human miRNAs show RNA editing of sequences to yield products different from those encoded by their DNA.  miRNA are implicated in cellular roles as diverse as developmental timing in worms, cell death and fat metabolism in flies, haematopoiesis in mammals, and leaf development and floral patterning in plants

The final miRNA gene product is a ∼22 nt functional RNA molecule. The mature miRNA (designated miR-#) is processed from a characteristic stem–loop sequence (called a pre-mir), which in turn may be excised from a longer primary transcript (or pri-mir). It is processed by the same enzyme (DICER) that processes short hairpin RNA, forming interfering RNA, which provides and additional level of control.

MiRNA controls gene expression by binding to complementary regions of messenger transcripts in the 3’ untranslated region to repress their translation or regulate degradation. What makes the mechanism more powerful (or complicated) is the imperfect but specific binding motif associates with a large number of mRNAs in the 3’ untranslated region having the complimentary motif.  Conversely then, each mRNA can potentially associate with a number miRNA. Mature processed cytosolic miRNA can act in a manner akin to small interfering(si)RNA, and form the RNA-induced silencing complex (RISC) to block translation. Computational methods have been used to identify potential gene targets based on complimentarity between the miRNA and mRNA sequences.

Gerstein et al. explored the “Architecture of the human regulatory network derived from ENCODE data” Nature 489:91-100 (06 Sep 2012) focusing on the regulation of transcription factors (TF) and association between TF and miRNAs, miRNA and miRNA, protein-protein interactions, and protein phosphorylation. Not surprisingly, not all TF are the upstream factor in each network.

These new and remarkably detailed examinations of the different elements within and transcribed from the human genome perhaps do more to aid our knowledge of why we have stumbled in attempts to eradicate diseases, initially by focusing on a single gene or constellation of coding regions. The miRNA wikipedia is also being re-written on a daily basis and new disease associations made*.  As an example of a pathological state that may be linked to miRNA controlled elements, in vitro as well as in small population studies have examined miRNA species in diabetogenic conditions and patients with diabetes (Type I and Type II).

Diabetes and miRNA

In adult β-cell islets, miR-375 is low when glucose is freely available and low miR-375 induces insulin secretion. Interestingly, miR-375 is found only in brain and β-cells which share a secretion pathway.

Diabetic Complications

Organ specific miRNA have been identified in liver, skeletal muscle, kidney, vascular, and adipose tissue which are responsive to transient or sustained hyperglycemia.

miR-17-5p and miR-132 were reported to show significant differences between obese and non obese omental fat and were also abnormal in the blood of obese subjects.  Altered expression of miR-17-5p and miR-132 were found to correlate significantly with BMI, fasting blood glucose and glycosylated hemoglobin. (Kloting et al. PLoS ONE 4(3), e4699 (2009).

Clinical practice related to miRNA in diabetes may be possible as one group has identified eight miRNAs (miR-144, miR-146a, miR-150, miR-182, miR-192, miR-29a, miR-30d and miR-320) as potential ‘signature miRNAs’ that could distinguish prediabetic patients from those with overt T2D (Karolina DS, Armugam A, Tavintharan S et al. MicroRNA 144 impairs insulin signaling by inhibiting the expression of insulin receptor substrate 1 in Type 2 diabetes mellitus. PLoS ONE 6(8), e22839 (2011).

Due to the autoimmune component of T1D, the constellation of miRNA would be expected to be different: upregulation of miR-510 and underexpression of miR-191 and miR-342 were observed in the Tregs (regulatory T-cells) of T1D patients (Hezova R, Slaby O, Faltejskova P et al. microRNA-342, microRNA-191 and microRNA-510 are differentially expressed in T regulatory cells of Type 1 diabetic patients. Cell. Immunol. 260(2),70–74 (2010).

Taken together with the “physical” mapping of miRNA genes in the context of the 3-dimensional genome provided by the ENCODE studies and new understanding of potential concerted regulatory mechanisms, the miRNA data for tissues and specific cell types involved in disease pathology form a new approach to either detecting or possibly correcting gene (coding or non-coding) dysregulation.  miRNA mimics and anti-miRNA agents are being developed as new therapeutic modalities.

References

Bartel, DP et al. MicroRNAs: Genomics, Biogenesis, Mechanism, and Function” Cell 2004, 116:281-297.

Fernandez-Valverde, SL et al. MicroRNAs in beta-cell Biology, insulin resistance, diabetes and its complications. Diabetes July 2011 60 (7):1825-31.

Kantharidis, et al.  Diabetes Complications: The MicroRNA Perspective http://diabetes.diabetesjournals.org/content/60/7/1832.short

MEDSCAPE Review article: “miRNAs and Diabetes Mellitus: miRNAs in Diabetic Complicatons”  http://www.medscape.org/viewarticle/763729_6

*Based on initial studies in the worm C. elegans showing the temporal appearance of 21- and 22-nt RNAs during development, a family of highly conserved micro RNA sequences (miRNA) existing in invertebrates and vertebrates, were cataloged by Tuschl et al. at the Max-Planck-Institute and others (see Eddy, SR  Non-coding RNA genes and the modern RNA world Nature Reviews Genetics, 2:920-929, 2001). The sequence-specific post-transcriptional regulatory mechanisms mediated by these miRNAs have been associated with certain disease states such as cancer miR-21) and more specifically, lung cancer (miR-124) or breast cancer (miR-7, miR-21) and new species and function continue to be found (see http://www.mirbase.org/ ).

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Expanding the Genetic Alphabet and Linking the Genome to the Metabolome

English: The citric acid cycle, also known as ...

English: The citric acid cycle, also known as the tricarboxylic acid cycle (TCA cycle) or the Krebs cycle. Produced at WikiPathways. (Photo credit: Wikipedia)

Expanding the Genetic Alphabet and Linking the Genome to the Metabolome

 

Reporter& Curator:  Larry Bernstein, MD, FCAP

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Unlocking the diversity of genomic expression within tumorigenesis and “tailoring” of therapeutic options

1. Reshaping the DNA landscape between diseases and within diseases by the linking of DNA to treatments

In the NEW York Times of 9/24,2012 Gina Kolata reports on four types of breast cancer and the reshaping of breast cancer DNA treatment based on the findings of the genetically distinct types, which each have common “cluster” features that are driving many cancers.  The discoveries were published online in the journal Nature on Sunday (9/23).  The study is considered the first comprehensive genetic analysis of breast cancer and called a roadmap to future breast cancer treatments.  I consider that if this is a landmark study in cancer genomics leading to personalized drug management of patients, it is also a fitting of the treatment to measurable “combinatorial feature sets” that tie into population biodiversity with respect to known conditions.   The researchers caution that it will take years to establish transformative treatments, and this is clearly because in the genetic types, there are subsets that have a bearing on treatment “tailoring”.   In addition, there is growing evidence that the Watson-Crick model of the gene is itself being modified by an expansion of the alphabet used to construct the DNA library, which itself will open opportunities to explain some of what has been considered junk DNA, and which may carry essential information with respect to metabolic pathways and pathway regulation.  The breast cancer study is tied to the  “Cancer Genome Atlas” Project, already reported.  It is expected that this work will tie into building maps of genetic changes in common cancers, such as, breast, colon, and lung.  What is not explicit I presume is a closely related concept, that the translational challenge is closely related to the suppression of key proteomic processes tied into manipulating the metabolome.

Saha S. Impact of evolutionary selection on functional regions: The imprint of evolutionary selection on ENCODE regulatory elements is manifested between species and within human populations. 9/12/2012. PharmaceuticalIntelligence.Wordpress.com

Hawrylycz MJ, Lein ES, Guillozet-Bongaarts AL, Shen EH, Ng L, et al. An anatomically comprehensive atlas of the adult human brain transcriptome. Nature  Sept 14-20, 2012

Sarkar A. Prediction of Nucleosome Positioning and Occupancy Using a Statistical Mechanics Model. 9/12/2012. PharmaceuticalIntelligence.WordPress.com

Heijden et al.   Connecting nucleosome positions with free energy landscapes. (Proc Natl Acad Sci U S A. 2012, Aug 20 [Epub ahead of print]).  http://www.ncbi.nlm.nih.gov/pubmed/22908247

2. Fiddling with an expanded genetic alphabet – greater flexibility in design of treatment (pharmaneogenesis?)

Diagram of DNA polymerase extending a DNA stra...

Diagram of DNA polymerase extending a DNA strand and proof-reading. (Photo credit: Wikipedia)

A clear indication of this emerging remodeling of the genetic alphabet is a new
study led by scientists at The Scripps Research Institute appeared in the
June 3, 2012 issue of Nature Chemical Biology that indicates the genetic code as
we know it may be expanded to include synthetic and unnatural sequence pairing (Study Suggests Expanding the Genetic Alphabet May Be Easier than Previously Thought, Genome). They infer that the genetic instructions for living organisms
that is composed of four bases (C, G, A and T)— is open to unnatural letters. An expanded “DNA alphabet” could carry more information than natural DNA, potentially coding for a much wider range of molecules and enabling a variety of powerful applications. The implications of the application of this would further expand the translation of portions of DNA to new transciptional proteins that are heretofore unknown, but have metabolic relavence and therapeutic potential. The existence of such pairing in nature has been studied in Eukariotes for at least a decade, and may have a role in biodiversity. The investigators show how a previously identified pair of artificial DNA bases can go through the DNA replication process almost as efficiently as the four natural bases.  This could as well be translated into human diversity, and human diseases.

The Romesberg laboratory collaborated on the new study and his lab have been trying to find a way to extend the DNA alphabet since the late 1990s. In 2008, they developed the efficiently replicating bases NaM and 5SICS, which come together as a complementary base pair within the DNA helix, much as, in normal DNA, the base adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G). It had been clear that their chemical structures lack the ability to form the hydrogen bonds that join natural base pairs in DNA. Such bonds had been thought to be an absolute requirement for successful DNA replication, but that is not the case because other bonds can be in play.

The data strongly suggested that NaM and 5SICS do not even approximate the edge-to-edge geometry of natural base pairs—termed the Watson-Crick geometry, after the co-discoverers of the DNA double-helix. Instead, they join in a looser, overlapping, “intercalated” fashion that resembles a ‘mispair.’ In test after test, the NaM-5SICS pair was efficiently replicable even though it appeared that the DNA polymerase didn’t recognize it. Their structural data showed that the NaM-5SICS pair maintain an abnormal, intercalated structure within double-helix DNA—but remarkably adopt the normal, edge-to-edge, “Watson-Crick” positioning when gripped by the polymerase during the crucial moments of DNA replication. NaM and 5SICS, lacking hydrogen bonds, are held together in the DNA double-helix by “hydrophobic” forces, which cause certain molecular structures (like those found in oil) to be repelled by water molecules, and thus to cling together in a watery medium.

The finding suggests that NaM-5SICS and potentially other, hydrophobically bound base pairs could be used to extend the DNA alphabet and that Evolution’s choice of the existing four-letter DNA alphabet—on this planet—may have been developed allowing for life based on other genetic systems.

3.  Studies that consider a DNA triplet model that includes one or more NATURAL nucleosides and looks closely allied to the formation of the disulfide bond and oxidation reduction reaction.

This independent work is being conducted based on a similar concep. John Berger, founder of Triplex DNA has commented on this. He emphasizes Sulfur as the most important element for understanding evolution of metabolic pathways in the human transcriptome. It is a combination of sulfur 34 and sulphur 32 ATMU. S34 is element 16 + flourine, while S32 is element 16 + phosphorous. The cysteine-cystine bond is the bridge and controller between inorganic chemistry (flourine) and organic chemistry (phosphorous). He uses a dual spelling, using  sulfphur to combine the two referring to the master catalyst of oxidation-reduction reactions. Various isotopic alleles (please note the duality principle which is natures most important pattern). Sulfphur is Methionine, S adenosylmethionine, cysteine, cystine, taurine, gluthionine, acetyl Coenzyme A, Biotin, Linoic acid, H2S, H2SO4, HSO3-, cytochromes, thioredoxin, ferredoxins, purple sulfphur anerobic bacteria prokaroytes, hydrocarbons, green sulfphur bacteria, garlic, penicillin and many antibiotics; hundreds of CSN drugs for parasites and fungi antagonists. These are but a few names which come to mind. It is at the heart of the Krebs cycle of oxidative phosphorylation, i.e. ATP. It is also a second pathway to purine metabolism and nucleic acids. It literally is the key enzymes between RNA and DNA, ie, SH thiol bond oxidized to SS (dna) cysteine through thioredoxins, ferredoxins, and nitrogenase. The immune system is founded upon sulfphur compounds and processes. Photosynthesis Fe4S4 to Fe2S3 absorbs the entire electromagnetic spectrum which is filtered by the Allen belt some 75 miles above earth. Look up chromatium vinosum or allochromatium species.  There is reasonable evidence it is the first symbiotic species of sulfphur anerobic bacteria (Fe4S4) with high potential mvolts which drives photosynthesis while making glucose with H2S.
He envisions a sulfphur control map to automate human metabolism with exact timing sequences, at specific three dimensional coordinates on Bravais crystalline lattices. He proposes adding the inosine-xanthosine family to the current 5 nucleotide genetic code. Finally, he adds, the expanded genetic code is populated with “synthetic nucleosides and nucleotides” with all kinds of customized functional side groups, which often reshape nature’s allosteric and physiochemical properties. The inosine family is nature’s natural evolutionary partner with the adenosine and guanosine families in purine synthesis de novo, salvage, and catabolic degradation. Inosine has three major enzymes (IMPDH1,2&3 for purine ring closure, HPGRT for purine salvage, and xanthine oxidase and xanthine dehydrogenase.

English: DNA replication or DNA synthesis is t...

English: DNA replication or DNA synthesis is the process of copying a double-stranded DNA molecule. This process is paramount to all life as we know it. (Photo credit: Wikipedia)

3. Nutritional regulation of gene expression,  an essential role of sulfur, and metabolic control 

Finally, the research carried out for decades by Yves Ingenbleek and the late Vernon Young warrants mention. According to their work, sulfur is again tagged as essential for health. Sulfur (S) is the seventh most abundant element measurable in human tissues and its provision is mainly insured by the intake of methionine (Met) found in plant and animal proteins. Met is endowed with unique functional properties as it controls the ribosomal initiation of protein syntheses, governs a myriad of major metabolic and catalytic activities and may be subjected to reversible redox processes contributing to safeguard protein integrity.

Consuming diets with inadequate amounts of methionine (Met) are characterized by overt or subclinical protein malnutrition, and it has serious morbid consequences. The result is reduction in size of their lean body mass (LBM), best identified by the serial measurement of plasma transthyretin (TTR), which is seen with unachieved replenishment (chronic malnutrition, strict veganism) or excessive losses (trauma, burns, inflammatory diseases).  This status is accompanied by a rise in homocysteine, and a concomitant fall in methionine.  The ratio of S to N is quite invariant, but dependent on source.  The S:N ratio is typical 1:20 for plant sources and 1:14.5 for animal protein sources.  The key enzyme involved with the control of Met in man is the enzyme cystathionine-b-synthase, which declines with inadequate dietary provision of S, and the loss is not compensated by cobalamine for CH3- transfer.

As a result of the disordered metabolic state from inadequate sulfur intake (the S:N ratio is lower in plants than in animals), the transsulfuration pathway is depressed at cystathionine-β-synthase (CβS) level triggering the upstream sequestration of homocysteine (Hcy) in biological fluids and promoting its conversion to Met. They both stimulate comparable remethylation reactions from homocysteine (Hcy), indicating that Met homeostasis benefits from high metabolic priority. Maintenance of beneficial Met homeostasis is counterpoised by the drop of cysteine (Cys) and glutathione (GSH) values downstream to CβS causing reducing molecules implicated in the regulation of the 3 desulfuration pathways

4. The effect on accretion of LBM of protein malnutrition and/or the inflammatory state: in closer focus

Hepatic synthesis is influenced by nutritional and inflammatory circumstances working concomitantly and liver production of  TTR integrates the dietary and stressful components of any disease spectrum. Thus we have a depletion of visceral transport proteins made by the liver and fat-free weight loss secondary to protein catabolism. This is most accurately reflected by TTR, which is a rapid turnover protein, but it is involved in transport and is essential for thyroid function (thyroxine-binding prealbumin) and tied to retinol-binding protein. Furthermore, protein accretion is dependent on a sulfonation reaction with 2 ATP.  Consequently, Kwashiorkor is associated with thyroid goiter, as the pituitary-thyroid axis is a major sulfonation target. With this in mind, it is not surprising why TTR is the sole plasma protein whose evolutionary patterns closely follow the shape outlined by LBM fluctuations. Serial measurement of TTR therefore provides unequaled information on the alterations affecting overall protein nutritional status. Recent advances in TTR physiopathology emphasize the detecting power and preventive role played by the protein in hyper-homocysteinemic states.

Individuals submitted to N-restricted regimens are basically able to maintain N homeostasis until very late in the starvation processes. But the N balance study only provides an overall estimate of N gains and losses but fails to identify the tissue sites and specific interorgan fluxes involved. Using vastly improved methods the LBM has been measured in its components. The LBM of the reference man contains 98% of total body potassium (TBK) and the bulk of total body sulfur (TBS). TBK and TBS reach equal intracellular amounts (140 g each) and share distribution patterns (half in SM and half in the rest of cell mass). The body content of K and S largely exceeds that of magnesium (19 g), iron (4.2 g) and zinc (2.3 g).

TBN and TBK are highly correlated in healthy subjects and both parameters manifest an age-dependent curvilinear decline with an accelerated decrease after 65 years. Sulfur Methylation (SM) undergoes a 15% reduction in size per decade, an involutive process. The trend toward sarcopenia is more marked and rapid in elderly men than in elderly women decreasing strength and functional capacity. The downward SM slope may be somewhat prevented by physical training or accelerated by supranormal cytokine status as reported in apparently healthy aged persons suffering low-grade inflammation or in critically ill patients whose muscle mass undergoes proteolysis.

5.  The results of the events described are:

  • Declining generation of hydrogen sulfide (H2S) from enzymatic sources and in the non-enzymatic reduction of elemental S to H2S.
  • The biogenesis of H2S via non-enzymatic reduction is further inhibited in areas where earth’s crust is depleted in elemental sulfur (S8) and sulfate oxyanions.
  • Elemental S operates as co-factor of several (apo)enzymes critically involved in the control of oxidative processes.

Combination of protein and sulfur dietary deficiencies constitute a novel clinical entity threatening plant-eating population groups. They have a defective production of Cys, GSH and H2S reductants, explaining persistence of an oxidative burden.

6. The clinical entity increases the risk of developing:

  • cardiovascular diseases (CVD) and
  • stroke

in plant-eating populations regardless of Framingham criteria and vitamin-B status.
Met molecules supplied by dietary proteins are submitted to transmethylation processes resulting in the release of Hcy which:

  • either undergoes Hcy — Met RM pathways or
  • is committed to transsulfuration decay.

Impairment of CβS activity, as described in protein malnutrition, entails supranormal accumulation of Hcy in body fluids, stimulation of activity and maintenance of Met homeostasis. The data show that combined protein- and S-deficiencies work in concert to deplete Cys, GSH and H2S from their body reserves, hence impeding these reducing molecules to properly face the oxidative stress imposed by hyperhomocysteinemia.

Although unrecognized up to now, the nutritional disorder is one of the commonest worldwide, reaching top prevalence in populated regions of Southeastern Asia. Increased risk of hyperhomocysteinemia and oxidative stress may also affect individuals suffering from intestinal malabsorption or westernized communities having adopted vegan dietary lifestyles.

Ingenbleek Y. Hyperhomocysteinemia is a biomarker of sulfur-deficiency in human morbidities. Open Clin. Chem. J. 2009 ; 2 : 49-60.

7. The dysfunctional metabolism in transitional cell transformation

A third development is also important and possibly related. The transition a cell goes through in becoming cancerous tends to be driven by changes to the cell’s DNA. But that is not the whole story. Large-scale techniques to the study of metabolic processes going on in cancer cells is being carried out at Oxford, UK in collaboration with Japanese workers. This thread will extend our insight into the metabolome. Otto Warburg, the pioneer in respiration studies, pointed out in the early 1900s that most cancer cells get the energy they need predominantly through a high utilization of glucose with lower respiration (the metabolic process that breaks down glucose to release energy). It helps the cancer cells deal with the low oxygen levels that tend to be present in a tumor. The tissue reverts to a metabolic profile of anaerobiosis.  Studies of the genetic basis of cancer and dysfunctional metabolism in cancer cells are complementary. Tomoyoshi Soga’s large lab in Japan has been at the forefront of developing the technology for metabolomics research over the past couple of decades (metabolomics being the ugly-sounding term used to describe research that studies all metabolic processes at once, like genomics is the study of the entire genome).

Their results have led to the idea that some metabolic compounds, or metabolites, when they accumulate in cells, can cause changes to metabolic processes and set cells off on a path towards cancer. The collaborators have published a perspective article in the journal Frontiers in Molecular and Cellular Oncology that proposes fumarate as such an ‘oncometabolite’. Fumarate is a standard compound involved in cellular metabolism. The researchers summarize that shows how accumulation of fumarate when an enzyme goes wrong affects various biological pathways in the cell. It shifts the balance of metabolic processes and disrupts the cell in ways that could favor development of cancer.  This is of particular interest because “fumarate” is the intermediate in the TCA cycle that is converted to malate.

Animation of the structure of a section of DNA...

Animation of the structure of a section of DNA. The bases lie horizontally between the two spiraling strands. (Photo credit: Wikipedia)

The Keio group is able to label glucose or glutamine, basic biological sources of fuel for cells, and track the pathways cells use to burn up the fuel.  As these studies proceed, they could profile the metabolites in a cohort of tumor samples and matched normal tissue. This would produce a dataset of the concentrations of hundreds of different metabolites in each group. Statistical approaches could suggest which metabolic pathways were abnormal. These would then be the subject of experiments targeting the pathways to confirm the relationship between changed metabolism and uncontrolled growth of the cancer cells.

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Reporter: Aviva Lev-Ari, PhD, RN

Glucose in the ICU — Evidence, Guidelines, and Outcomes

Brian P. Kavanagh, M.B., F.R.C.P.C.

September 7, 2012 (10.1056/NEJMe1209429)

Just over a decade ago, a single-center Belgian study showed that normalization of blood glucose in critically ill patients lowered hospital mortality by more than 30%.1 Although subsequent studies were unable to reproduce these findings, the appeal of such a straightforward intervention was too great to resist: guidelines from professional organizations2,3 were published, and editorial commentary4 highlighted initiatives by the Institute for Healthcare Improvement, the Joint Commission on Accreditation of Healthcare Organizations, and the Volunteer Hospital Association that incorporated tight glucose control as a standard. Indeed, the prestigious Codman Award of the Joint Commission was presented in 2004 for a program of glycemic control in critical care that “saved” patients’ lives.5 Tight glucose control for critically ill patients was in vogue.

The publication in 2009 of a large international trial (the Normoglycemia in Intensive Care Evaluation–Survival Using Glucose Algorithm Regulation [NICE-SUGAR] study6) followed that of several negative trials. The NICE-SUGAR study, which involved more than 6100 patients, showed that tight glycemic control didn’t decrease mortality — it increased it. Most guidelines were hastily revised. However, in the same year a separate study by Vlasselaers et al.7 in pediatric intensive care unit (ICU) patients, most of whom had undergone cardiac surgery, showed that normalizing glucose decreased mortality from 6% to 3%, keeping open the question — at least in critically ill children.

The study by Agus et al.8 now reported in the Journal provides new key data. A total of 980 children (up to 36 months of age) admitted to an ICU after cardiac surgery were randomly assigned to usual care or tight glucose control. The results are clear — there was no significant difference in the incidence of health care–associated infections (the primary outcome) or in any of the secondary outcomes, including survival. Moreover, the rate of hypoglycemia (blood glucose level <40 mg per deciliter [2.2 mmol per liter]) in the intervention group (3%) was far less than that previously reported (25%).7 These findings contrast sharply with those of Vlasselaers et al.,7 who found that secondary infections, length of stay, and mortality were reduced. Faced with contradictory results from two large clinical trials, how does the clinician know which results are correct?

First, biologic plausibility is important in attributing a survival benefit to a specific intervention. In the first pediatric ICU study, the additional deaths in the control group did not appear to be due to causes related to hyperglycemia,7 a finding that suggests that the benefit was unlikely to be reproducible. The current authors, exclusively studying children after cardiac surgery, recognized that mortality in this population is usually due to prohibitive anatomy or surgical challenge; these are circumstances not amenable to correction by metabolic control.

Second, might differences in the target plasma glucose explain the discrepant findings? Agus et al. aimed for a higher target range of plasma glucose in the intervention group (80 to 110 mg per deciliter [4.4 to 6.1 mmol per liter]) than was targeted in the first pediatric study (infants, 50 to 80 mg per deciliter [2.8 to 4.4 mmol per liter]; children, 70 to 100 mg per deciliter [3.9 to 5.6 mmol per liter]).7 Perhaps the lower glucose target is preferable? The weight of evidence is against this, and if this target were used, the incidence and severity of hypoglycemia would have been greater, as previously reported.7 Hypoglycemia is never to a patient’s benefit, and its negative impact on neurocognitive development in children is of particular concern.

It seems that — as in adults — claims for survival benefit in critically ill children are incorrect. Furthermore, there is no reason why the effects of glucose control in children would be opposite to those in adults. In aggregate, the data do not support a basis for embarking on a pediatric megatrial.

Assuming the results of the NICE-SUGAR study6 are generalizable, we must be grateful for the future lives saved by avoiding the practice of normalizing glucose in the ICU. At the same time, we should reflect on why a large study with mortality as an end point was needed in the first place.

Perhaps the most important question from a decade of studying glucose control in the ICU is how influential practice guidelines advocating tight glucose control were developed2,3 yet turned out to be harmful — an issue noted in the lay press.9 Guideline writers, reflecting on the experience, must accept that there are multiple sources of clinical knowledge10 and must pay careful attention to trial characteristics — especially study reproducibility — in order to provide advice that genuinely helps clinicians. Clinicians in turn should use guidelines wisely, recognizing that no single source of knowledge is sufficient to guide clinical decisions.10

Is the door closed on studying glucose homeostasis in the critically ill? No, but it should be closed on the routine normalization of plasma glucose in critically ill adults and children.

Disclosure forms provided by the author are available with the full text of this article at NEJM.org.

This article was published on September 7, 2012, at NEJM.org.

SOURCE INFORMATION

From the Department of Critical Care Medicine and Anesthesia, Hospital for Sick Children, University of Toronto, Toronto.

Source:

http://www.nejm.org/doi/full/10.1056/NEJMe1209429?query=OF

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