Cellular Metabolism and Disease: What Do Metabolic Outliers Teach Us?
Open accessAbstract
An understanding of metabolic pathways based solely on biochemistry textbooks would underestimate the pervasive role of metabolism in essentially every aspect of biology. It is evident from recent work that many human diseases involve abnormal metabolic states--often genetically programmed--that perturb normal physiology and lead to severe tissue dysfunction. Understanding these metabolic outliers is now a crucial frontier in disease-oriented research. This Review discusses the broad impact of metabolism in cellular function and how modern concepts of metabolism can inform our understanding of common diseases like cancer and also considers the prospects of developing new metabolic approaches to disease treatment.
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Written from the paper’s full text.
TL;DR
This review argues that metabolism pervades every aspect of biology and that genetically defined metabolic outliers—inborn errors of metabolism and cancer—can reveal disease mechanisms and therapeutic opportunities. It highlights cancer metabolic reprogramming, including the Warburg effect and mutations in SDH, FH, IDH1/2, and PHGDH, and discusses prospects for metabolic imaging and in vivo flux studies.
Key findings
- Metabolism is far broader than textbook biochemistry: KEGG annotates more than 8,700 reactions and 16,000 metabolites, and core metabolic pathways are integrated with signaling through PI3K/Akt/mTOR, AMPK, acetyl-CoA, sirtuins, and other mechanisms.
- Inborn errors of metabolism (IEMs) are the largest category of heritable human diseases, with some 500 recognized IEMs; newborn screening programs now detect more than 20 individual disorders from a single blood sample and reveal marked phenotypic heterogeneity, including clinically silent cases.
- Cancer is a paradigm of genetically defined metabolic abnormality: many tumors out-compete surrounding tissue for glucose (Warburg effect), and mutations in SDH and FH act as tumor suppressors, IDH1/2 mutations produce the oncometabolite 2-HG, and PHGDH amplification/overexpression can promote malignant phenotypes.
- Metabolic imaging and flux analysis are promising frontiers: FDG-PET is established, newer PET agents target glutamine/glutamate, MRS can quantify metabolites such as glycine and 2-HG in gliomas, and hyperpolarized 13C can produce a transient sensitivity gain of 10,000-fold or more.
Methods
- Narrative review synthesizing literature across biochemistry, genetics, inborn errors of metabolism, cancer metabolism, and metabolic imaging.
- No primary experimental data, systematic search strategy, inclusion criteria, or meta-analysis are reported.
- The paper discusses examples from human genetics, newborn screening, cancer genomics, metabolomics, and preclinical models to support its conceptual arguments.
Limitations
- The paper states that metabolomics alone does not present a complete view of metabolism and can produce misleading results; elevated metabolite levels often reflect decreased rather than increased pathway flux, and it may be impossible to infer which pathway is affected from abnormal metabolite levels alone.
- The paper notes that technical challenges remain for combined metabolomics–metabolic flux studies and that key mechanisms are unresolved, such as how G6Pase deficiency affects hepatocellular differentiation, whether PHGDH is a bona fide oncogene, and which nutrients produce 2-HG in IDH1/2-mutant tumors in vivo.
- Evident from the text: as a review, it provides no primary data or systematic evidence synthesis, so its conclusions depend on the cited literature and selected examples.
Model-written summary. Check it against the paper before relying on it.
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Claims the paper makes
0 of 112 cited sources checked · 0 supported · 0 flagged
- Premisecitation
Glucose and glutamine collaborate in the hexosamine pathway to modify nutrient transporters and growth factor receptors, enabling their expression on the cell membrane.
“But they also collaborate in another biochemical pathway to produce hexosamines, which modify nutrient transporters and growth factor receptors, enabling their expression on the cell membrane (Figure 2).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Wellen et al., 2010 source
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- Premisecitation
Metabolite GWAS also found associations with drug toxicity, Crohn's disease and other conditions not conventionally thought to be related to intermediary metabolism.
“However, there were also associations with drug toxicity, Crohn’s disease and other conditions not conventionally thought to be related to intermediary metabolism (Suhre et al., 2011).”
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- Premisenone given
Much of the metabolic variation among individuals is genetically defined.
“Much of the metabolic variation among individuals is genetically defined.”
Quote in the paperNot a substantial claim - Interpretationreasoning
Generating sufficient quantities of a metabolite for protein modification requires access to nutrients in excess of the levels needed to run basic bioenergetic programs.
“These modifications can signal states of nutrient abundance, because generating sufficient quantities of the requisite metabolite for protein modification requires access to nutrients in excess of the levels needed to run basic bioenergetic programs.”
Quote in the paperSubstantial claim - Premisecitation
Other polymorphisms associated with metabolite levels had previously been shown to associate with cardiovascular disorders, gout and type-2 diabetes, all of which involve changes in core metabolic pathways.
“Other polymorphisms had previously been shown to associate with cardiovascular disorders, gout and type-2 diabetes, all of which are known to involve changes in core metabolic pathways (Suhre et al., 2011).”
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- Premisecitation
AMPK regulates a p53-dependent cell-cycle checkpoint activated by glucose deprivation in cultured cells, limiting growth in energetically unfavorable states.
“Interestingly, AMPK also regulates a p53-dependent cell-cycle checkpoint activated by glucose deprivation in cultured cells, thereby limiting growth in energetically unfavorable states (Jones et al., 2005).”
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- Premisecitation
Most newborn screening programs now detect more than 20 individual disorders from a single blood sample.
“Most programs now detect more than 20 individual disorders from a single blood sample (Chace et al., 2002).”
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- Premisecitation
Many cellular proteins besides histones are acetylated, including most enzymes in core metabolic pathways.
“Many other cellular proteins besides histones are acetylated, including most of the enzymes in core metabolic pathways (Zhao et al., 2010).”
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- Premisecitation
Some polymorphisms associated with metabolite levels changed the coding sequence of a metabolic enzyme directly related to the variable metabolite.
“There were several examples in which a polymorphism changed the coding sequence of a metabolic enzyme directly related to the variable metabolite.”
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Pyruvate dehydrogenase's crucial role in brain development is evident in the profound central nervous system dysfunction resulting from mutation of PDH's catalytic subunit.
“Similarly, glucose oxidation in the citric acid cycle produces most of the energy for the brain, but the crucial role for pyruvate dehydrogenase (PDH) in brain development is evident in the profound central nervous system dysfunction resulting from mutation of PDH’s catalytic subunit (Robinson et al., 1996).”
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Genome-wide association studies of metabolite abundance identified relatively common alleles that accounted for significant fractions of variation in metabolite levels, sometimes more than 20% of total variance.
“Surprisingly, these studies identified a number of relatively common alleles that accounted for significant fractions of the variation in metabolite levels, sometimes more than 20% of the total variance (Gieger et al., 2008; Illig et al., 2010).”
Quote in the paperSubstantial claim0 of 2 sources checked - Premisecitation
In glucose-limiting conditions, budding yeast collectively oscillate through a metabolic cycle linked to synchronized cell growth.
“When budding yeast are cultured in glucose-limiting conditions, they collectively oscillate through a metabolic cycle that is linked to synchronized cell growth (Tu et al., 2005).”
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- Premisecitation
Sirtuins are key evolutionarily conserved factors linking caloric restriction to longevity.
“Sirtuins are key evolutionarily-conserved factors linking caloric restriction to longevity.”
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- Premisecitation
Loss of function of acetyl-CoA synthetase or ATP-citrate lyase reduces histone acetylation, with global consequences on gene expression.
“Loss of function of these enzymes reduces histone acetylation, with global consequences on gene expression (Takahashi et al., 2006; Wellen et al., 2009).”
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Over-expression of sirtuins in model systems ameliorates a variety of age-related phenotypes including cancer, diabetes and neurodegeneration.
“Over-expression of sirtuins in model systems ameliorates a variety of age-related phenotypes including cancer, diabetes and neurodegeneration (Guarente, 2011).”
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- Premisecitation
Mitochondrial fatty acid oxidation's specific role in human energy homeostasis became obvious from severe, life-threatening hypoketotic hypoglycemia elicited by prolonged fasting in children with diminished function of the pathway.
“Mitochondrial fatty acid oxidation was understood to be an efficient bioenergetic pathway, but its specific role in human energy homeostasis became obvious from the severe, life-threatening hypoketotic hypoglycemia elicited by prolonged fasting in children with diminished function of the pathway (Houten and Wanders, 2010).”
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- Premisecitation
IEMs once thought to be highly penetrant and severe now appear to be clinically silent in most individuals.
“In other cases, IEMs once thought to be highly penetrant and severe now appear to be clinically silent in most individuals (Alfardan et al., 2010).”
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- Premisecitation
Peak levels of acetyl-CoA are accompanied by histone acetylation at specific regions of chromatin containing growth genes.
“Peak levels of acetyl-CoA are accompanied by histone acetylation at specific regions of chromatin containing growth genes.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Cai et al., 2011 source
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- Premisecitation
Profiling plasma lipids in large populations has uncovered sequence variations that substantially impact lipid phenotypes.
“Profiling plasma lipids in large populations has uncovered sequence variations that substantially impact lipid phenotypes (Cohen et al., 2005; Teslovich et al., 2010).”
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Warburg observed that carcinoma slices from rats and humans consumed much more glucose and secreted much more lactate than normal tissue, even when presented with enough oxygen to metabolize glucose completely to CO2.
“Warburg observed that carcinoma slices from rats and humans consumed much more glucose and secreted much more lactate than normal tissue, even when presented with enough oxygen to metabolize glucose completely to CO2.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Warburg, 1956 source
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- Interpretationreasoning
In yeast, extracellular nutrients stimulate gene expression via an acetyl-CoA-transmitted signal that culminates in a commitment to cell growth/division.
“Thus, in these cells, extracellular nutrients stimulate gene expression via an acetyl-CoA-transmitted signal that culminates in a commitment to cell growth/division.”
Quote in the paperNot a substantial claim - Interpretationreasoning
Deacetylation of CPS by SIRT5 likely enables the liver to accommodate increased amino acid degradation and ammonia production stimulated by fasting.
“This likely enables the liver to accommodate the increased amino acid degradation and ammonia production stimulated by the fasting state.”
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Growth factor-induced signaling coordinates metabolism to meet the rising demands of proliferation, including maintaining a bioenergetic state permissive for growth.
“Growth factor-induced signaling coordinates these functions, including maintaining a bioenergetic state permissive for growth (Lum et al, 2005).”
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- Interpretationcitation
Cancer is a prime example of a common human disease with genetically-defined, pathological metabolic perturbations.
“Cancer is a prime example of a common human disease with genetically-defined, pathological metabolic perturbations.”
Quote in the paperSubstantial claim - Premisecitation
Clinically silent disease has been detected in asymptomatic mothers of babies subjected to screening programs, apparently because small amounts of the mother's metabolites are transferred to the unaffected baby through the placenta, breast milk or other routes.
“In some cases, clinically silent “disease” has been detected in the asymptomatic mothers of babies subjected to screening programs, apparently because small amounts of the mother’s metabolites are transferred to the unaffected baby through the placenta, breast milk or other routes (Eichhorst et al., 2010).”
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- Interpretationnone given
Many human diseases involve abnormal metabolic states, often genetically programmed, that perturb normal physiology and lead to severe tissue dysfunction.
“It is evident from recent work that many human diseases involve abnormal metabolic states – often genetically programmed – that perturb normal physiology and lead to severe tissue dysfunction.”
Quote in the paperNot a substantial claim - Premisecitation
In both mammals and bacteria, enzyme acetylation fluctuates according to which nutrients are available to the cell.
“In both mammals and bacteria, enzyme acetylation fluctuates according to which nutrients are available to the cell (Wang et al., 2010; Zhao et al., 2010).”
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Many human oncogenes and tumor suppressors regulate glucose metabolism.
“First, many human oncogenes and tumor suppressors regulate glucose metabolism (Figure 3A) (DeBerardinis, 2008; Jones and Thompson, 2009).”
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- cites Jones and Thompson, 2009 source
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- Interpretationreasoning
The ability of tumors to out-compete surrounding tissue for glucose explains the success of FDG-PET to image tumors of many histological types.
“This trait explains the success of 18fluoro-2-deoxyglucose positron emission tomography (FDG-PET) to image tumors of many histological types.”
Quote in the paperSubstantial claim - Interpretationreasoning
Metabolic reprogramming in tumors can occur as the direct effect of enzyme mutations.
“Second, metabolic reprogramming can occur as the direct effect of enzyme mutations.”
Quote in the paperSubstantial claim - Interpretationnone given
The metabolic idiosyncrasies of tumors are genetically defined, resulting from the same mutations that promote malignancy.
“As in IEMs, the metabolic idiosyncrasies of tumors are genetically defined, resulting from the same mutations that promote malignancy.”
Quote in the paperSubstantial claim - Premisecitation
High levels of fumarate can modify cysteine residues through succination, converting sulfhydryl groups on cysteine to S-(2-succinyl)-cysteine (2SC), in some cases interfering with protein function.
“Interestingly, because of its electrophilic properties, high levels of fumarate can modify cysteine residues through a process termed succination. This process converts sulfhydryl groups on cysteine to S-(2-succinyl)-cysteine (2SC), in some cases interfering with protein function (Alderson et al., 2006).”
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- Interpretationreasoning
These effects chronically poise SDH- and FH-deficient cells for glycolysis, regardless of whether or not oxygen is available.
“These effects chronically poise SDH- and FH-deficient cells for glycolysis, regardless of whether or not oxygen is available.”
Quote in the paperSubstantial claim - Interpretationreasoning
Cancer is a paradigm for how perturbed metabolism at the cellular level contributes to disease.
“Thus, cancer is a paradigm for how perturbed metabolism at the cellular level contributes to disease.”
Quote in the paperSubstantial claim - Premisecitation
Accumulation of reactive oxygen species, an independent trigger for HIF stabilization, may contribute to this process in some cases of defective SDH or FH.
“Accumulation of reactive oxygen species, an independent trigger for HIF stabilization, may contribute to this process in some cases of defective SDH or FH (Guzy et al., 2008; Sudarshan et al., 2009).”
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Cancer is associated with metabolic mutations confined to the tumor, in which metabolic enzymes behave genetically as oncogenes or tumor suppressors.
“Recently it has become apparent that cancer is also associated with metabolic mutations confined to the tumor. In these diseases, the metabolic enzymes behave genetically as oncogenes or tumor suppressors (Figure 3A) (Frezza et al., 2011a; Thompson, 2009).”
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- cites Thompson, 2009 source
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- Premisecitation
Cell growth downstream of PI3K/Akt/mTOR requires induction of de novo lipid synthesis via mTOR, due in part to increased nuclear localization of SREBP, which activates expression of lipogenic enzymes.
“Cell growth downstream of this pathway requires the induction of de novo lipid synthesis via mTOR, and this effect is due in part to increased nuclear localization of sterol regulatory element-binding protein (SREBP), a basic helix-loop-helix leucine zipper transcription factor that activates expression of a suite of lipogenic enzymes (Porstmann et al., 2008).”
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- Premisecitation
Genomic sequencing of gliomas and acute myelogenous leukemia identified mutations in two isoforms of NADP+-dependent isocitrate dehydrogenase (IDH1 and IDH2).
“Genomic sequencing of gliomas (Parsons et al., 2008; Yan et al., 2009) and acute myelogenous leukemia (Mardis et al., 2009) identified mutations in two isoforms of NADP+-dependent isocitrate dehydrogenase (IDH1 and IDH2).”
Quote in the paperSubstantial claim0 of 3 sources checked - Premisecitation
The PI3K/Akt/mTOR pathway is essential to cancer metabolic reprogramming because it regulates both nutrient uptake and allocation of carbon and nitrogen into biosynthetic pathways.
“The PI3K/Akt/mTOR pathway is essential to this process because it regulates both nutrient uptake and the allocation of carbon and nitrogen into biosynthetic pathways (Zoncu et al., 2011).”
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- Premisenone given
Many tumors can out-compete surrounding tissue for glucose.
“After Warburg, generations of cancer biologists and biochemists have refined his hypothesis and attempted to provide mechanistic explanations for it – but basically these studies have confirmed the central observation that many tumors can out-compete surrounding tissue for glucose.”
Quote in the paperSubstantial claim - Premisecitation
Tumor-promoting mutations in oncogenes and tumor suppressors tend to converge on a metabolic phenotype of enhanced glycolysis and energy production, contributing to self-sufficiency of growth and evasion of growth-suppressive signals.
“Tumor-promoting mutations in these genes tend to converge on a metabolic phenotype of enhanced glycolysis and energy production, thereby contributing to self-sufficiency of growth and evasion of growth-suppressive signals.”
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- cites Jones and Thompson, 2009 source
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- Premisecitation
Metabolic flux studies in cancer cells have validated the model that aggressive tumor growth requires metabolic restructuring, emphasizing integration of glycolysis, glutamine metabolism and fatty acid synthesis.
“Metabolic flux studies in cancer cells have validated this model, emphasizing the integration of these three core pathways (DeBerardinis et al., 2007).”
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- Interpretationreasoning
G6Pase deficiency mimics the Warburg effect and other oncogene-dependent metabolic phenomena, with shunting of glucose-6-phosphate into lactate and other metabolite pools.
“But it is noteworthy that G6Pase deficiency mimics the Warburg effect and other oncogene-dependent metabolic phenomena, with the shunting of glucose-6-phosphate into lactate and other metabolite pools.”
Quote in the paperSubstantial claim - Interpretationreasoning
The mechanisms connecting dysfunctional SDH/FH to malignancy are probably multi-factorial.
“The mechanisms connecting dysfunctional SDH/FH to malignancy are probably multi-factorial (Figure 3A).”
Quote in the paperNot a substantial claim - Interpretationreasoning
In IEMs with increased cancer risk due to mutagens or cirrhosis, the connection between metabolism and malignancy is probably indirect.
“In these cases the connection between metabolism and malignancy is probably indirect.”
Quote in the paperSubstantial claim - Premisecitation
Cells lacking FH have high levels of succination on KEAP1, an electrophile sensor and negative regulator of Nrf2.
“Cells lacking FH were shown to have high levels of succination on Kelch-like ECH-associated protein 1 (KEAP1), an electrophile sensor and negative regulator of the transcription factor Nuclear Factor E2-related factor 2 (Nrf2) (Adam et al., 2011; Ooi et al., 2011).”
Quote in the paperSubstantial claim0 of 2 sources checked - Premisecitation
Mutations in succinate dehydrogenase (SDH) were identified in dominantly inherited familial paraganglioma.
“Mutations in succinate dehydrogenase (SDH), an oxidoreductase complex that functions in both the ETC and TCA cycle, were identified in dominantly-inherited familial paraganglioma (Baysal, 2008; Baysal et al., 2000).”
Quote in the paperSubstantial claim0 of 2 sources checked - Interpretationreasoning
Dysfunctional mitochondrial metabolism and elevations of dicarboxylic intermediates of the TCA cycle promote aberrant signaling in tumor cells.
“Although it is still unclear how best to exploit any of these effects for cancer therapy, these findings collectively demonstrate that dysfunctional mitochondrial metabolism and elevations of dicarboxylic intermediates of the TCA cycle promote aberrant signaling in tumor cells.”
Quote in the paperSubstantial claim - Premisecitation
Strong evidence implicates dysfunctional cell signaling stimulated by succinate and/or fumarate, which accumulate to high levels in SDH/FH-deficient tumors.
“Strong evidence implicates dysfunctional cell signaling stimulated by succinate and/or fumarate, which accumulate to high levels in the tumors.”
Quote in the paperSubstantial claim0 of 2 sources checked - Interpretationreasoning
Failure to generate glucose from glycogenolysis or gluconeogenesis in G6Pase deficiency results in a large flux into other pathways supplied by glucose-6-phosphate in the liver, including glycolysis, lipid synthesis and nucleotide metabolism.
“The failure to generate glucose from either of these two pathways results in a large flux into other pathways supplied by glucose-6-phosphate in the liver, including glycolysis, lipid synthesis and nucleotide metabolism.”
Quote in the paperSubstantial claim - Premisenone given
IDH1 and IDH2 normally oxidize isocitrate to α-ketoglutarate, with NADP+ reduced to NADPH.
“These enzymes normally oxidize isocitrate to α-ketoglutarate, with NADP+ reduced to NADPH in the process.”
Quote in the paperSubstantial claim - Interpretationcitation
Aggressive tumor growth requires a restructuring of metabolism to meet the bioenergetic and biosynthetic demands of rapid cell growth and to protect the cells against stresses induced by a harsh microenvironment.
“One common hypothesis to unify these metabolic pathways is that aggressive tumor growth requires a restructuring of metabolism to meet the bioenergetic and biosynthetic demands of rapid cell growth and to protect the cells against stresses induced by a harsh microenvironment (Deberardinis et al., 2008; Semenza, 2010; Shanware et al., 2011).”
Quote in the paperSubstantial claim0 of 3 sources checked - Premisecitation
Mutations in fumarate hydratase (FH) were identified in familial syndromes characterized by susceptibility to renal cell cancer and leiomyomatosis.
“Mutations in the TCA cycle enzyme fumarate hydratase (FH) were identified in familial syndromes characterized by susceptibility to renal cell cancer and leiomyomatosis (smooth muscle tumors of the uterus and skin) (Tomlinson et al., 2002).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Tomlinson et al., 2002 source
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- Premisereasoning
G6Pase-deficient patients develop severe elevations of lactic acid, lipids and uric acid in the bloodstream.
“Along with massive accumulation of glycogen and fat in the liver, G6Pase-deficienct patients develop severe elevations of lactic acid, lipids and uric acid in the bloodstream.”
Quote in the paperSubstantial claim - Premisecitation
Hyperpolarization has been used successfully to quantify oncogene-driven metabolic activities in experimental tumors.
“Hyperpolarization has been used successfully to quantify oncogene-driven metabolic activities in experimental tumors (Hu et al., 2011).”
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- Premisecitation
Successful quantification of significant metabolites like glycine and 2-HG has already been reported for human gliomas.
“Successful quantification of significant metabolites like glycine and 2-HG has already been reported for human gliomas (Choi, 2011a; Choi et al., 2011b)”
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- cites Choi et al., 2011b
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A large fraction of children with (L)-2-hydroxyglutaric aciduria have developed brain tumors or other types of cancer.
“A large fraction of children with this disease have developed brain tumors or other types of cancer (Moroni et al., 2004).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Moroni et al., 2004 source
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- Rests on an assumption: Children with (L)-2-hydroxyglutaric aciduria accumulate the (L)-isomer of 2-HG in all body fluids.
- Premisecitation
The importance of additional nutrients besides glucose to tumor metabolism has prompted the development of several new PET agents for cancer, including glutamate and glutamine.
“The importance of additional nutrients besides glucose to tumor metabolism has prompted the development of several new PET agents for cancer, including glutamate and glutamine (Koglin et al., 2011; Qu et al., 2011).”
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- cites Qu et al., 2011
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- Interpretationreasoning
The presence of 2-HG in IDH-mutant tumors mirrors one of the best-established connections between an IEM and cancer.
“The presence of 2-HG in these tumors is compelling because it mirrors one of the best-established connections between an IEM and cancer.”
Quote in the paperSubstantial claim - Premisecitation
Up to half of patients with (D)-2-hydroxyglutaric aciduria contain heterozygous active-site mutations in IDH2.
“up to half of patients with (D)-2-hydroxyglutaric aciduria contain heterozygous active-site mutations in IDH2 (Kranendijk et al., 2010).”
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- Premisecitation
High concentrations of 2-HG inhibited the function of α-ketoglutarate-dependent histone demethylases and 5-methylcytosine hydroxylases in vitro.
“high concentrations of 2-HG inhibited the function of α-ketoglutarate-dependent histone demethylases and 5-methylcytosine hydroxylases in vitro”
Quote in the paperSubstantial claim0 of 2 sources checked- cites Figueroa et al., 2010 source
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- cites Xu et al., 2011
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- Interpretationreasoning
Active-site mutations in IDH1 and IDH2 seem to confer oncogenic properties to the enzyme.
“Thus, active-site mutations in IDH1 and IDH2 seem to confer oncogenic properties to the enzyme”
Quote in the paperSubstantial claim- Rests on an assumption: Children with (L)-2-hydroxyglutaric aciduria accumulate the (L)-isomer of 2-HG in all body fluids.
- Interpretationreasoning
Production of the oncometabolite 2-HG may be the crucial factor that tips susceptible populations of cells into a transformed state.
“production of the oncometabolite 2-HG may be the crucial factor that tips susceptible populations of cells into a transformed state.”
Quote in the paperSubstantial claim- Rests on an assumption: Children with (L)-2-hydroxyglutaric aciduria accumulate the (L)-isomer of 2-HG in all body fluids.
- Premisecitation
Mutations in IDH1/2 and in the 5-methylcytosine hydroxylase TET2 occur frequently in acute myelogenous leukemia.
“mutations in IDH1/2 and in the 5-methylcytosine hydroxylase TET2 occur frequently in acute myelogenous leukemia”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Figueroa et al., 2010 source
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- Interpretationnone given
2-HG exerts its effects by influencing some of the more than 50 mammalian dioxygenases that use α-ketoglutarate as a substrate.
“Recent data suggest that 2-HG exerts its effects by influencing some of the more than 50 mammalian dioxygenases that use α-ketoglutarate as a substrate”
Quote in the paperSubstantial claim- Rests on an assumption: The more than 50 mammalian dioxygenases that use α-ketoglutarate as a substrate regulate crucial processes including methylation of histones and DNA.
- Interpretationreasoning
High levels of PHGDH define another class of genetically-defined metabolic outliers with vulnerabilities that could perhaps be exploited therapeutically in cancer.
“Therefore high levels of PHGDH define another class of genetically-defined metabolic outliers with vulnerabilities that could perhaps be exploited therapeutically in cancer.”
Quote in the paperSubstantial claim- Rests on an assumption: PHGDH is an enzyme required to produce the amino acids serine and glycine from glucose.
- Rests on an assumption: Serine and glycine are crucial intermediates in biosynthetic processes including the production of nucleotides, proteins, glutathione, creatine, and methylated DNA.
- Interpretationcitation
Metabolic imaging using hyperpolarization of 13C and other stable isotopes has considerable translational potential in human disease because of its high sensitivity, integration with MRI, lack of the need for radioactive tracers, and ability to probe the flux of specific enzymatic reactions in vivo.
“metabolic imaging using hyperpolarization of 13C and other stable isotopes has considerable translational potential in human disease because of its high sensitivity, integration with MRI, lack of the need for radioactive tracers, and in particular its ability to probe the flux of specific enzymatic reactions in vivo (Kurhanewicz et al., 2011).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Kurhanewicz et al., 2011 source
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- Interpretationreasoning
IDH1/2 mutations have the potential to exert tremendous effects on cellular function and differentiation because widespread methylation changes of histones and DNA could broadly influence epigenetics.
“Because widespread methylation changes of histones and DNA could broadly influence epigenetics, IDH1/2 mutations have the potential to exert tremendous effects on cellular function and differentiation”
Quote in the paperSubstantial claim- Rests on an assumption: The more than 50 mammalian dioxygenases that use α-ketoglutarate as a substrate regulate crucial processes including methylation of histones and DNA.
- Premisecitation
The region of chromosome 1p12 encoding PHGDH is amplified in a significant fraction of tumors.
“the region of chromosome 1p12 encoding PHGDH is amplified in a significant fraction of tumors”
Quote in the paperSubstantial claim0 of 2 sources checked- cites Locasale et al., 2011 source
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- cites Possemato et al., 2011 source
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- Rests on an assumption: PHGDH is an enzyme required to produce the amino acids serine and glycine from glucose.
- Rests on an assumption: Serine and glycine are crucial intermediates in biosynthetic processes including the production of nucleotides, proteins, glutathione, creatine, and methylated DNA.
- Interpretationcitation
The mutual exclusivity of IDH1/2 and TET2 mutations suggests that the two types of mutation exert redundant effects on the cell.
“suggesting that the two different types of mutation exert redundant effects on the cell”
Quote in the paperSubstantial claim - Premisecitation
Cell lines derived from tumors with PHGDH amplification tend to be highly dependent on PHGDH expression.
“cell lines derived from these tumors tend to be highly dependent on PHGDH expression”
Quote in the paperSubstantial claim0 of 2 sources checked- cites Locasale et al., 2011 source
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- cites Possemato et al., 2011 source
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- Rests on an assumption: PHGDH is an enzyme required to produce the amino acids serine and glycine from glucose.
- Rests on an assumption: Serine and glycine are crucial intermediates in biosynthetic processes including the production of nucleotides, proteins, glutathione, creatine, and methylated DNA.
- Premisecitation
High levels of PHGDH protein expression relative to normal tissue correlate with disease severity in breast cancer patients.
“High levels of PHGDH protein expression relative to normal tissue correlates with disease severity in breast cancer patients (Pollari et al., 2011).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Pollari et al., 2011 source
Not checked in the free run.
- Rests on an assumption: PHGDH is an enzyme required to produce the amino acids serine and glycine from glucose.
- Rests on an assumption: Serine and glycine are crucial intermediates in biosynthetic processes including the production of nucleotides, proteins, glutathione, creatine, and methylated DNA.
- Premisecitation
Tumor tissue and cell lines expressing mutant IDH1 or IDH2 produced large quantities of (D)-2-hydroxyglutarate (2-HG), which is vanishingly scarce when only wild-type enzymes were expressed.
“This suspicion was confirmed by metabolomics: tumor tissue and cell lines expressing mutant IDH1 or IDH2 produced large quantities of a metabolite, (D)-2-hydroxyglutarate (2-HG), that is vanishingly scarce when only the wild-type enzymes were expressed (Dang et al., 2009).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Dang et al., 2009 source
Not checked in the free run.
- Premisecitation
Primary IDH1- or IDH2-mutant tumors showed evidence of extensively altered histone and DNA methylation in vivo.
“primary IDH1- or IDH2-mutant tumors showed evidence of extensively altered histone and DNA methylation in vivo”
Quote in the paperSubstantial claim0 of 2 sources checked- cites Figueroa et al., 2010 source
Not checked in the free run.
- cites Xu et al., 2011
Not checked in the free run.
- Premisecitation
Even large accumulations of 2-HG do not cause wholesale perturbations of metabolite levels in IDH1-mutant tumors.
“Surprisingly, even large accumulations of 2-HG do not cause wholesale perturbations of metabolite levels in IDH1-mutant tumors (Dang et al., 2009).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Dang et al., 2009 source
Not checked in the free run.
- Interpretationreasoning
Because metabolism involves so many intersecting pathways, it may be impossible to infer which pathway(s) are affected when abnormal levels of a metabolite are observed.
“because metabolism involves so many intersecting pathways, it may be impossible to infer which pathway(s) are affected when abnormal levels of a metabolite are observed.”
Quote in the paperSubstantial claim- Rests on an assumption: An elevated level of a metabolite in newborn screening tests almost always reflects decreased rather than increased flux of the pathway.
- Premisecitation
Tumor cells with mutations in the TCA cycle or ETC, or with hypoxia-induced suppression of oxidative metabolism, use reductive carboxylation of α-KG to produce citrate and other precursors during growth.
“tumor cells with mutations in the TCA cycle or ETC (Mullen et al., 2011), or with hypoxia-induced suppression of oxidative metabolism (Metallo et al., 2011; Scott et al., 2011; Wise et al., 2011) use reductive carboxylation of α-KG to produce citrate and other precursors during growth.”
Quote in the paperSubstantial claim0 of 3 sources checked - Premisereasoning
In reductive carboxylation, NADPH-dependent isoforms of IDH act in reverse with respect to their conventional role as oxidative decarboxylases.
“In this reaction, NADPH-dependent isoforms of IDH act in reverse with respect to their conventional role as oxidative decarboxylases”
Quote in the paperSubstantial claim - Premisecitation
IDH1/2 and TET2 mutations were found to be mutually exclusive in acute myelogenous leukemia.
“the mutations were found to be mutually exclusive”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Figueroa et al., 2010 source
Not checked in the free run.
- Interpretationreasoning
Combined metabolomics-metabolic flux studies have tremendous value because they could produce a quantitative and comprehensive readout of the variation in metabolic pathway activity, leading to a deeper understanding of metabolic individuality and the biological basis of disease in humans.
“Combined metabolomics-metabolic flux studies, despite their technical challenges, have tremendous value because they could produce a quantitative and comprehensive readout of the variation in metabolic pathway activity, leading to a deeper understanding of metabolic individuality and the biological basis of disease in humans.”
Quote in the paperSubstantial claim - Interpretationreasoning
Unlike FH and SDH, the data for IDH1 and IDH2 were more consistent with a gain-of-function referable to the altered enzymatic active site than with tumor suppressor loss.
“Thus, unlike FH and SDH, it was difficult to make a case for IDH1 and IDH2 as tumor suppressors. The data were more consistent with a gain-of-function referable to the altered enzymatic active site.”
Quote in the paperSubstantial claim
- May combine two claims. 32
- Classified as probably not a substantial claim. 7
May combine two claims.
PremisecitationA rise in intracellular acetyl-CoA occurs in phase with induction of growth genes, and a bolus of extracellular nutrients convertible to acetyl-CoA causes yeast cells to short-circuit the metabolic cycle and enter directly into growth.
“A rise in intracellular acetyl-CoA occurs in phase with the induction of growth genes, and a bolus of extracellular nutrients that can be readily converted to acetyl-CoA causes cells to short-circuit the metabolic cycle and enter directly into growth (Cai et al., 2011).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Cai et al., 2011 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationThere are now some 500 recognized IEMs, making this the largest category of heritable human diseases.
“There are now some 500 recognized IEMs (Childs et al., 2001), making this the largest category of heritable human diseases.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Childs et al., 2001
Not checked in the free run.
May combine two claims.
PremisecitationAltered cellular metabolism is a hallmark of cancer, contributing to malignant transformation and to the initiation, growth and maintenance of tumors.
“Altered cellular metabolism is a hallmark of cancer, contributing to malignant transformation and to the initiation, growth and maintenance of tumors (Hanahan and Weinberg, 2011).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Hanahan and Weinberg, 2011 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationThe PI3K/Akt/mTOR pathway stimulates a rapid increase in essential nutrient uptake and the proper allocation of nutrients into catabolic and anabolic pathways to produce energy and macromolecules.
“In particular, the PI3K/Akt/mTOR pathway stimulates both a rapid increase in essential nutrient uptake and the proper allocation of these nutrients into catabolic and anabolic pathways to produce energy and macromolecules, respectively (Gibbons et al., 2009).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Gibbons et al., 2009
Not checked in the free run.
May combine two claims.
PremisecitationAcetyl-CoA groups used to modify histones are predominantly produced by acetyl-CoA synthetase in yeast and ATP-citrate lyase in mammalian cells, both of which enter the nucleus to produce a localized acetyl-CoA pool.
“The acetyl-CoA groups used to modify histones are predominantly produced by acetyl-CoA synthetase in yeast and ATP-citrate lyase in mammalian cells, both of which enter the nucleus to produce a localized acetyl-CoA pool for this purpose (Figure 2).”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites Takahashi et al., 2006
Not checked in the free run.
- cites Wellen et al., 2009 source
Not checked in the free run.
May combine two claims.
PremisecitationSynthesis of plasmalogens and oxidation of fatty acids 24-26 carbons in length occur in peroxisomes, as realized when abnormal levels of these metabolites were observed in patients with peroxisomal dysfunction.
“Synthesis of plasmalogens and oxidation of fatty acids 24-26 carbons in length occur in the peroxisomes, but this was only realized when abnormal levels of these metabolites were observed in patients with peroxisomal dysfunction (Wanders and Waterham, 2006).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Wanders and Waterham, 2006 source
Not checked in the free run.
May combine two claims.
PremisecitationThe vast majority of IEMs result from recessively inherited loss-of-function mutations in enzymes and transporters, although several are caused by mutations that either stimulate basal enzymatic activity or evoke altogether new functions.
“The vast majority of IEMs result from recessively inherited loss-of-function mutations in enzymes and transporters, although several are caused by mutations that either stimulate basal enzymatic activity or evoke altogether new functions (Kranendijk et al., 2010; Stanley et al., 1998).”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites Kranendijk et al., 2010 source
Not checked in the free run.
- cites Stanley et al., 1998
Not checked in the free run.
May combine two claims.
InterpretationcitationThese studies prove that a wide range of human metabolic diversity is genetically programmed and emphasize intimate connections between metabolism and health.
“These studies prove that a wide range of human metabolic diversity is genetically programmed, and they emphasize the intimate connections between metabolism and health.”
Quote in the paperSubstantial claimMay combine two claims.
PremisecitationUnless glucose is present in adequate amounts to supply flux through the hexosamine pathway, cells lose the ability to respond to growth factor signaling and no longer take up the full complement of nutrients required for growth.
“Unless glucose is present in adequate amounts to supply flux through the hexosamine pathway, cells lose the ability to respond to growth factor signaling and no longer take up the full complement of nutrients required for growth (Wellen et al., 2010).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Wellen et al., 2010
Not checked in the free run.
May combine two claims.
PremisecitationAMPK inactivates energy-consuming growth-promoting pathways like protein and lipid synthesis and activates catabolism of fatty acids and other fuels, rebalancing energy supply with demand.
“By phosphorylating a number of key targets, AMPK inactivates energy-consuming, growth-promoting pathways like protein and lipid synthesis, and activates catabolism of fatty acids and other fuels. This enables the cell to re-balance energy supply with demand.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Hardie, 2011 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationAMPK localizes to chromatin and phosphorylates histone H2B on serine 36, facilitating its effects on gene expression.
“AMPK also coordinates the expression of stress response genes by localizing to chromatin and phosphorylating histone H2B on serine 36, and this activity facilitates AMPK’s effects on gene expression (Bungard et al., 2010).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Bungard et al., 2010
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationAMPK is a fuel sensor activated during compromised bioenergetic states such as acute nutrient deprivation and hypoxia.
“This serine-threonine kinase is a “fuel sensor” activated during compromised bioenergetic states such as acute nutrient deprivation and hypoxia (Hardie, 2011).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Hardie, 2011 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationCPS is deacetylated by SIRT5 during fasting.
“For example, the urea cycle enzyme carbamoyl phosphate synthetase (CPS) is deacetylated by the sirtuin SIRT5 during fasting (Nakagawa et al., 2009).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Nakagawa et al., 2009 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
InterpretationreasoningMetabolism impacts, or is impacted by, virtually every other cellular process, and no area of biological research is totally free from the influence of metabolism.
“Rather, metabolism impacts, or is impacted by, virtually every other cellular process; there is no longer any space in biological research that is totally free from the influence of metabolism.”
Quote in the paperNot a substantial claimMay combine two claims.
PremisecitationBoth succinate and fumarate aberrantly increase the function of hypoxia inducible factors (HIFs).
“Furthermore, both succinate and fumarate aberrantly increase the function of hypoxia inducible factors (HIFs).”
Quote in the paperSubstantial claim0 of 2 sources checkedMay combine two claims.
Premisenone givenG6Pase catalyzes the final common step in glycogenolysis and gluconeogenesis, and G6Pase deficiency results in extreme fasting intolerance and hypoglycemia.
“G6Pase catalyzes the final common step in glycogenolysis and gluconeogenesis, and G6Pase deficiency results in extreme fasting intolerance and hypoglycemia.”
Quote in the paperSubstantial claimMay combine two claims.
PremisecitationBoth succinate and fumarate interfere with processes potentially involved in tumor suppression, including c-Jun-mediated apoptosis in pheochromocytoma cells and AMPK signaling.
“Both metabolites have been demonstrated to interfere with processes potentially involved in tumor suppression, including c-Jun-mediated apoptosis in pheochromocytoma cells (Lee et al., 2005) and AMPK signaling (Tong et al., 2011).”
Quote in the paperSubstantial claim0 of 2 sources checked- cites Lee et al., 2005 source
Not checked in the free run.
- cites Tong et al., 2011
Not checked in the free run.
May combine two claims.
PremisecitationLoss-of-function mutations have been identified in all four subunits of the SDH complex and in SDH5.
“Loss-of-function mutations have been identified in all four subunits of the SDH complex (Baysal, 2008; Burnichon et al., 2010), and in SDH5, which encodes a protein involved in incorporation of SDH’s flavin adenine dinucleotide cofactor (Hao et al., 2009).”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites Baysal, 2008
Not checked in the free run.
- cites Burnichon et al., 2010
Not checked in the free run.
- cites Hao et al., 2009 source
Not checked in the free run.
May combine two claims.
Premisenone givenG6Pase deficiency in Glycogen Storage Disease Type 1a is a risk factor for hepatocellular adenomas and HCC, but cirrhosis is not a prominent feature.
“Glucose-6-phosphatase (G6Pase) deficiency in Glycogen Storage Disease Type 1a is a risk factor for hepatocellular adenomas and HCC, but cirrhosis is not a prominent feature.”
Quote in the paperSubstantial claimMay combine two claims.
Premisenone givenIDH1 and IDH2 mutations in cancer are somatically acquired, present on only one allele, and confined to the enzyme's active site.
“IDH1 and IDH2 mutations in cancer are somatically acquired, present on only one allele, and confined to the enzyme’s active site.”
Quote in the paperSubstantial claimMay combine two claims.
PremisecitationmTOR's influence on SREBP involves phosphorylation of Lipin-1; mTOR-dependent Lipin-1 phosphorylation causes it to be retained in the cytosol, whereas mTOR inhibition leads to dephosphorylation and nuclear translocation of Lipin-1, where it is involved with depletion of nuclear SREBP.
“Recent work demonstrated that mTOR’s influence on SREBP involves phosphorylation of Lipin-1, a phosphatidic acid phosphatase. mTOR-dependent Lipin-1 phosphorylation causes it to be retained in the cytosol, whereas mTOR inhibition led to the dephosphorylation of Lipin-1 and its translocation to the nucleus, where it was involved with depletion of nuclear SREBP (Peterson et al., 2011).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Peterson et al., 2011
Not checked in the free run.
May combine two claims.
InterpretationreasoningNrf2 induces expression of genes involved in defense against reactive oxygen species, perhaps enabling malignant FH-deficient cells to tolerate high levels of oxidants.
“Nrf2 induces expression of a suite of genes involved in defense against reactive oxygen species, perhaps enabling malignant FH-deficient cells to tolerate high levels of exogenous or endogenous oxidants.”
Quote in the paperSubstantial claimMay combine two claims.
PremisecitationBoth succinate and fumarate are competitive PHD inhibitors, and massive accumulation of these metabolites in cells lacking SDH or FH activity elicits a hypoxic response even under oxygen-replete conditions.
“Both succinate and fumarate are competitive PHD inhibitors, and the massive accumulation of these metabolites in cells lacking SDH or FH activity elicit a hypoxic response even under oxygen-replete condition (Isaacs et al., 2005; Selak et al., 2005).”
Quote in the paperSubstantial claim0 of 2 sources checkedMay combine two claims.
InterpretationreasoningReprogramming metabolism into a platform that promotes cell growth and proliferation is an essential component of growth-factor signaling pathways and of malignancy resulting from constitutive activation of these pathways.
“Thus reprogramming metabolism into a platform that promotes cell growth and proliferation is an essential component of growth-factor signaling pathways and of malignancy resulting from constitutive activation of these pathways.”
Quote in the paperSubstantial claimMay combine two claims.
PremisecitationThe pathway of heme synthesis from glutamine followed by degradation via HMOX1 is enhanced in FH-deficient cells, and silencing HMOX1 prevents these cells from forming colonies.
“The pathway of heme synthesis from glutamine followed by degradation via HMOX1 is enhanced in FH-deficient cells, and silencing HMOX1 prevents these cells from forming colonies (Frezza et al., 2011b).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Frezza et al., 2011b
Not checked in the free run.
May combine two claims.
PremisecitationTumor tissue has additional metabolic characteristics, most consistently the tendency to metabolize glutamine and to synthesize fatty acids, both of which promote tumor growth in experimental models.
“Other work has identified additional metabolic characteristics of tumor tissue, most consistently the tendency to metabolize glutamine and to synthesize fatty acids, both of which promote tumor growth in experimental models (DeBerardinis and Cheng, 2010; Swinnen et al., 2006).”
Quote in the paperSubstantial claim0 of 2 sources checked- cites DeBerardinis and Cheng, 2010 source
Not checked in the free run.
- cites Swinnen et al., 2006
Not checked in the free run.
May combine two claims.
PremisecitationBoth HIF-1α and HIF-2α are dispensable for the formation of hyperplastic renal cysts in mice lacking expression of FH in the kidney, suggesting additional consequences of these enzyme deficiencies.
“However both HIF-1α and HIF-2α are dispensable for the formation of hyperplastic renal cysts in mice lacking expression of FH in the kidney (Adam et al., 2011), suggesting additional consequences of these enzyme deficiencies.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Adam et al., 2011 source
Not checked in the free run.
May combine two claims.
PremisereasoningCancer mutations are in general acquired somatically and associated with metabolic effects that appear to increase fitness and growth at the cellular level.
“Cancer mutations are in general acquired somatically and associated with metabolic effects that appear to increase fitness and growth at the cellular level.”
Quote in the paperSubstantial claimMay combine two claims.
PremisecitationMany IEMs with increased cancer risk, particularly hepatocellular carcinoma, either involve accumulation of mutagens or cause cirrhosis, an independent risk factor for HCC.
“Many of these diseases either involve the accumulation of mutagens or cause cirrhosis, an independent risk factor for HCC (Erez et al., 2011).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Erez et al., 2011
Not checked in the free run.
May combine two claims.
InterpretationreasoningIn families with SDH- or FH-deficient tumors, affected individuals inherit one mutation and their tumors display loss of the wild-type allele; thus both SDH and FH are tumor suppressors.
“In families with SDH- or FH-deficient tumors, affected individuals inherit one mutation and their tumors display loss of the wild-type allele. Thus, both SDH and FH are tumor suppressors.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationMagnetic resonance spectroscopy at 1.5-Tesla has been used for decades to produce semi-quantitative, non-invasive measurements of abundant metabolite pools in cancer.
“Magnetic resonance spectroscopy (MRS) at 1.5-Tesla has been used for decades to produce semi-quantitative, non-invasive measurements of abundant metabolite pools in cancer (Glunde and Bhujwalla, 2011).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Glunde and Bhujwalla, 2011
Not checked in the free run.
May combine two claims.
Premisecitation2-HG is produced from NADPH-dependent reduction of α-ketoglutarate to 2-HG, a neomorphic enzyme activity that occurs very efficiently when both mutant and wild-type alleles are expressed together.
“This metabolite is produced from the NADPH-dependent reduction of α-ketoglutarate to 2-HG (Fig. 3A,B), a neomorphic enzyme activity that occurs very efficiently when both mutant and wild-type alleles are expressed together (Pietrak et al., 2011).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Pietrak et al., 2011
Not checked in the free run.
May combine two claims.
InterpretationreasoningMetabolomics methods do not present a complete view of metabolism and in some cases can produce misleading results.
“While methods to catalog and quantify small molecules in biological fluids (metabolomics) are highly informative, they do not present a complete view of metabolism and in some cases can produce misleading results.”
Quote in the paperSubstantial claim- Rests on an assumption: An elevated level of a metabolite in newborn screening tests almost always reflects decreased rather than increased flux of the pathway.
May combine two claims.
PremisecitationThe presence of IDH1/2 mutations in gliomas is associated with both lower histological grade and a slower rate of disease progression.
“the presence of IDH1/2 mutations in gliomas is associated with both lower histological grade and a slower rate of disease progression”
Quote in the paperSubstantial claim0 of 2 sources checkedMay combine two claims.
PremisecitationOver-expressing PHGDH was sufficient to promote anchorage independence in breast epithelial cells and to disturb cell polarity, phenotypes taken to be consistent with malignancy.
“over-expressing PHGDH was sufficient to promote anchorage independence in breast epithelial cells and to disturb cell polarity, phenotypes taken to be consistent with malignancy”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Locasale et al., 2011 source
Not checked in the free run.
- Rests on an assumption: PHGDH is an enzyme required to produce the amino acids serine and glycine from glucose.
- Rests on an assumption: Serine and glycine are crucial intermediates in biosynthetic processes including the production of nucleotides, proteins, glutathione, creatine, and methylated DNA.
May combine two claims.
PremisecitationSimilar approaches focusing on a handful of metabolites have already been used successfully in humans to measure gluconeogenesis and the urea cycle in vivo, and to compare metabolism between lung tumors and surrounding tissue.
“Similar approaches focusing on a handful of metabolites have already been used successfully in humans to measure gluconeogenesis and the urea cycle in vivo, and to compare metabolism between lung tumors and surrounding tissue (Fan et al., 2009; Landau et al., 1996; Yudkoff et al., 2010).”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites Fan et al., 2009
Not checked in the free run.
- cites Landau et al., 1996 source
Not checked in the free run.
- cites Yudkoff et al., 2010
Not checked in the free run.
The paper relies on this without support.
Children with (L)-2-hydroxyglutaric aciduria accumulate the (L)-isomer of 2-HG in all body fluids.
“Children with (L)-2-hydroxyglutaric aciduria, an autosomal recessive condition caused by deficiency of (L)-2-HG dehydrogenase, which converts 2-HG to α-ketoglutarate, accumulate the (L)-isomer of 2-HG in all body fluids.”
The paper relies on this without support.
The more than 50 mammalian dioxygenases that use α-ketoglutarate as a substrate regulate crucial processes including methylation of histones and DNA.
“These enzymes regulate a number of crucial processes including methylation of histones and DNA.”
The paper relies on this without support.
PHGDH is an enzyme required to produce the amino acids serine and glycine from glucose.
“phosphoglycerate dehydrogenase (PHGDH), an enzyme required to produce the amino acids serine and glycine from glucose”
The paper relies on this without support.
Serine and glycine are crucial intermediates in biosynthetic processes including the production of nucleotides, proteins, glutathione, creatine, and methylated DNA.
“Serine and glycine are crucial intermediates in a variety of biosynthetic processes including the production of nucleotides, proteins, glutathione, creatine, and methylated DNA.”
The paper relies on this without support.
An elevated level of a metabolite in newborn screening tests almost always reflects decreased rather than increased flux of the pathway.
“An elevated level of a metabolite in these screening tests almost always reflects decreased rather than increased flux of the pathway”
The paper relies on this without support.
SLC2A1 is a HIF-1 transcriptional target and encodes the predominant glucose transporter in cancer cells, GLUT1.
“SLC2A1 is a HIF-1 transcriptional target and encodes the predominant glucose transporter in cancer cells, GLUT1.”
The paper relies on this without support.
GLUT1 is the major transporter at the blood-brain barrier and is responsible for supplying glucose to the brain.
“GLUT1 is also the major transporter at the blood-brain barrier and is responsible for supplying glucose to the brain.”
The paper relies on this without support.
GLUT1 deficiency most commonly involves severe central nervous system manifestations including seizures, mental retardation and poor growth of the postnatal brain.
“GLUT1 deficiency has a wide phenotypic spectrum but its most common form involves severe central nervous system manifestations including seizures, mental retardation and poor growth of the postnatal brain.”
The paper relies on this without support.
Severe LDHA deficiency causes Glycogen Storage Disease Type XI, which causes exercise intolerance, cramps and occasional myoglobinuria in adolescents and adults, but is not associated with severe dysfunction of major homeostatic organs.
“Severe LDHA deficiency is also a well-characterized human disease, Glycogen Storage Disease Type XI. This disorder causes exercise intolerance, cramps and occasional myoglobinuria in adolescents and adults, but is not associated with severe dysfunction of major homeostatic organs.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Steady-state metabolite levels provide no measurement of metabolite flux, that is, the speed or direction of metabolite flow through a given pathway.
“One caution of measuring steady-state metabolite levels is that these data provide no measurement of metabolite flux, that is, the speed or direction of metabolite flow through a given pathway (115).”
From Fueling Immunity: Insights into Metabolism and Lymphocyte Function (2013) · cites this paper as [115]
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Self-citationRecurring mutations found by sequencing an acute myeloid leukemia genome
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Succinate links TCA cycle dysfunction to oncogenesis by inhibiting HIF-α prolyl hydroxylase
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Fundamentals of Cancer Metabolism
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“The drastic decreases in HK2 and LDHA, the two key enzymes supporting aerobic glycolysis (DeBerardinis and Thompson, 2012; Dang, 2012), are consistent with neurons not having high flux aerobic glycolysis and exhibiting low lactate production.”
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- Authors
- DeBerardinis, R. J., & Thompson, C. B.
- Affiliations
- The University of Texas Southwestern Medical Center (US)
- Memorial Sloan Kettering Cancer Center (US)
- Corresponding author
- DeBerardinis, Ralph J.
- Thompson, Craig B.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-03
- Volume
- 148
- Issue
- 6
- Pages
- 1132-1144
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3337773
- OpenAlex
- W2162790428
- Cited by
- 858
- References
- 100
- Citations by year
- 2026: 45 · 2025: 49 · 2024: 71 · 2023: 82 · 2022: 65 · 2021: 89 · 2020: 73 · 2019: 63 · 2018: 60 · 2017: 40 · 2016: 42 · 2015: 59 · 2014: 61 · 2013: 40 · 2012: 19
- FWCI
- 4.28
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Cancer Institute (R01CA105463, R01CA157996)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer, Hypoxia, and Metabolism
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Cancer and biochemical research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolism, Diabetes, and Cancer
- Keywords
- cellular metabolism, metabolic disorders, genetic metabolic disorders, cancer metabolism, metabolic therapy, tissue dysfunction, metabolic pathways
- MeSH terms
- Animals, Humans, Metabolic Diseases, Neoplasms, Metabolic Networks and Pathways
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-10.
Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-10.
Statistics and arithmetic are recomputed, not judged.
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