Metabolism, Molecular Hypometabolism And Inflammation .

Shoemaker RC (2020) Metabolism, molecular hypometabolism and inflammation: Complications of proliferative physiology include metabolic acidosis, pulmonaryhypertension, T reg cell deficiency, insulin resistance and neuronal injuryillness, characterized by chronic fatigue [2-4]. of a particular type,called chronic inflammatory response syndrome (CIRS). Of note is theincreased production of inflammatory compounds that accompaniessuppression of production of ribosomal mRNA [4].Nearly all CIRS cases also meet the case definition for ChronicFatigue Syndrome (CFS) [5] and Severe Exercise-Induced Disease(SEID), though CFS and SEID have no specific biomarkers [6] CIRShas at least 15 biomarkers [7]. For these individuals, compromise ofmetabolism may be adaptive, providing the potential for cell survivalin the face of an inflammatory or ribotoxin-mediated attack on proteinsynthesis at the sarcin-ricin loop [8] (SRL), an evolutionarily conservedstructure located between the large and small subunits of ribosomes.Found in all living organisms, and directly involved with initiation,elongation, and termination of amino acid chains, one may speculateas to the source of the paucity of papers on the incredibly importantrole in the metabolism of ribosomal protein production played bythe SRL (number of papers on [metabolism, SRL] 177) compared to[metabolism, ribosomes] ( 44,400).Added to decreased protein production and innate immuneinflammation in MHM is the severe cellular impairment created bythe simultaneous suppression of nuclear-encoded mitochondrialgenes. While putative mitochondrial dysfunction in CFS and CIRShas many proponents, we must account for differential gene activityfor mitochondrial genes that have migrated to the nucleus over severalbillion years. While nuclear-encoded mitochondrial genes number inthe hundreds, only 37 genes remain in the mitochondrial genome [9].Specifically, genes for ETC and ATP synthases were noted by Dr. Ryanto be suppressed, as were translocases. Translocases move nuclear geneencoded products out of the cytosol, across the outer mitochondrialmembrane, in conjunction with porins, small electrically chargedchannels (voltage-dependent anion channels, VDAC) that permitentry of ions, solutes, ADP and pyruvate against a gradient into theintermembranous space [10-13]. There, specific carriers will completedelivery across the inner mitochondrial membrane to the matrix.Failure of entry of pyruvate into the mitochondrial matrixcompartment from the cytosol has very important consequencesfor metabolism (see below). Survival adaptations using MHM aremaintained at a cost, however, as organisms with MHM are alive butmight not be vigorous in either of two main cellular energy processes, (i)proliferation and (ii) conservation. The literature is relatively silent onsurvival with MHM. Indeed, with mitochondrial gene suppression, asshown by measurable abnormalities in the amount of mRNA producedby nuclear-encoded mitochondrial genes, little is published on energyproduction in patients with CIRS or SEID. They have a deficiencyof translocases. For perspective, while [metabolism, mitochondria]yields 167,000 papers, nuclear-encoded mitochondrial genes areonly referenced by 1471 papers under [metabolism, nuclear-encodedmitochondrial genes] and only 4 for [metabolism, fatigue, and voltagedependent anion channels]. Given that the estimates of the prevalenceof the chronic fatiguing illnesses in the US alone exceed 50,000,000cases, with that number increasing yearly, it was disturbing to find thedearth of papers on [metabolism, CIRS] ( 1334) and [metabolism,ribotoxins], the source of SRL injury ( 72).Fortunately, a diagnostic and treatment protocol that identifies andcorrects the transcriptomic abnormalities of MHM has been in wideuse [2,4]. since 2010, with correction of MHM noted in over 90% ofcases (manuscript in preparation). This paper will review the impactof MHM on metabolism as those pathways interact with inflammationseen in CIRS, with particular attention to aerobic glycolysis andTrends Diabetes Metab, 2020doi: 10.15761/TDM.1000118VDAC effects on metabolic acidosis, grey matter nuclear atrophy andpulmonary hypertension in CIRS. We follow that thread with studydata on 112 patients with CIRS.SEID, CIRS and metabolismThe recent addition of transcriptomic testing to the approach topatients with chronic fatiguing illnesses, defined as multisystem, multisymptom illnesses, including Severe Exercise Intolerance Disease(SEID), fibromyalgia, Post Lyme disease and chronic inflammatoryresponse syndrome (CIRS), among others, has demonstrated not only(i) commonality of the complexity and near universality of responsesof genes of inflammation and coagulation, but also (ii) the relationshipof suppression of production of ribosomal mRNA and nuclearencoded mitochondrial genes to multiple facets of glucose metabolism,especially aerobic glycolysis [14,15], resulting in neuronal injury,including cognitive impairment [16-20], and pulmonary hypertension(see PAH below) These findings in chronic illnesses parallel the findingsof acute sepsis (systemic inflammatory response syndrome, SIRS),with excessive inflammation, coagulation, and immunosuppressionpersisting beyond the treatment of infection [21].Each of these elements is consistent with the classic observationsof Lewis Thomas that the host immune response, once initiated, canbecome the disease. When combined with disturbances in glycolysisand pyruvate uptake into mitochondria through VDAC, identified inpart by transcriptomics, it is clear that ongoing maladaptive responsesto immune and metabolic initiators underlie multiple sources ofSEID (excluding CIRS) typified by the absence of objective diagnosticparameters without which there are no guides to physiology-basedtherapies.For patients who survive sepsis, a chronic illness called persistentinflammation and catabolism syndrome (PICS) [21], often develops.While we have chosen the term CIRS to describe “chronic PICS” andother related illnesses related to chronic inflammation, the illnessconcepts are the same. The difference is that CIRS literature has data onmany recognized biomarkers and a published treatment protocol [7],but PICS does not.These biomarkers include symptom clusters for CIRS acquiredfollowing environmental exposures to biotoxins and inflammagensin water-damaged buildings (WDB), finding at least 8 of 13 clusterspresent. Proteomic biomarkers compared to controls [4] include(i) increased relative risk for specific HLA haplotypes; (ii) presenceof a distinctive deficit seen in visual contrast sensitivity (VCS); (iii)reduction of mean levels of melanocyte-stimulating hormone (MSH);(iv) dysregulation of ACTH to cortisol and (v) ADH to osmolality; (vi)elevated C4a, (vii) TGF beta-1, and (viii) MMP9; (ix) suppression ofvascular endothelial growth factor (VEGF); (x) increased incidence ofantigliadin and (xi) anticardiolipin antibodies [7]. Functional CIRSWDB biomarkers include (a) a distinctive “fingerprint” of volumetricabnormalities [22-24] seen on NeuroQuant ; (b) reduction of VO2max and (c) anaerobic threshold shown by pulmonary stress testing;(d) elevated pulmonary artery pressures at rest, or (e) after exercise onechocardiogram; (f) transcriptomics.Focus on molecular hypometabolismThe advances of understanding the physiology associated withMHM brought to light by use of transcriptomics are highlighted by theapplication of differential gene activation, stratified by age, comparingcases to controls for mRNA for ribosomal genes for the small ribosomesubunit and differentiating those mRNA findings from the largeVolume 3: 2-15

Shoemaker RC (2020) Metabolism, molecular hypometabolism and inflammation: Complications of proliferative physiology include metabolic acidosis, pulmonaryhypertension, T reg cell deficiency, insulin resistance and neuronal injuryribosomal subunit. Further, transcriptomics allows us to understandmRNA findings on mitoribosomes, both large and small subunits.These findings are important when evaluating NeuroQuant, looking atthe role of commensal multiple antibiotic-resistant coagulase-negativestaphylococci (MARCoNS), now found to make unidentified polycyclicether toxins (unpublished). The role of mitochondrial gene suppressionin association with MARCoNS is fertile ground for continued research.When taken as a whole, with a correction for the high and lownumber of copies of mRNA, combined with an adjustment for age, wehave seen that transcriptomics will identify molecular hypometabolismaccurately in patients with CIRS and SEID. We also see thesefundamental abnormalities in less commonly represented illnessesin our data set, including multiple sclerosis and cancer, for example.Disorders of inflammation, metabolism, and loss of regulation ofdifferential gene activation, commonly seen in CIRS, SEID, and otherchronic fatiguing illnesses, hold importance by defining pathologicalabnormalities in metabolism that may apply to other chronic illnesses.Changes in MHM with therapy also provide a window on thetreatment of CIRS, as the use of a peer-reviewed protocol [4] showsthe correction of suppression of ribosomal and nuclear-encodedmitochondrial genes, especially translocases. The completion of initialtreatment is marked by an overshoot of the number of copies of targetedgenes compared to controls, with a return to control levels with the useof intranasal vasoactive intestinal polypeptide (VIP). The changes inindividual mRNA counts seen in each of the MHM entities, are parallelin shape when graphed, describing the “CIRS curve” [25].Metabolism overviewTrying to simplify the known biochemical pathways of metabolismruns the risk of oversimplification. Conversely, a more detaileddiscussion of metabolism creates a learning curve for the new readerwith the use of multiple lengthy and often unfamiliar terms forreactants in a given metabolic pathway, especially given the ubiquity ofacronyms. Looking at a typical metabolic pathway, say glycolysis leadingto pyruvate production and then with pyruvate entering into the Krebscycle and ETC, we see a deluge of names of new reaction products inthe pathways, with each term also identified by a new acronym thatinteracts with others making another new compound with its ownacronym, produced by a catalyzing enzyme with its new name and itsacronym. Suffice to say, metabolism can be presented to students inwhat seems to be an inordinately complicated manner when the namesof compounds and definitions of acronyms are not used frequently. Itremains concerning that many physicians in primary care learned thesepathways in medical school only to lose recollection of pathways andenzymes over time due to lack of daily use.Like inflammation, metabolism is present in every physiologicalfunction; metabolism can regulate energy and growth, as well as directthe fate of cells, i.e., living or dying, not being functional or creatingdisease [1]. As always, regulation of metabolism and metabolic fluxis under control of gene activity. Differences in gene activity createdifferences in the regulation of metabolic activity. As we will see,metabolism can regulate the differentiation of immune cells, includingthe reduction of the production of T regulatory cells, under conditionsof proliferation.We will focus on glucose, pyruvate, Warburg physiology, insulinreceptor substrate 2 (IRS2), proteins, and amino acids, in the discussionsbelow. Each of the sections that follow will look at the major sections ofthis initial discussion in greater detail.Trends Diabetes Metab, 2020doi: 10.15761/TDM.1000118Metabolic complications: metabolic acidosis specifics ofglycolysis and pyruvateOnce glucose enters the cell, often by the facilitated transportfrom a family of solute carriers, called Glut 1 (SLC2A1) and Glut4 (SLC2A4), it enters into a cytosolic pathway called glycolysis (alsocalled the Embden-Meyerhof pathway). This series of enzymaticsteps can generate needed precursors that can be used for othermetabolic pathways, small amounts of ATP and pyruvate. Glycolysisis an evolutionarily conserved process used by all living organisms. Asseen with the SRL, evolutionary conservation means all the possiblemutations and nucleotide polymorphisms that surely had to occur overthree billion years amount to no replacement of the glycolysis genes orpathway.Glycolysis is a ten-step pathway of intracytoplasmic conversion of a6-carbon ring, glucose, to create two copies of a three-carbon fragment,pyruvate. As an example of the abstruse names and the plethora ofacronyms, we will use the glycolysis pathway as a typical example ofjargon in metabolism, highlighted in the text that follows.There are two phases to glycolysis. The first is called the “preparatoryphase,” and the second is the “payoff phase.” The preparatory phaseconsumes two ATP to place phosphate moieties strategically onmetabolites, with the return of a total of four ATP in the payoff phase.Diversion of metabolic precursors to other pathways subtracts from thenet four generated ATP [26, 27].The conversion of glucose to the first metabolite, glucose6-phosphate, is accomplished at the cost of one ATP to fuel animportant enzyme, hexokinase. As an aside, hexokinase has recentlybecome the focus of much attention in degenerative central nervoussystem diseases, especially Alzheimer’s, as Apo E2 patients rarely willhave Alzheimer’s and have a rich endowment of hexokinase, but Apo E4is associated with CNS deterioration, with reduced hexokinase [28-30].Once the first change of glucose has been made by hexokinase, the firstdiversion of glucose from its ultimate goal of producing pyruvate canoccur. Here, glucose 6-phosphate can be shunted to participate in thesynthesis of a storage compound, glycogen, a complex carbohydrate.A second diversion occurs when glucose-6-phosphate dehydrogenase(G6PD) is activated to convert G-6-P to ribose-5-P, the first step of thepentose phosphate shunt, a significant source of metabolites, especiallynucleotides, needed for added cell division. This shunt is a crucialdiversion used in proliferative physiology.If glycolysis continues, the next step is to make fructose 6-phosphateby an enzyme phosphohexose isomerase. Fructose 6-phosphate isprimed with its new stereochemistry, and at a cost of one additionalATP, the enzyme phospho-fructokinase-1 will add a phosphate groupmaking fructose 1,6-bisphosphate. We can see where this change isheaded, as now the 6-carbon ring can be cleaved into two pieces. Notethat fructose-6-phosphate can lead to the hexosamine biosyntheticshunt, part of the cell’s metabolic response to stressors such as infection,ischemia or trauma, for example (see HBP below).This cleavage is accomplished by the enzyme aldolase, known forits role in muscular diseases, to make glyceraldehyde 3-phosphate anddihydroxyacetone phosphate, with the latter then converted by triosephosphate isomerase, thus making two molecules of glyceraldehyde3-phosphate. If the word glycerol seems to be hidden in glyceraldehyde,there can be a diversion of glyceraldehyde to make glycerol. Alternatively,dihydroxyacetone phosphate can be diverted to participate in thesynthesis of lipids. This step marks the crossover from the preparatoryVolume 3: 3-15

Shoemaker RC (2020) Metabolism, molecular hypometabolism and inflammation: Complications of proliferative physiology include metabolic acidosis, pulmonaryhypertension, T reg cell deficiency, insulin resistance and neuronal injuryphase to the payoff phase. Now the two molecules of glyceraldehyde3-phosphate can be converted by oxidation and phosphorylation usingthe enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH) tomake two molecules of 1,3 biphosphoglycerate. GAPDH is a vitallyimportant enzyme that serves as a rate-controlling regulator of pyruvateproduction that, in turn, serves as a vital component of GAIT (seebelow) as will be discussed. GAIT provides a mechanism for cellularfeedback control to downregulate inflammatory cytokine responsesand maintain metabolism. GAPDH has other important roles as well.GAPDH will also generate reduced NADH in this pathway inthe next step, which is then used to facilitate the production of twoadditional ATP. Step 7 uses phosphoglycerate kinase to make twocopies of a single phosphate molecule, 3-phosphoglycerate. Cleaving aphosphate group from each permits conversion of ADP to make a totalof two ATP for each pyruvate. Remember, two ATP were consumed inthe preparatory phase; now, two sets of two ATP are returned, makinga net yield of positive two molecules of ATP. 3-phosphoglycerate canbe converted to an amino acid, serine, fueling the production of otheramino acids needed for protein synthesis.Next, moving one phosphate is a necessary step to manufacture oftwo copies of 2-phosphoglycerate by phosphoglycerate mutase. Each2-phosphoglycerate is converted by enolase to phosphoenolpyruvate.This compound is further converted by pyruvate kinase to make pyruvate.Pyruvate, if it can traverse the outer mitochondrial membrane and reachthe mitochondrial matrix, feeds into the Krebs cycle (tricarboxylic acidpathway, TCA) where it can be converted to acetyl-CoA by pyruvatedehydrogenase (PDH), leading to lipid synthesis. PDH can be blockedby pyruvate kinase (PDK1). PDK1 is induced by hypoxia-induciblefactor 1 alpha (HIF-1α), a compound that also activates the conversionof pyruvate to lactate. Further, HIF-1α can increase uptake of glucosethrough Glut 1 and 4 and activate hexokinase, setting off glycolysis.HIF-1α is important in aerobic glycolysis (see the section on PAHbelow). Interest in the use of PDK1 as a possible chemotherapy agent isnoted, as use aerobic glycolysis typifies many cancers. HIF-1α also hasa significant role in suppression of the production of T regulatory (reg)cells by activating the production of T effector cells.As complex as the glycolysis pathway is with its multiple diversions,a basic tenet of metabolism is that the activation of one pathway willchange the activity of competing pathways [31]. Add to that concept theidea that metabolism adapts to environmental change, which in turncreates a stimulus for differential gene activation, controlling discreteelements of metabolic pathways and inflammation. All of these changescreate a cellular environment in which two consecutive measurementsof gene activity and metabolism rarely are going to be similar unlessthe initiating stressor (exposure to ribotoxins, for example) is constant.Here is the putative role for inflammation controlling gene activation,with metabolic changes driven by gene activation that, are themselvesregulated by inflammation. An exciting finding is that medicationsassociated with salutary health effects [2,4,24] that change geneactivation and inflammation will restore regulation of abnormalities ofmetabolism.A prime example of gene activation, inflammation, and metaboliccontrol comes from a review of the effect of the Randle cycle onglycolysis. As each pathway is mutually reciprocal on the other, anincrease of the Randle cycle decreases glycolysis, in favor of fatty acidoxidation with its enriched source of ATP production. Increasing fattyacid oxidation, as follows a rise in IRS 2, activating Glut1 and Glut4,will suppress glucose catabolism, but at the cost of increasing oxygenTrends Diabetes Metab, 2020doi: 10.15761/TDM.1000118consumption: burning fatty acids costs oxygen. Citrate, part of theKrebs cycle, will suppress phosphofructokinase, increasing glucose-6phosphate, shunting the glycolysis pathway to increasing the storageof glycogen. This part of the Randle cycle creates the “second wind,”as well-trained athletes know, as increased energy (9.3 calories/gram)comes from fatty acid oxidation, compared to 3.4 calories/gram fromglucose oxidation.Simply stated, direct fat burn stores glycogen. Fatty acid oxidation,in turn, generates acetyl CoA, which blocks pyruvate dehydrogenase,preventing pyruvate from being converted into acetyl CoA. This stepleads to aerobic glycolysis and production of lactate, especially ifpyruvate is also blocked from entering mitochondria across the VDACby inflammation-induced reduction of translocases. The combinationof the development of hypoxemia (from FAO) and aerobic glycolysis isthe development of pulmonary hypertension [32]. Blocking fatty acidoxidation in isolated myocytes of the right ventricle leads to increasedpyruvate burn and less oxygen consumption [32].Meanwhile, the Krebs cycle is the site of the conversion ofglutamine to glutamate, making available a free amino group crucialto glycosylation, discussed below. To find these ten metabolic stepsevolutionary conserved seems surprising at first glance, and yet natureworks in predictable ways. The amount of enzymatic work to make justtwo net ATP seems excessive, but the production of so many buildingblocks has two important additional benefits: (i) the manufacture of areservoir of compounds needed for cell proliferation; and (ii) speed ofATP production. A theme in metabolism both in health and diseaseis the dual role of glucose in (i) energy conservation versus (ii) energyexpenditure to support cell proliferation.Glucose remains the coin of the metabolic realm as it leads to theproduction of pyruvate that can be further processed by an enzyme,lactate dehydrogenase (LDH), to generate lactic acid (lactate). Inturn, lactate is moved by transport molecules out of the cell. Excessiveamounts of lactate production can be suspected by seeing a widenedanion gap in peripheral blood. However, even this seemingly simplecalculation can be complicated by further metabolism of lactate incapillary beds adjacent to where it was produced, with reconversion topyruvate, reducing the anion gap.Pyruvate is the cellular metabolic treasure; it plays a dominant role incell proliferation versus cellular conservation of energy primarily basedon where pyruvate is further metabolized. Mitochondrial production ofATP depends on the delivery of pyruvate into the mitochondrial matrix.If delivery is compromised, cytosolic metabolism will be the default sitefor pyruvate metabolism. If there is too much pyruvate being madein the cytosol, or too little being consumed, look for suppression ofGAPDH gene(s) to reduce pyruvate production, possibly contributingto insulin resistance. Some rapidly dividing cells will use the conversionof pyruvate to lactate as its primary source of ATP through “aerobicglycolysis,” also called the Warburg Effect [33,34]. At first glance, thislow yield conversion of pyruvate to make ATP, compared to whatKrebs cycle and ETC pathways in the mitochondrial matrix wouldbring, seems dysfunctional. What benefit does a rapidly dividing cellglean from “wasting” the ability to create molecules used for energy?Cancer cells commonly use this so-called “Warburg physiology,” toproduce lactate, export it from the dividing cell, creating an adversemicroclimate that serves as a defense to prevent T-cells from attackinggrowing cancer cells. Cells at the surface of the developing tumor usethe reverse of cellular fermentation by reconverting lactate back topyruvate as a source of ATP [34].Volume 3: 4-15

Shoemaker RC (2020) Metabolism, molecular hypometabolism and inflammation: Complications of proliferative physiology include metabolic acidosis, pulmonaryhypertension, T reg cell deficiency, insulin resistance and neuronal injuryIn CIRS, we worry about the Warburg Effect because it underliesthe pathologic development of clinically significant metabolic acidosis,pulmonary hypertension [35]; it underlies abnormalities, includingmetabolism in branched-chain glycans (see below) that will lead toinsulin resistance. Further, we also see multiple examples of injury toneuronal tissue associated with the Warburg Effect, both peripherally,creating peripheral neuropathy and centrally, possibly contributing todementing illnesses, as discussed. The marker for the Warburg Effectthat can harm CIRS patients, the anion gap, one that is readily calculated,but not so readily confirmed, is due to fermentation of pyruvate tomake lactate. Excess lactic acid adds to or widens, the normal aniongap. To calculate the anion gap, add values of sodium (Na ) to thoseof potassium (K ), and from that sum, subtract the sum of CO2 andchloride (Cl-). If the number is 10-12, that is a normal anion gap.Beyond a gap of 14 or 15, however, we become concerned regarding theexcessive presence of compounds that are anionic and contribute to thewidened anion gap. The body uses lactic acid and bicarbonate to helpregulate pH tightly; metabolic acidosis is commonly found in multipledisea

[Metabolism, glucose] brought 435,000 matches, but [disorders of glucose metabolism] had only 177,000 matches. So here is a massive scientific database on metabolism and disorders of metabolism of proteins and