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Mitochondria: Origin from oxygen free environment, role in aerobic glycolysis, metabolic adaptation

Posted in Biological Networks, Gene Regulation and Evolution, Biomarkers & Medical Diagnostics, CANCER BIOLOGY & Innovations in Cancer Therapy, Cardiovascular Pharmacogenomics, Cell Biology, Signaling & Cell Circuits, Chemical Biology and its relations to Metabolic Disease, Computational Biology/Systems and Bioinformatics, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Genome Biology, Glycobiology: Biopharmaceutical Production, Pharmacodynamics and Pharmacokinetics, International Global Work in Pharmaceutical, Metabolomics, Molecular Genetics & Pharmaceutical, Nutrigenomics, Nutrition, Personalized and Precision Medicine & Genomic Research, Pharmacotherapy of Cardiovascular Disease, Population Health Management, Genetics & Pharmaceutical, Population Health Management, Nutrition and Phytochemistry, Scientist: Career considerations, Systemic Inflammatory Response Related Disorders, Technology Transfer: Biotech and Pharmaceutical, tagged Acetyl-CoA, Adenosine triphosphate, anaerobic and aerobic gycolysis, ATP, ATP demands, Cellular respiration, Citric acid cycle, fermentation, gluconeogenesis, hydrophobic interaction, N:S, overflow at branch points, oxidative stress, Pasteur effect, PFK 2, plant protein diet, protein calorie malnutrition, pyruvate dehydrogenase, Saccharomyces cerevisiae, SIRT3, synthetic small DNA ligands, TCA cycle intermediates, Warburg Effect on September 26, 2012| 26 Comments »

 

English: A diagram of cellular respiration including glycolysis, Krebs cycle, citric acid cycle, and the electron transport chain (Photo credit: Wikipedia)

Reporter and Curator: Larry H Bernstein, MD, FACP

Introduction

Mitochondria are essential for life, and are critical for the generation of ATP. Otto Warburg won the Nobel Prize in 1918 for his studies of respiration and he described a situation of impaired respiration in cancer cells causing them to produce lactic acid, like bacteria. This has been termed facultative anaerobic glycolysis. The metabolic explanation for mitochondrial respiration had to await the Nobel discoveries of the Krebs cycle and high energy ~P in acetyl CoA by Fritz Lippman. The Krebs cycle generates 16 ATPs I respiration compared to 2 ATPs through glycolysis. The discovery of the genetic code with the “Watson-Crick” model and the identification of DNA polymerase opened a window for contuing discovery leading to the human genome project at 20th century end that has now been followed by “ENCODE” in the 21st century. This review opens a rediscovery of the metabolic function of mitochondria and adaptive functions with respect to cancer and other diseases.

Function in aerobic and anaerobic metabolism

Two-carbon compounds – the TCA, the pentose phosphate pathway, together with gluconeogenesis and the glyoxylate cycle are essential for the provision of anabolic precursors. Yeast environmental diversity mostly leads to a vast metabolic complexity driven by carbon and the energy available in environmental habitats. This resulted in much early research on analysis of yeast metabolism associated with glucose catabolism in Saccharomyces cerevisiae, under both aerobic and anaerobic environments. Yeasts may be physiologically classified with respect to the type of energy-generating process involved in sugar metabolism, namely non-, facultative- or obligate fermentative. The nonfermentative yeasts have exclusively a respiratory metabolism and are not capable of alcoholic fermentation from glucose, while the obligate-fermentative yeasts – “natural respiratory mutants” – are only capable of metabolizing glucose through alcoholic fermentation. Most of the yeasts identified are facultative-fermentative ones, and depending on the growth conditions, the type and concentration of sugars and/or oxygen availability, may display either a fully respiratory or a fermentative metabolism or even both in a mixed respiratory-fermentative metabolism (e.g., S. cerevisiae). The sugar composition of the media and oxygen availability are the two main environmental conditions that have a strong impact on yeast metabolic physiology, and three frequently observed effects associated with the type of energy-generating processes involved in sugar metabolism and/or oxygen availability are Pasteur, Crabtree and Custer. In modern terms the Pasteur effect refers to an activation of anaerobic glycolysis in order to meet cellular ATP demands owing to the lower efficiency of ATP production by fermentation compared with respiration. In 1861 Pasteur observed that S. cerevisiae consume much more glucose in the absence of oxygen than in its presence. S. cerevisiae only shows a Pasteur at low growth rates and at resting-cell conditions, where a high contribution of respiration to sugar catabolism occurs owing to the loss of fermentative capacity. The Crabtree effect is defined as the occurrence of alcoholic fermentation under aerobic conditions, explained by a theory involving “limited respiratory capacities” in the branching point of pyruvate metabolism. The Custer effect is known as the inhibition of alcoholic fermentation by the absence of oxygen. It is thought that the Custer effect is caused by reductive stress.

Glycolysis

Once inside the cell, glucose is phosphorylated by kinases to glucose 6-phosphate and then isomerized to fructose 6-phosphate, by phosphoglucose isomerase. The next enzyme is phospho-fructokinase, which is subject to regulation by several metabolites, and further phosphorylates fructose 6-phosphate to fructose 1,6-bisphosphate. These steps of glycolysis require energy in the form of ATP. Glycolysis leads to pyruvate formation associated with a net production of energy and reducing equivalents. Approximately 50% of glucose 6-phosphate is metabolized via glycolysis and 30% via the pentose phosphate pathway in Crabtree negative yeasts. However, about 90% of the carbon going through the pentose phosphate pathway reentered glycolysis at the level of fructose 6-phosphate or glyceraldehyde 3-phosphate. The pentose phosphate pathway in Crabtree positive yeasts (S. cerevisiae) is predominantly used for NADPH production but not for biomass production or catabolic reactions.
Pyruvate branch point. At the pyruvate (the end product of glycolysis) branching point, pyruvate can follow three different metabolic fates depending on the yeast species and the environmental conditions. On the other hand, the carbon flux may be distributed between the respiratory and fermentative pathways. Pyruvate might be directly converted to acetyl–cofactor A (CoA) by the mitochondrial multienzyme complex pyruvate dehydrogenase (PDH) after its transport into the mitochondria by the mitochondrial pyruvate carrier. Alternatively, pyruvate can also be converted to acetyl–CoA in the cytosol via acetaldehyde and to acetate by the so-called PDH-bypass pathway. Compared with cytosolic pyruvate decarboxylase, the mitochondrial PDH complex has a higher affinity for pyruvate and therefore most of the pyruvate will flow through the PDH complex at low glycolytic rates. However, at increasing glucose concentrations, the glycolytic rate will increase and more pyruvate is formed, saturating the PDH bypass and shifting the carbon flux through ethanol production. In the yeast S. cerevisiae, the external glucose level controls the switch between respiration and fermentation.

Rodrigues F, Ludovico P and Leão C. Sugar Metabolism in Yeasts: an Overview of Aerobic and Anaerobic Glucose Catabolism. In Molecular and Structural Biology. Chapter 6. qxd 07/23/05 P117
Eriksson P, Andre L, Ansell R, Blomberg A, Adler L (1995) Cloning and characterization of GPD2, a second gene encoding sn-glycerol 3-phosphate dehydrogenase (NAD+) in Saccharomyces cerevisiae, and its comparison with GPD1. Mol Microbiol 17:95–107.
Flikweert MT, van der Zanden L, Janssen WM, Steensma HY, van Dijken JP, Pronk JT (1996)Pyruvate decarboxylase: an indispensable enzyme for growth of Saccharomyces cerevisiae on glucose. Yeast 12:247–257.

Biogenesis of mitochondrial structures from aerobically grown S. cerevisiae

Under aerobic conditions S. cerevisiae forms mitochondria which are classical in their properties,
but the number, morphology, and enzyme activity of these mitochondria are also affected by catabolite repression, but it cannot respire under anaerobic conditions and lacks cytochromes. These structures were isolated from anaerobically grown yeast cells and contain malate and succinate dehydrogenases, ATPase, and DNA characteristic of yeast mitochondria. These lipid-complete structures consist predominantly of double-membrane vesicles enclosing a dense matrix which contains a folded inner membrane system bordering electron-transparent regions similar to the cristae of mitochondria.

• The morphology of the structures is critically dependent on their lipid composition
• Their unsaturated fatty acid content is similar to that of mitochondria from aerobically grown cells
• The structures from cells grown without lipid supplements have simpler morphology – a dense granular matrix surrounded by a double membrane but have no obvious folded inner membrane system within the matrix
• The lipid-depleted structures are only isolated in intact form from protoplasts
• The synthesis of ergosterol and unsaturated fatty acids is oxygen-dependent and anaerobically grown cells may be depleted of these lipid components
• The cytology of anaerobically grown yeast cells is profoundly affected by both lipid-depletion and catabolite repression
• Lipid-depleted anaerobic cells, membranous mitochondrial profiles were not demonstrable
• The structures from the aerobically and anaerobically grown cells are markedly different in morphology and fatty acid composition, but both contain mitochondrial DNA and a number of mitochondrial enzymes

The phospholipid composition of various strains of Saccharomyces cerevisiae, wild type and petite (cytoplasmic respiratory deficient) yeasts and derived mitochondrial mutants grown under conditions designed to induce variations in the complement of mitochondrial were fractionated into various subcellular fractions and analyzed for cytochrome oxidase (in wild type) and phospholipid composition . 90% or more of the phospholipid, cardiolipin was found in the mitochondrial membranes of wild type and petite yeast . Cardiolipin content differed markedly under various growth conditions .

• Stationary yeast grown in glucose had better developed mitochondria and more cardiolipin than repressed log phase yeast .
• Aerobic yeast contained more cardiolipin than anaerobic yeast .
• Respiration-deficient cytoplasmic mitochondrial mutants, both suppressive and neutral, contained less cardiolipin than corresponding wild types .
• A chromosomal mutant lacking respiratory function had normal cardiolipin content .
• Log phase cells grown in galactose and lactate, which do not readily repress the development of mitochondrial membranes, contained as much cardiolipin as stationary phase cells grown in glucose .
• Cytoplasmic mitochondrial mutants respond to changes in the glucose concentration of the growth medium by variations in their cardiolipin content in the same way as wild type yeast does under similar growth conditions.
• It is of interest that the chromosomal petite, which as far as can be ascertained has qualitatively normal mitochondrial DNA and a normal cardiolipin content when grown under maximally derepressed conditions .

Thus, the genetic defect in this case probably does not diminish the mass of inner mitochondrial membrane under appropriate conditions . This suggests the cardiolipin content of yeast is a good indicator of the state of development of mitochondrial membrane.
Jakovcic S, Getz Gs, Rabinowitz M, Jakob H, Swift H. Cardiolipin Content Of Wild Type and Mutant Yeasts in Relation to Mitochondrial Function and Development. JCB 1971. jcb.rupress.org
Jakovcic S, Haddock J, Getz GS, Rabinowitz M, Swift H. Biochem J. 1971; 121 :341 .
EPHRUSSI, B . 1953 . Nucleocytoplasmic Relations in Microorganisms . Clarendon Press, Oxford.

Mitochondria, hydrogenosomes and mitosomes

Before and after the publication of an unnoticed article in 1905 by Mereschkowsky there were many publications dealing with plant “chimera’s” and cytoplasmic inheritance in plants, which should have favoured the interpretation of plastids as “semi-autonomous” symbiotic entities in the cytoplasm of the eukaryotic plant cell. Twenty years after Mereschkowsky’s plea for an endosymbiotic origin of plastids, Wallin (1925, 1927) postulated the “bacterial nature of mitochondria”. And so it is one of the mysteries of the 20th century that an endosymbiotic origin of plastids had not been generally accepted before the 1970s, primarily because one cannot experience the consequences of mutations in the mitochondrial genome by naked eye.

• Mitochondrial DNA is usually present in multiple copies in one and the same mitochondrion and those in the hundreds to thousands of mitochondria in a single cell are not necessarily identical.
• The random partitioning of the mitochondria in mitosis (and meiosis) frequently results in a more or less biased distribution of the diverent mitochondria in the daughter cells, eventually causing diverent phenotypes in different tissues obscuring the maternal inheritance
• It was not until the 1990s that certain diseases—which had been interpreted as being X-chromosomal with incomplete penetrance—eventually turned out to be

Lastly, the vast majority of mitochondrial proteins are encoded in the nucleus and, consequently, mutations in the corresponding genes exhibit a Mendelian, and not a cytoplasmic, maternal inheritance
In the 1970s and 1980s the unequivocal demonstration of mitochondrial DNA occurred
and mitochondrial mutations at the DNA level provided the final proof for the role of such mutations in a wealth of hereditary diseases in man.

• The genomics era provided the tools to prove the endosymbiont-hypothesis for the origin of the eukaryotic cell

Since DNA does not arise de novo, the genomes of organisms and organelles provide a historical record for the evolution of the eukaryotic cell and its organelles. The DNA sequences of two to three genomes of the eukaryotic cell turned out to be a record of the evolution of the eukaryotic life on earth. The analysis of organelle genomes unequivocally revealed a cyanobacterial origin for plastids and an -proteobacterial origin for mitochondria. Both plastids and mitochondria appear to be monophyletic, i.e. plastids derived from one and the same cyanobacterial ancestor, and mitochondria from one and the same -proteobacterial ancestor.
The evolution of the eukaryotic cell appears to have involved one (in the case of animals) or two (in the case of plants) events that took place 1.5 to 2 billion years ago. However, it appears that symbioses involving one or the other eubacterium arose repeatedly during the billions of years available. For example, photosynthetic algae by phagotrophic eukaryotes, negating the hypothesis of a single eukaryotic event, rather than stringent selection shaping the diversity of present-day life. Recent hypotheses for the origin of the nucleus have postulated that introns, which could be acquired by the uptake of the -proteobacterial endosymbiont, forced the nucleus-cytosol compartmentalization. Lateral gene transfer among eukaryotes is more frequent than was assumed earlier, and “mitochondrial genes” in the nuclear genomes of amitochondrial organisms are not necessarily the consequence of a transient presence of a DNA-containing mitochondrial-like organelle.
To cope with the obvious ubiquity of “mitochondrial” genes and the chimerism of the DNA of present day eukaryotes, the hydrogen hypothesis postulates that an archaeal host took up a eubacterial symbiont that became the ancestor of mitochondria and hydrogenosomes. The hydrogen hypothesis has the potential to explain both the monophyly of the mitochondria, and the existence of “anaerobic” and “aerobic” variants of one and the same original organelle. Based on these observations we have only the terms “mitochondrion”, “hydrogenosome” and “mitosome” to classify the various variants of the mitochondrial family.
Hackstein JHP, Joachim Tjaden J , Huynen M. Mitochondria, hydrogenosomes and mitosomes: products of evolutionary tinkering! Curr Genet (2006) 50:225–245. DOI 10.1007/s00294-006-0088-8.

Lineages

A look at the phylogenetic distribution of characterized anaerobic mitochondria among animal lineages shows that these are not clustered but spread across metazoan phylogeny. The biochemistry and the enzyme equipment used in the facultatively anaerobic mitochondria of metazoans is nearly identical across lineages, strongly indicating a common origin from an archaic metazoan ancestor. The organelles look like hydrogenosomes – anaerobic forms of mitochondria that generate H2 and adenosine triphosphate (ATP) from pyruvateoxidation and which were previously found only in unicellular eukaryotes. The animals harbor structures resembling prokaryotic endosymbionts, reminiscent of the methanogenic endosymbionts found in some hydrogenosome-bearing protists; fluorescence of F420, a typical methanogen cofactor, or lack thereof, will bring more insights as to what these structures are. If we follow the anaerobic lifestyle further back into evolutionary history, beyond the origin of the metazoans, we see that the phylogenetic distribution of eukaryotes with facultative anaerobic mitochondria, eukaryotes with hydrogenosomes and eukaryotes that possess mitosomes (reduced forms of mitochondria with no direct role in ATP synthesis) the picture is similar to that seen for animals. In all six of the major lineages (or supergroups) of eukaryotes that are currently recognized, forms with anaerobic mitochondria have been found. The newest additions to the growing collection of anaerobic mitochondrial metabolisms are the denitrifying foraminiferans. A handful of about a dozen enzymes make the difference between a ‘normal’ O2-respiring mitochondrion found in mammals, and the energy metabolism of eukaryotes with anaerobic mitochondria, hydrogenosomes or mitosomes. Notably, the full complement of those enzymes, once thought to be specific to eukaryotic anaerobes, surprisingly turned up in the green alga Chlamydomonas reinhardtii , which produces O2 in the light, has typical O2-respiring mitochondria but, within about 30 min of exposure to heterotrophic, anoxic and dark conditions, expresses its anaerobic biochemistry to make H2 in the same way as trichomonads, the group in which hydrogenosomes were discovered. Chlamydomonas provides evidence which indicates that the ability to inhabit oxygen-harbouring, as well as anoxic environments, is an ancestral feature of eukaryotes and their mitochondria. The prokaryote inhabitants have existed for well over a billion years, and have reached this new habitat by dispersal, not by adaptive evolution de novo and in situ. Indeed, geochemical evidence has shown that methanogenesis and sulphate reduction, and the niches in which they occur, are truly ancient.
Mentel and Martin. Anaerobic mitochondria: more common all the time. BMC Biology 2010; 8:32. BioMed Central Ltd. http://www.biomedcentral.com/1741-7007/8/32.

Anaerobic mitochondrial enzymes

Mitochondria from the muscle of the parasitic nematode Ascaris lumbricoides var. suum function anaerobically in electron transport-associated phosphorylations under physiological conditions. These helminth organelles have been fractionated into inner and outer membrane, matrix, and inter-membrane space fractions. The distributions of enzyme systems were determined and compared with corresponding distributions reported in mammalian mitochondria. Succinate and pyruvate dehydrogenases as well as NADH oxidase, Mg++-dependent ATPase, adenylate kinase, citrate synthase, and cytochrome c reductases were determined to be distributed as in mammalian mitochondria. In contrast with the mammalian systems, fumarase and NAD-linked “malic” enzyme were isolated primarily from the intermembrane space fraction of the worm mitochondria. These enzymes are required for the anaerobic energy-generating system in Ascaris and would be expected to give rise to NADH in the intermembrane space.
Pyruvate kinase activity is barely detectable in Ascaris muscle. Therefore, rather than giving rise to cytoplasmic pyruvate, CO2 is fixed into phosphoenolpyruvate, resulting in the formation of oxalacetate which, in turn, is reduced by NADH to form malate regenerating glycolytic NAD . Ascaris muscle mitochondria utilize malate anaerobically as their major substrate by means of a dismutation reaction. The “malic” enzyme in the mitochondrion catalyzes theoxidation of malate to form pyruvate, CO2, and NADH. This reaction serves to generate intramitochondrial reducing power in the form of NADH. Concomitantly, fumarase catalyzes thedehydration of an equivalent amount of malate to form fumarate which, in turn, is reduced by an NADH-linked fumarate reductase to succinate. The flavin-linked fumarate reductase reaction results in a site I electron transport-associated phosphorylation of ADP, giving rise to ATP. This identifies a proton translocation system to obtain energy generation.
Rew RS, Saz HJ. Enzyme Localization in the Anaerobic Mitochondria Of Ascaris Lumbricoides. The Journal Of Cell Biology 1974; 63: 125-135. jcb.rupress.org

Mitochondrial redox status

Tumor cells are characterized by accelerated growth usually accompanied by up-regulated pathways that ultimately increase the rate of ATP production. These cells can suffer metabolic reprogramming, resulting in distinct bioenergetic phenotypes, generally enhancing glycolysis channeled to lactate production. These investigators showed metabolic reprogramming by means of inhibitors of histone deacetylase (HDACis), sodium butyrate and trichostatin. This treatment was able to shift energy metabolism by activating mitochondrial systems such as the respiratory chain and oxidative phosphorylation that were largely repressed in the untreated controls.
Amoêdo ND, Rodrigues MF, Pezzuto P, Galina A, et al. Energy Metabolism in H460 Lung Cancer Cells: Effects of Histone Deacetylase Inhibitors. PLoS ONE 2011; 6(7): e22264. doi:10.1371/ journal.pone.0022264
Antioxidant pathways that rely on NADPH are needed for the reduction of glutathione and maintenance of proper redox status. The mitochondrial matrix protein isocitrate dehydrogenase 2 (IDH2) is a major source of NADPH. NAD+-dependent deacetylase SIRT3 is essential for the prevention of age related hearing loss of caloric restricted mice. Oxidative stress resistance by SIRT3 was mediated through IDH2. Inserting SIRT3 Nε-acetyl-lysine into position 413 of IDH2 and has an activity loss by as much as 44-fold. Deacetylation by SIRT3 fully restored maximum IDH2 activity. The ability of SIRT3 to protect cells from oxidative stress was dependent on IDH2, and the deacetylated mimic, IDH2K413R variant was able to protect Sirt3-/- MEFs from oxidative stress through increased reduced glutathione levels. The increased SIRT3 expression protects cells from oxidative stress through IDH2 activation. Together these results uncover a previously unknown mechanism by which SIRT3 regulates IDH2 under dietary restriction. Recent findings demonstrate that IDH2 activities are a major factor in cancer, and as such, these results implicate SIRT3 as a potential regulator of IDH2-dependent functions in cancer cell metabolism.
Wei Yu, Dittenhafer-Reed KE and JM Denu. SIRT3 Deacetylates Isocitrate Dehydrogenase 2 (IDH2) and Regulates Mitochondrial Redox Status. JBC Papers in Press. Published on March 13, 2012 as Manuscript M112.355206. http://www.jbc.org
Computationally designed drug small molecules targeted for metabolic processes: a bridge from the genome to repair of dysmetabolism
New druglike small molecules with possible anticancer applications were computationally designed. The molecules formed stable complexes with antiapoptotic BCL-2, BCL-W, and BFL-1 proteins. These findings are novel because, to the best of the author’s knowledge, molecules that bind all three of these proteins are not known. A drug based on them should be more economical and better tolerated by patients than a combination of drugs, each targeting a single protein. The calculated drug-related properties of the molecules were similar to those found in most commercial drugs. The molecules were designed and evaluated following a simple, yet effective procedure. The procedure can be used efficiently in the early phases of drug discovery to evaluate promising lead compounds in time- and cost-effective ways.
Keywords: small molecule mimetics, antiapoptotic proteins, computational drug design.

Tardigrades

Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant.
Keywords: RNA, expressed sequence tag, cluster, protein family, adaptation, tardigrada, transcriptome

Epicrisis

This discussion has disparate pieces that are tied together by dysfunctional changes that are

• adaptations from metabolic process in the channeling of energy dependent of mitochondrial enzymes in interaction with three to 6 carbon carbohydrates, high energy phosphate, oxygen and membrane lipid structures, as well as
• proteins rich or poor in sulfur linked with genome specific targets, and semisynthetic modifications, oxidative stress
• leading to a new approach to pharmaceutical targeted drug design.

Related articles

• Determinants of Brain Cell Metabolic Phenotypes and Energy Substrate Utilization Unraveled with a Modeling Approach (ploscompbiol.org)
• Mitochondria and Cancer: An overview of mechanisms (pharmaceuticalintelligence.com)
• Making a molecular micromap: Imaging the yeast 26S proteasome at near-atomic resolution (phys.org)
• Fermentation (ahschoolapbio2013.wordpress.com)
• Nitric Oxide has a ubiquitous role in the regulation of glycolysis -with a concomitant influence on mitochondrial function (pharmaceuticalintelligence.com)
• What Causes Aging and How Does Dietary Restriction Increase Life Span? (understandnutrition.com)
• Diaz-Cano SJ. Tumor heterogeneity: mechanisms and bases for a reliable application of molecular marker design. Int J Mol Sci 2012; 13(2):1951-2011 PMID 22408433Bernstein LH. Expanding the Genetic Alphabet and linking the genome to the metabolome.PharmaIntell.wordpress.com. luly 24, 2012.
• Sainani K. Meet the Skeptics: Why Some Doubt Biomedical Models – and What it Takes to Win Them Over.  IMAG Futures meeting.   2009
• Ritusaxena. ENCODE: the key to unlocking the secrets of complex genetic diseases.  PharmaIntell.wordpress.com  2012.
• Ritusaxena. Scientists use natural agents for prostate cancer bone metastasis treatment. PharmaIntell.wordpress.com. 2012
• Ritusaxena. β Integrin emerges as an important player in mitochondrial dysfunction associated Gastric Cancer. PharmaIntell.wordpress.com 2012

 

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Expanding the Genetic Alphabet and Linking the Genome to the Metabolome

Posted in Bio Instrumentation in Experimental Life Sciences Research, Biological Networks, Gene Regulation and Evolution, Biomarkers & Medical Diagnostics, CANCER BIOLOGY & Innovations in Cancer Therapy, Cell Biology, Signaling & Cell Circuits, Chemical Biology and its relations to Metabolic Disease, Chemical Genetics, Computational Biology/Systems and Bioinformatics, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Genome Biology, Genomic Testing: Methodology for Diagnosis, Liver & Digestive Diseases Research, Medical and Population Genetics, Metabolomics, Molecular Genetics & Pharmaceutical, Nutrigenomics, Nutrition, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Analytics, Pharmaceutical Industry Competitive Intelligence, Pharmaceutical R&D Investment, Population Health Management, Genetics & Pharmaceutical, Population Health Management, Nutrition and Phytochemistry, Proteomics, Scientist: Career considerations, Systemic Inflammatory Response Related Disorders, Technology Transfer: Biotech and Pharmaceutical, tagged adenine, ATP, biodiversity, Cancer - General, Cancer Genome Atlas, cystathionine beta synthase, cytosine, DNA, fumarate, gene modification, genetic code, genetic engineering, genetics, genome, guanine, H2S, homocysteine, inosine, malnutrition, metabolome, methionine, Nature (journal), Nature Chemical Biology, Nucleic acid double helix, nucleosides, oncometabolite, oxidative stress, proteome, regulatory pathways, S-adenosylmethionine, Scripps Research Institute, Sulfur, synthetic nucleotides, thymidine, Warburg Effect, Watson-Crick Model, xanthine on September 24, 2012| 13 Comments »

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 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 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. 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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• Molecular milestone: scientists unravel the human genome – Fox News (foxnews.com)
• The Story of You: Encode and the human genome – video | Martin Robbins (guardian.co.uk)
• Science takes a giant leap in its understanding of genetics (jessiebaldwin.wordpress.com)
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• The ENCODE delusion (scienceblogs.com)

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Breast Cancer, drug resistance, and biopharmaceutical targets

Posted in Biomarkers & Medical Diagnostics, CANCER BIOLOGY & Innovations in Cancer Therapy, Cell Biology, Signaling & Cell Circuits, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Genome Biology, Genomic Testing: Methodology for Diagnosis, International Global Work in Pharmaceutical, Molecular Genetics & Pharmaceutical, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Analytics, Pharmaceutical Industry Competitive Intelligence, Population Health Management, Genetics & Pharmaceutical, Regulated Clinical Trials: Design, Methods, Components and IRB related issues, Technology Transfer: Biotech and Pharmaceutical on September 18, 2012| 2 Comments »

Breast Cancer, drug resistance, and biopharmaceutical targets
Reporter: Larry H Bernstein, MD
There has been a continuing improvement in breast cancer treatment and extended survival, that is rapidly changing with respect to disease free survival and decreased toxicity. This is a snapshot of recently published work.
1. Breast Cancer Drug Resistance Linked to Gene Family
Two related proteins have been implicated in the mechanisms that allow breast cancer, and potentially other tumor types, to resist therapy with tyrosine kinase inhibitors (TKIs).
Case Western Reserve University
FAM83A and FAM83B have been identified by separate research groups reporting in parallel in the Journal of Clinical Investigation. The proteins may represent promising new therapeutic targets.
Researchers at Case Western Reserve University used a validation-based insertional mutagenesis (VBIM) strategy to generate libraries of HEM1 immortalized human mammary epithelieal cells (HMECs) that carried unique, single genetic alterationsto identify genes that promoted anchorage-independent growth (AIG), and tumorigenicity, and then carried out further cell-based assays to see which of the identified genes could promote tumor growth independently of RAS.

• Expression of FAM83B was found to promote AIG and tumorigenesis, in naïve HME1 cells, and FAM83B-expressing cells were also shown to be capable of forming tumors in immunodeficient mice, confirming its function as a transforming oncogene.
• FAM83B expression levels were associated with specific cancer subtypes, with increased tumor grade, and with decreased overall survival. For example, increased expression of FAM83B was significantly associated with estrogen receptor– (ER-) and progesterone receptor–negative (PR-negative) breast tumors, with higher grade and poor outcome.
• FAM83B also binds with a downstream RAS effector, CRAF, and this binding increased MAPK and mTOR signaling, and reduced sensitivity to EGFR-TKIs.

The Case Western Reserve group concludes that knocking out FAM83B inhibited the proliferation and malignant phenotype of tumor-derived cells or RAS-transformed HMECs.
The authors say targeting FAM38B therapeutically may increase the sensitivity of breast cancer to EGFR-TKI therapy. Given the requirement for FAM83B as an activator of CRAF/MAPK in EGFR and RAS signaling, the levels of FAM83B and FAM83A may be important to consider when determining which patients receive TKI treatment.
MW Jackson., RCipriano, et al. “FAM83B mediates EGFR- and RAS-driven oncogenic transformation.” J Clin Invest 2012.

Lawrence Berkeley National Laboratory-led team
The Berkely group also identified this potential target for addressing drug resistance in breast cancer and potentially other tumor types. The  team have reported in the same issue of JCI that a gene known as FAM83A has oncogenic properties, and when overexpressed in cancer cells confers resistance to EGFR-tyrosine kinase inhibitor (EGFR-TKI) drugs and also promotes tumor proliferation and invasion.

• FAM38A had coincidentally previously been identified as highly expressed in lung cancer. The researchers found that, while normal tissue didn’t produce the FAM38A, it was highly expressed in malignant tissue.
• They hypothesized that resistance to EGFR-TKIs may occur in part as a result of a molecular mechanism that triggers phosphorylation signaling downstream of EGFRs.
• They developed a novel three-dimensional cell culture assay based on the phenotypic reversion of malignant cells into phenotypically nonmalignant cells, to screen for genes involved in EGFR-TKI resistance both in normal and cancerous human cell lines.
• FAM83A is expressed in every breast cancer cell line they looked at and was particularly elevated in those that were more resistant to EGFR-TKI treatment.
• FAM38A interacts with and triggers phosphorylation of signaling proteins downstream of EGFR, that act to block the therapeutic effects of EGFR-TKIs.
• When breast cancer cells were treated with an shRNA that blocked FAM38A expression, the cells became less proliferative and more sensitive to EGFR-TKI treatment. Conversely, FAM83A overexpression led to elevated invasiveness.

Mechanistically, FAM83A was shown to interact with and cause phosphorylation of CRAF and PI3K, upstream of MAPK and downstream of EGFR. This finding correlates well with the mechanism reported for FAM38B by the Case Western team.
The published data highlights the potential importance of this family of proteins as potential drug targets, and helps explain existing data demonstrating a clinical correlation between high FAM83A expression and poor cancer prognosis. Moreover, Dr. Bissell states the finding also reveals a whole new family of potential oncogenes that could be a target for all types of cancer, including breast cancer.
Bissell et al. “FAM83A confers EGFR-TKI resistance in breast cancer cells and in mice.” Journal of Clinical Investigation 2012
GEN News Highlights : Sep 12, 2012

2. Targets Identified to Prevent Breast Cancer Spread
Hypoxia-inducible factor 1 (HIF-1) and platelet-derived growth factor B (PDGF-B) may represent promising therapeutic targets for preventing breast cancer from spreading to the lymph nodes and metastasizing to other organs. The protein’s role in lymphatic dissemination of cancer hasn’t been well understood.

Researchers at the Johns Hopkins University School of Medicine and partners in Italy have found that HIF-1 promotes lymphatic metastasis of breast cancer directly by activating the gene encoding PDGF-B, which triggers the growth of new lymphatic vessels.

• Previous work by Gregg L. Semenza, M.D., and colleagues had shown that knocking out HIF-1α or HIF2α in mice implanted with human breast cancer cells (BCCs) slowed tumor growth and lung metastasis.
• Treating animals with the HIF-1 inhibitor digoxin similarly impaired primary tumor growth and lung metastasis.
• Mice injected with HIF-1 knockdown human BCC cells exhibited 76% fewer cancer cells in their lymph nodes after 24 days than animals injected with unengineered BCC cells, supporting a role for HIF-1 in the spread of breast cancer to lymph nodes.
• HIF-1 binds directly to the gene for PDGF-B, which is overexpressed under the hypoxic conditions found in tumors, and triggers the growth of lymphatic vessels.
• Moreover, coexpression of HIF-1α and PDGF-B was also found in invasive breast carcinomas, and this coexpression correlated with survival and response to chemotherapy, the researchers stress.
• PDGF-B produced as a result of HIF-1 binding is released from the tumor cells and binds to its cognate receptor PDGFRβ, which is upregulated on lymphatic endothelial cells (LEC) under hypoxic conditions.
• This PDGFβ signaling triggers LEC proliferation and migration, and the growth of lymphatic vessels.
• When the researchers turned off PDGFRβ signalling by blocking HIF-1 or PDGF-B using either RNA interference, or chemical inhibitors (digoxin or the tyrosine kinase inhibitor imatinib), both lymphatic vessel density and lymph node metastasis were significantly reduced.

Reporting their findings in PNAS, the investigators suggest:
highlighting HIF-1 and PDGF-B as potential therapeutic targets for breast cancer their results suggest that co-expression of the two proteins may help to identify lymph node-negative patients who are at a high risk for developing lymph node metastasis
GL Semenza, et al. “Hypoxia-inducible factor 1-dependent expression of platelet-derived growth factor B promotes lymphatic metastasis of hypoxic breast cancer cells.” PNAS 2012.
GEN News Highlights : Sep 12, 2012

3. how tamoxifen-resistant breast-cancer cells grow and proliferate
A study by researchers at the Ohio State University Comprehensive Cancer Center (OSUCCC – James) has discovered how tamoxifen-resistant breast-cancer cells grow and proliferate.
It suggests that an experimental agent might offer a novel targeted therapy for tamoxifen-resistant breast cancer.

• Like a second door that opens after the first door closes, a signaling pathway called hedgehog (Hhg) can promote the growth of breast-cancer cells after tamoxifen shuts down the pathway activated by the hormone estrogen.
• A second signaling pathway, called PI3K/AKT, is also involved. Activation of the Hhg pathway renders tamoxifen treatment ineffective and enables the tumor to resume its growth and progression.
• The researchers found that the tumors with an activated Hhg pathway had a worse prognosis.
• an experimental drug called vismodegib, which blocks the Hhg pathway, inhibits the growth of tamoxifen-resistant human breast tumors in an animal model. The drug is in clinical trials testing for other types of cancer.

This study has identified targeted therapies that could be an alternative to chemotherapy for these resistant tumors. The study is published in the journal Cancer Research  2012.
### Follow Ronald’s contributions at Boston Biotech & Golden Triangle Biotech ###
Possible therapy for tamoxifen-resistant breast cancer identified cphi-online.com

EGF Signalling (Photo credit: TheJCB)

Related articles

• How breast cancer spreads (eurekalert.org)
• How breast cancer spreads: Researchers find key to lymph node metastasis in mice (medicalxpress.com)
• PARP inhibitors may have clinical utility in HER2-positive breast cancers (eurekalert.org)
• Lack of oxygen in cancer cells leads to growth and metastasis (eurekalert.org)
• Protein Linked To Therapy Resistance In Breast Cancer (medicalnewstoday.com)

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Nitric Oxide has a Ubiquitous Role in the Regulation of Glycolysis – with a Concomitant Influence on Mitochondrial Function

Posted in Biological Networks, Gene Regulation and Evolution, Bone Disease and Musculoskeletal Disease, CANCER BIOLOGY & Innovations in Cancer Therapy, Cell Biology, Signaling & Cell Circuits, Disease Biology, Small Molecules in Development of Therapeutic Drugs, HTN, Human Immune System in Health and in Disease, Infectious Disease & New Antibiotic Targets, Innovations in Neurophysiology & Neuropsychology, Medical Devices R&D Investment, Metabolomics, Nitric Oxide in Health and Disease, Nutrigenomics, Pharmaceutical Industry Competitive Intelligence, Pharmacotherapy of Cardiovascular Disease, Systemic Inflammatory Response Related Disorders, Technology Transfer: Biotech and Pharmaceutical, tagged adaptive compensatory glycolysis, aerobic glycolysis, Doctor of Philosophy, Endothelium, health, Larry H. Bernstein, lymphokines, mitochondrial dysfunction, nitric oxide, Nitric oxide synthase, Pasteur effect, Phosphofructokinase-2, Platelet, resident-cell-based, skeletal muscle and myocardial, Therapy, Vascular smooth muscle, Warburgh effect on September 16, 2012| 27 Comments »

Nitric Oxide has a Ubiquitous Role in the Regulation of Glycolysis – with a Concomitant Influence on Mitochondrial Function

 

Reporter, Editor, and Topic Co-Leader: Larry H. Bernstein, MD, FACP, Clinical Pathologist and Biochemist

 

 

Apoptosis signaling pathways (Photo credit: AJC1)

This discussion is a followup on a series of articles elucidating the importance of NO, eNOS, iNOS, cardiovascular and vascular endothelium effects, and therapeutic targets.

This mechanism of action and signaling actions have been introduced so that we identify endocrine, paracrine, and such effects in the normal, stressed, and dysfunctional state. The size and breadth of this vital adaptive process is now further explored.

The title is short, befitting a subtitle.  The full topic may be considered “Nitric Oxide has a ubiquitous role in the regulation of glycolysis -with a concomitant influence on mitochondrial function that is active in endothelium, platelets, vascular smooth muscle and neural cells and the balance has a role in chronic inflammation, asthma, hypertension, sepsis and cancer”.

Vascular endothelium (Photo credit: Wikipedia)

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• Interaction of Nitric Oxide and Prostacyclin in Vascular Endothelium (pharmaceuticalintelligence.com)
• Nitric oxide: role in Cardiovascular health and disease (pharmaceuticalintelligence.com)
• Nitric Oxide: Chemistry and function (pharmaceuticalintelligence.com)
• Nitric Oxide in bone metabolism (pharmaceuticalintelligence.com)
• Can Erectile Dysfunction Indicate Heart Attack Risk? (everydayhealth.com)
• Nitric Oxide Signalling Pathways (pharmaceuticalintelligence.com)
• Endothelial Dysfunction, Diminished Availability of cEPCs, Increasing CVD Risk for Macrovascular Disease – Therapeutic Potential of cEPCs (pharmaceuticalintelligence.com)
• Nitric Oxide production in Systemic sclerosis

 

 

Nitric Oxide Synthase (Photo credit: Wikipedia)

 

 

Nitric Oxide has a ubiquitous role in the regulation of glycolysis with a concomitant influence on mitochondrial function that is active in endothelium, platelets, vascular smooth muscle and neural cells and the balance has a role in chronic inflammation, asthma, hypertension, sepsis and cancer.

Uncoupling of aerobic glycolysis
Potential cytotoxic mediators of endothelial cell (EC) apoptosis include increased formation of reactive oxygen and nitrogen species (ROSRNS) during the atherosclerotic process. Nitric oxide (NO) has a biphasic action on oxidative cell killing with low concentrations protecting against cell death, whereas higher concentrations are cytotoxic. High levels of NO can be produced by inducible nitric-oxide synthase in response to cytokine stimulation, primarily from macrophages, and elevated levels of NO is injurious to endothelium.Ccytochrome c release and caspase activation are involved in NO induced apoptosis. ROS also induces mitochondrial DNA damage in ECs, and this damage is accompanied by a decrease in mitochondrial RNA (mtRNA) transcripts, mitochondrial protein synthesis, and cellular ATP levels. Mitochondria have been recognized to play a pivotal role in the signaling cascade of apoptosis leading to atherosclerosis-induced damage in endothelial cells.
The processes involved in the signaling pathways leading to apoptosis are complex but have some degree of convergence between cell types including those in the vasculature. Release of cytochrome c from mitochondria is a proapoptotic signal, which activates several downstream signaling events including formation of the apoptosome and activation of caspases. Ubiquinol cytochrome c reductase (complex III) is a site for ROS formation, and cytochrome c oxidase (complex IV) is a target for the interaction of NO in mitochondria.
The impact of the inhibition of mitochondrial protein synthesis is particularly important in NO-dependent cytotoxicity, and depends also on other factors such as glycolysis. These authors examined whether the inhibition of mitochondrial protein synthesis by chloramphenicol increases the susceptibility of endothelial cells to undergo NO-dependent apoptosis in glucose-free media. Bovine aortic endothelial cells were treated with chloramphenicol, which resulted in a decreased ratio of mitochondrial complex IV to cytochrome c and increased oxidant production in the cell. Inhibition of mitochondrial protein synthesis was associated with a greater susceptibility of the cells to apoptosis induced by NO in glucose-free medium.
Inhibition of mitochondrial protein synthesis results in increased endothelial cell susceptibility to nitric oxide-induced apoptosis. A Ramachandran, DR Moellering, E Ceaser, S Shiva, J Xu, and V Darley-Usmar. PNAS May 14, 2002: 99(10): 6643–6648 http://www.pnas.orgcgidoi10.1073pnas.102019899

Nitric oxide (NO) is a ubiquitous signaling molecule whose physiological roles mediated through the activation of the soluble guanylate cyclase are now clearly recognized. At physiological concentrations, NO also inhibits the mitochondrial enzyme cytochrome c oxidase (complex IV) in competition with oxygen, and recently we have suggested that the interplay between the two gases allows this enzyme to act as an oxygen sensor in cells. In addition, NO plays a variety of patho-physiological roles, some of which also may be the consequence of its action at a mitochondrial level. We have characterized the sequence of events that follow inhibition of complex IV by continuous exposure to NO.
The mitochondrion is a key organelle in the control of cell death. Nitric oxide (NO) inhibits complex IV in the respiratory chain and is reported to possess both proapoptotic and antiapoptotic actions. We investigated the effects of continuous inhibition of respiration by NO on mitochondrial energy status and cell viability. Serum-deprived human T cell leukemia (Jurkat) cells were exposed to NO at a concentration that caused continuous and complete (;85%) inhibition of respiration. Serum deprivation caused progressive loss of mitochondrial membrane potential (Dcm) and apoptotic cell death. In the presence of NO, Dcm was maintained compared to controls, and cells were protected from apoptosis. Similar results were obtained by using staurosporin as the apoptotic stimulus. As exposure of serum-deprived cells to NO progressed (>5 h), however, Dcm fell, correlating with the appearance of early apoptotic features and a decrease in cell viability. Glucose deprivation or iodoacetate treatment of cells in the presence of NO resulted in a collapse of Dcm, demonstrating involvement of glycolytic ATP in its maintenance. Under these conditions cell viability also was decreased. Treatment with oligomycin and or bongkrekic acid indicated that the maintenance of Dcm during exposure to NO is caused by reversal of the ATP synthase and other electrogenic pumps. Thus, blockade of complex IV by NO initiates a protective action in the mitochondrion to maintain Dcm; this results in prevention of apoptosis. It is likely that during cellular stress involving increased generation of NO this compound will trigger a similar sequence of events, depending on its concentration and duration of release. (mitochondrial membrane potential ; apoptosis ; necrosis)

The effect of nitric oxide on cell respiration: A key to understanding its role in cell survival or death. B Beltra, A Mathur, MR Duchen, JD. Erusalimsky, and S Moncada. PNAS Dec 19, 2000; 97(26):4602–14607.

Another study by this group shows that inhibition of respiration by exogenous nitric oxide (NO) in Jurkat cells leads to mitochondrial membrane hyperpolarization dependent on the utilization of glycolytic ATP by the F1Fo-ATPase and other transporters acting in reverse mode. This process also occurs in astrocytes, which are highly glycolytic cells, but not in neurons , which do not invoke glycolysis to maintain ATP concentrations. In addition, this hyperpolarization correlates with protection against apoptotic cell death. Others found an early phase of mitochondrial hyperpolarization after treatment of a variety of cells with different pro-apoptotic stimuli, which precedes the generation of free. At present, no satisfactory explanation has been proposed to explain the mechanism of hyperpolarization, the reasons why free radicals are released from the mitochondrion, or the connection of these phenomena with apoptosis.
The authors surmise that a pro-apoptotic stimulus, anti-Fas Ab, leads to release of endogenous NO from Jurkat cells in sufficient amounts to inhibit cell respiration and cause a hyperpolarization dependent on the reversal of the F1Fo-ATPase. Moreover, the reduction of the mitochondrial electron transport chain, after inhibition of cytochrome oxidase by NO, leads to generation of superoxide anion (O2). They suggest the process is a cellular defense response that may be overcome by pro-apoptotic mechanisms that occur in parallel.

Inhibition of mitochondrial respiration by endogenous nitric oxide: A critical step in Fas signaling. B Beltran, M Quintero, E Garcıa-Zaragoza, E O’Connor, JV. Esplugues, and Salvador Moncada. PNAS June 25, 2002 99(13): 8892–8897. http://www.pnas.orgcgidoi10.1073pnas.092259799

Nitric oxide has been shown to render cells resistant to oxidative stress. Mechanisms proposed for the ability of nitric oxide to protect cells against oxidative stress include reactions of nitric oxide and the induction of adaptive responses that require protein synthesis. Nitric oxide forms iron complexes preventing the formation of strong oxidants. In addition, reactions of nitric oxide with lipid and or organic radicals protect against membrane peroxidation and peroxidative chemistry-induced cell injury. Exposure to low, nonlethal doses of nitric oxide induces adaptive responses that render cells resistant to lethal concentrations of nitric oxide and or peroxides, such as, the induction of hemoxygenase-1 (HO-1) and Mn superoxide dismutase. The up-regulation of HO-1 was accompanied by an increase in ferritin to account for the release of iron from HO-1, indicating a role of both iron heme and nonheme iron for peroxide-mediated cellular injury. Further, nitric oxide, by regulating critical mitochondrial functions such as respiration, membrane potential, and release of cytochrome c, is able to trigger defense mechanisms against cell death induced by pro-apoptotic stimuli.
This study investigates the potential contribution of nitric oxide’s ability to protect cells from oxidative stress, low steady state levels of nitric oxide generated by endothelial nitric oxide synthase (eNOS) and the mechanisms of protection against H2O2. Spontaneously transformed human ECV304 cells, which normally do not express eNOS, were stably transfected with a green fluorescent-tagged eNOS cDNA. The eNOS-transfected cells were found to be resistant to injury and delayed death following a 2-h exposure to H2O2 (50–150 mM). Inhibition of nitric oxide synthesis abolished the protective effect against H2O2 exposure. The ability of nitric oxide to protect cells depended on the presence of respiring mitochondria. ECV3041 eNOS cells with diminished mitochondria respiration are injured to the same extent as non-transfected ECV304 cells, and recovery of mitochondrial respiration restores the ability of nitric oxide to protect against H2O2-induced death. Nitric oxide had a profound effect in cell metabolism, because ECV3041eNOS cells had lower steady state levels of ATP and higher utilization of glucose via the glycolytic pathway than ECV304 cells. However, the protective effect of nitric oxide against H2O2 exposure is not reproduced in ECV304 cells after treatment with azide and oligomycin suggesting that the dynamic regulation of respiration by nitric oxide represent a critical and unrecognized primary line of defense against oxidative stress.

Dynamic regulation of metabolism and respiration by endogenously produced nitric oxide protects against oxidative stress. E Paxinou, M Weisse, Q Chen, JM Souza, et al. PNAS Sept 25, 2001; 98( 20): 11575–11580. http://www.pnas.orgycgiydoiy10.1073ypnas.201293198.

Nitric oxide (NO) mediates a variety of biological effects including relaxation of blood vessels, cytotoxicity of activated macrophages, and formation of cGMP by activation of glutamate receptors of neurons. NO has also been implicated for such pathophysiological conditions as destruction of tumor cells by macrophages, rheumatoid arthritis, and focal brain ischemia. Some of these effects of NO are associated with hypoxic conditions. O2 radicals and ions that result from reactivity of NO are presumed to be involved in NO cytotoxicity. These investigators report that adaptive cellular response controlled by the transcription factor hypoxia-inducible factor 1 (HIF-1) in hypoxia is suppressed by NO. Induction of erythropoietin and glycolytic aldolase A mRNAs in hypoxically cultured Hep3B cells, a human hepatoma cell line, was completely and partially inhibited, respectively, by the addition of sodium nitroprusside (SNP), which spontaneously releases NO. A reporter plasmid carrying four hypoxia-response element sequences connected to the luciferase structural gene was constructed and transfected into Hep3B cells. Inducibly expressed luciferase activity in hypoxia was inhibited by the addition of SNP and two other structurally different NO donors, S-nitroso-Lglutathione and 3-morpholinosydnonimine, giving IC50 values of 7.8, 211, and 490 mM, respectively. Inhibition by SNP was also observed in Neuro 2A and HeLa cells, indicating that the inhibition was not cell-type-specific. The vascular endothelial growth factor promoter activity that is controlled by HIF-1 was also inhibited by SNP (IC50 5 6.6 mM). Induction generated by the addition of cobalt ion (this treatment mimics hypoxia) was also inhibited by SNP (IC50 5 2.5 mM). Increased luciferase activity expressed by cotransfection of effector plasmids for HIF-1a or HIF-1a-like factor in hypoxia was also inhibited by the NO donor. We also showed that the inhibition was performed by blocking an activation step of HIF-1a to a DNA-binding form.
Inhibition of hypoxia-inducible factor 1 activity by nitric oxide donors in hypoxia. K Sogawa, K Numayama-Tsuruta, M Ema, M Abe, et al. Proc. Natl. Acad. Sci. USA (Biochemistry) June 1998; 95:7368–7373. 1998. The National Academy of Sciences 0027-8424.98.957368-6. http:yywww.pnas.org.

The role of nitrogen metabolism in the survival of prolonged periods of waterlogging was investigated in highly flood-tolerant, nodulated Lotus japonicus plants. Alanine production revealed to be a critical hypoxic pathway. Alanine is the only amino acid whose biosynthesis is not inhibited by nitrogen deficiency resulting from RNA interference silencing of nodular leghemoglobin. The metabolic changes that were induced following waterlogging can be best explained by the activation of alanine metabolism in combination with the modular operation of a split tricarboxylic acid pathway. The sum result of this metabolic scenario is the accumulation of alanine and succinate and the production of extra ATP under hypoxia. The importance of alanine metabolism is discussed with respect to its ability to regulate the level of pyruvate, and this and all other changes are discussed in the context of current models concerning the regulation of plant metabolism.
Glycolysis and the Tricarboxylic Acid Cycle Are Linked by Alanine Aminotransferase during Hypoxia Induced by Waterlogging of Lotus japonicus[W][OA]. M Rocha, F Licausi, WL Arau´ jo, A Nunes-Nesi, et al. Plant Physiology Mar 2010; 152: 1501–1513. http://www.plantphysiol.org 2010 Amer Soc Plant Biologists

DNA damage occurs in ischemia, excitotoxicity, inflammation, and other disorders that affect the central nervous system (CNS). Extensive DNA damage triggers cell death and in the mature CNS, this occurs primarily through activation of the poly(ADP-ribose) polymerase-1 (PARP-1) cell death pathway. PARP-1 is an abundant nuclear enzyme that, when activated by DNA damage, consumes nicotinamide adenine dinucleotide (NAD)+ to form poly(ADP-ribose) on acceptor proteins. The PARP-1 activation leads to cell death. We used mouse astrocyte cultures to explore the bioenergetic effects of NAD+ depletion by PARP-1 and the role of NAD+ depletion in this cell death program. PARP-1 activation led to a rapid but incomplete depletion of astrocyte NAD+, a near-complete block in glycolysis, and eventual cell death. Repletion of intracellular NAD restored glycolytic function and prevented cell death. The addition of non-glucose substrates to the medium, pyruvate, glutamate, or glutamine, also prevented astrocyte death after PARP-1 activation.
These findings suggest a sequence of events in which NAD+ depletion is a key event linking DNA damage to metabolic impairment and cell deathm. A similar scenario has been proposed by Zong et al. (2004), based on the finding that cell types that depend on aerobic glycolysis for ATP production exhibit a particularly high sensitivity to DNA damage and PARP-1 activation. In mature brain, glucose is normally the dominant metabolic substrate due to relatively slow transport of other metabolites across the blood– brain barrier. Oncein brain, glucose may be metabolized directly by neurons and glia or may be metabolized to lactate in glia and thelactate subsequently shuttled to neurons for oxidative metabolism (Dringen et al., 1993; Pellerin and Magistretti,1994; Wender et al., 2000; Dienel and Cruz, 2004). In either case, a block in glycolytic flux produced by NAD depletion will block energy metabolism in both neurons and glia in brain. Interestingly, the lactate shuttle hypothesis raises the possibility that activation of PARP-1 selectively in astroglia might also block energy metabolism in neurons.

These studies suggest PARP-1 activation leads to rapid depletion of the cytosolic but not the mitochondrial NAD+ pool. Depletion of the cytosolic NAD+ pool renders the cells unable to utilize glucose as a metabolic substrate. Under conditions where glucose is the only available metabolic substrate, this leads to cell death. This cell death pathway is particularly germane to brain because glucose is normally the only metabolic substrate that is transported rapidly across the blood–brain barrier. © 2004 Wiley-Liss, Inc.
Key words: mitochondria; permeability transition; poly(ADP-ribose) polymerase; ischemia; peroxynitrite
NAD+as a metabolic link between DNA damage and cell death. DNA damage induced by alkylating agents, oxidative stress, or other agents causes PARP-1 activation. PARP-1 activation leads to depletion in cytosolic NAD with, initially, a relative preservation of mitochondrial NAD and mitochondrial function. The depletion in cytosolic NAD+ blocks glycolysis, and in cells in which glucose is the primary energy substrate, this in turn leads to a block in substrate flux to mitochondria. The resulting mitochondrial dysfunction leads to mitochondrial permeability transition (MPT) and subsequent downstream events culminating in cell death.
NAD+ as a Metabolic Link Between DNA Damage and Cell Death. W Ying, CC Alano, P Garnier, and RA Swanson. Journal of Neuroscience Research 2005;79:216–223
Key words: glycolysis, mitochondrial energy production, nitric oxide
Abbreviations: NO, nitric oxide; SNAP, S-nitroso-N-acetylpenicyllamine; SNP, sodium nitroprusside.
The results indicate that: 1) in porcine platelets NO is able to diminish mitochondrial energy production through the inhibition of cytochrome oxidase, 2) the inhibitory effect of NO on platelet secretion (but not aggregation) can be attributed to the reduction of mitochondrial energy production.
Nitric oxide (NO) has been increasingly recognized as an important intra- and intercellular messenger molecule with a physiological role in vascular relaxation, platelet physiology, neurotransmission and immune responses (Moncada et al., 1991; Radomski et al., 1996; Szabó, 1996; Riedel et al., 1999; Titheradge 1999). In vitro NO is a strong inhibitor of platelet adhesion and aggregation (Radomski et al., 1996; Riedel et al., 1999;nSogo et al., 2000). In the blood stream, platelets remain in contact with NO that is permanently released from the endothelial cells and from activated macrophages (Moncada et al., 1991; Riedel et al., 1999; Titheradge 1999). It has been suggested that the activated platelet itself is able to produce NO (Lantoine et al., 1995; Zhou et al., 1995; Radomski et al., 1996). The mechanism responsible for the inhibitory effect of NO on platelet responses is not entirely clear. It is believed that the main intracellular target for NO in platelets is soluble cytosolic guanylate cyclase (Waldman & Walter 1989; Schmidt et al., 1993; Wang et al., 1998). NO activates the enzyme (Schmidt et al., 1993). Thus, elevated intracellular cGMP level inhibits platelet activation. There are suggestions, however, that elevated cGMP may not be the only intracellular factor directly involved in the inhibition of platelet activation (Gordge et al., 1998; Sogo et al., 2000; Beghetti et al., 2003).
Platelets are fairly active metabolically and have a total ATP turnover rate of about 3–8 times that of resting mammalian muscle (Akkerman, 1978; Akkerman et al., 1978; Holmsen, 1981; Niu et al., 1996). Platelets contain mitochondria which enable these cells to produce energy both in the oxidative and anaerobic way (Holmsen, 1981). Under aerobic conditions, ATP is produced by aerobic glycolysis using glucose or glycogen which can account for 30–50% of total ATP production, and by oxidative metabolism using glucose and glycogen (6–11%), amino-acids (7%) or free fatty acids (20–40%) (Holmsen 1981; Guppy et al., 1990; Niu et al., 1996).
The inhibition of mitochondrial respiration by removing oxygen or by respiratory chain blockers (antimycin A, cyanide, rotenone) results in the stimulation of glycolytic flux (Guppy et al., 1990). This phenomenon is known as Pasteur effect and indicates that in platelets glycolysis and mitochondrial respiration are tightly functionally connected (Akkerman, 1978; Holmsen, 1981; Guppy et al., 1995; Niu et al., 1996). It has been reported that the activation of human platelets by high concentration of thrombin is accompanied by an acceleration of lactate production and an increase in oxygen consumption (Akkerman & Holmsen, 1981; Niu et al., 1996).
The results presented here suggest that also porcine blood platelets stimulated by collagen produce more lactate. This indicates that both glycolytic and oxidativeATP production supports platelet responses. This also indicates that blocking of energy production in platelets may decrease their responses. It is well established that platelet responses have different metabolic energy (ATP) requirements increasing in the order: aggregation< dense and alfa granule secretion < acid hydrolase secretion (Holmsen et al., 1982; Verhoeven et al., 1984; Morimoto & Ogihara, 1996).
The present results indicate that exogenously added NO (in the form of NO donors)stimulates glycolysis in intact porcine platelets. Since in platelets glycolysis and mitochondrial respiration are tightly functionally connected, this can be interpreted to mean that the stimulatory effectof NO on glycolysis in intact platelets may be produced by non-functional mitochondria.This can be really the case since NO donors are able to inhibit both mitochondrial respiration and platelet cytochrome oxidase. Interestingly, the concentrations of NO donors inhibiting mitochondrial respiration and cytochrome oxidase were similar to those stimulating glycolysis in intact platelets.
Studies performed on intact J774 cells have shown that mitochondrial complex I is inhibited only after a prolonged (6–18 h) exposure to NO and that this inhibition appears to result from S-nitrosylation of critical thiols in the enzyme complex (Clementi et al., 1998). Further studies are needed to establish whether long term exposure of platelets to NO affects Mitochondrial complexes I and II.
Comparison of the concentrations of SNP and SNAP affecting cytochrome oxidase activityand mitochondrial respiration with those reducing the platelet responses indicates that NO cannot significantly reduce platelet aggregation through the inhibition of oxidative energy production. By contrast, the concentrations of the NO donors inhibiting platelet secretion, mitochondrial respiration and cytochrome oxidase were similar. This and the fact that the platelet release reaction strongly depends on the oxidative energy production may suggest that in porcine platelets NO can affect platelet secretion through the inhibition of mitochondrial energy production at the step of cytochrome oxidase.

Taking into account that platelets may contain NO synthase and are able to produce significant amounts of NO (Berkels et al., 1997)it seems possible that nitric oxide can function in these cells as a physiological regulator of mitochondrial energy production.
Nitric oxide and platelet energy metabolism. M Tomasiak, H Stelmach, T Rusak and J Wysocka. Acta Biochimica Polonica 2004; 51(3):789–803

These authors previously investigated the bioenergetic consequences of activating J774.A1 macrophages (MФ) with interferon (IFN)γ and lipopolysaccharide (LPS) and found that there is a nitric oxide (NO)-dependent mitochondrial impairment and stabilization of hypoxia inducible factor (HIF)-1α, which synergize to activate glycolysis and generate large
quantities of ATP. We now demonstrate, using TMRM fluorescence and time-lapse confocal microscopy, that these cells maintain a high mitochondrial membrane potential (ΔΨm) despite the complete inhibition of respiration. The maintenance of high ΔΨm is due to the utilization of a significant proportion of glycolytically generated ATP as a defence mechanism against cell death. This is achieved by the reverse functioning of FoF1-ATP synthase and adenine nucleotide translocase (ANT). Treatment of activated MФ with inhibitors of either of these enzymes, but not with inhibitors of the respiratory chain complexes I to IV, led to a collapse in ΔΨm and to an immediate increase in intracellular [ATP], due to the prevention of ATP hydrolysis by the FoF1-ATP synthase. This collapse in ΔΨm was followed by translocation of Bax from cytosol to the mitochondria, release of cytochrome c into the cytosol, activation of caspase 3 and 9 and subsequent apoptotic cell death. Our results indicate that during inflammatory activation “glycolytically competent cells” such as MФ utilize significant amounts of the glycolytically-generated ATP to maintain ΔΨm and thereby prevent apoptosis.

Activated macrophages utilize glycolytic ATP to maintain mitochondrial membranepotential and prevent apoptotic cell death. A Garedew, SO Henderson, S Moncada. Cell Death and Differentiation. 2010. DOI : 10.1038/cdd.2010.27
The effects of the sodium nitroprusside (SNP), a nitric oxide (NO) donor clinically used in the treatment of hypertensive emergencies on the energy production of rat reticulocytes were investigated. Rat reticulocyte-rich red blood cell suspensions were aerobically incubated without (control) or in the presence of different concentrations of SNP (0.1, 0.25, 0.5, 1.0 mM). SNP decreased total and coupled, but increased uncoupled oxygen consumption. This was accompanied by the stimulation of glycolysis, as measured by increased glucose consumption and lactate accumulation. Levels of all glycolytic intermediates indicate stimulation of hexokinase-phosphofructo kinase (HK-PFK), glyceraldehyde 3-phosphate dehydrogenase (GAPD) and pyruvate kinase (PK) activities in the presence of SNP. Due to the decrease of coupled oxygen consumption in the presence of SNP, ATP production via oxidative phosphorylation was significantly diminished. Simultaneous increase of glycolytic ATP production was not enough to provide constant ATP production. In addition, SNP significantly decreased ATP level, which was accompanied with increased ADP and AMP levels. However, the level of total adenine nucleotides was significantly lower, which was the consequence of increased catabolism of adenine nucleotides (increased hypoxanthine level). ATP/ADP ratio and adenylate energy charge level were significantly decreased. In conclusion, SNP induced inhibition of oxidative phosphorylation, stimulation of glycolysis, but depletion of total energy production in rat reticulocytes. These alterations were accompanied with instability of energy status.

Effects of Exogenous Donor of Nitric Oxide – Sodium Nitroprusside on Energy Production of Rat Reticulocytes. SD MALETIĆ, L M DRAGIĆEVIĆ-DJOKOVIĆ, BI OGNJANOVIĆ, RV ŽIKIĆ, AŠ ŠTAJN, MB SPASIĆ.
Physiol. Res. 2004;53: 439-447.

Key points to take from this:
1. The role of NO in regulating cellular death is in many organs and central to this function is the stabilization of mitochondria through sufficient levels of NO. High levels of eNO leads to mitochondrial dysfunction that increases the dependence of ATP generated from glycolysis.
2. This is accompanied by inhibition of oxidative phosphorylation and stimulation of glycolysis, which brings the discussion to a different domain – cancer growth and Warburgh Effect.
3. This is accompanied by PPAR activation, cytoplasmic NAD+ depletion, and inhibition of glycolysis (critical in cells dependent on aerobic glycolysis), depletion of total energy production, and apoptosis.
4. Maintenance of high glycolytic generation of ATP is essential for cellular defense, but the oxygen consumption is uncoupled.
5. NO donors inhibiting mitochondrial respiration and cytochrome oxidase are similar to those stimulating glycolysis

More    (pharmaceuticalintelligence.com)

• Nitric Oxide: a short historic perspective (pharmaceuticalintelligence.com)
• Cardiovascular Disease (CVD) and the Role of agent alternatives in endothelial Nitric Oxide Synthase (eNOS) Activation and Nitric Oxide Production (pharmaceuticalintelligence.com)

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