Coupling Krebs cycle metabolites to signalling in immunity and cancer

In the paper

“Recent data demonstrated that fumarate acts as a powerful inhibitor of the TET family of DNA demethylases and of a series of histone demethylases91,92.”

What the sources say

• ?Could not verify

  The paper’s discussion of fumarate and succination (section “Dimethyl fumarate: targeting glycolysis to treat MS,” page not identified in our copy) concerns GAPDH inhibition. Searches for TET-family DNA demethylases and histone demethylases found no passage addressing whether fumarate inhibits either group. (LLM, conf=0.76)

  cites [91] Angiari, S. & O’Neill, L. A. Dimethyl fumarate: targeting glycolysis to treat MS. Cell Res. 28, 613–615 (2018). sourceExperimental — accuracy not yet measured
• ?Could not verify

  The paper’s Abstract discusses fumarate and dimethyl fumarate modifying proteins, particularly GAPDH, but does not address inhibition of TET DNA demethylases or histone demethylases. Searches for those enzymes and for epigenetic demethylation found no passage supporting the attributed claim. (LLM, conf=0.72)

  cites [92] Kornberg, M. D. et al. Dimethyl fumarate targets GAPDH and aerobic glycolysis to modulate immunity. Science 360, 449–453 (2018). sourceExperimental — accuracy not yet measured

In the paper

“High levels of succinate or 2-HG inhibit α-KGDDs. These include the PHDs, the TET DNA demethylases, and the JMJDs154-156”

What the sources say

• Not checked yetcites [60] Lee, C. G., Jenkins, N. A., Gilbert, D. J., Copeland, N. G. & O’Brien, W. E. Cloning and analysis of gene regulation of a novel LPS-inducible cDNA. Immunogenetics 41, 263–270 (1995). source
• Not checked yetcites [61] Shin, J. H. et al. 1H NMR-based metabolomic profiling in mice infected with Mycobacterium tuberculosis. J. Proteome Res. 10, 2238–2247 (2011). source
• Not checked yetcites [62] Sugimoto, M. S. H. Y. et al. Non-targeted metabolite profiling in activated macrophage secretion. Metabolomics 8, 624–633 (2011). source
• Partly supported

  The passages labeled Abstract identify TET enzymes and Jumonji-domain histone demethylases as possible D2HG targets and state that succinate inhibits PHDs. The ROS section reports evidence consistent with D2HG inhibition of TET enzymes and says the authors concur that it blocks PHD-mediated modification, but it also notes conflicting PHD findings and no change in histone methylation in their cells. The copy does not establish that succinate inhibits TET enzymes or JMJDs, so the claim's unqualified grouping overstates the evidence. (LLM, conf=0.83)

  cites [154] Sasaki, M. et al. d-2-hydroxyglutarate produced by mutant IDH1 perturbs collagen maturation and basement membrane function. Genes Dev. 26, 2038–2049 (2012). sourceExperimental — accuracy not yet measured
• Partly supported

  The introduction (page unavailable) says elevated succinate and 2-HG are proposed to inhibit 2-oxoglutarate oxygenases. The paper reports 2-HG inhibition of a JmjC demethylase, but treats inhibition of TET enzymes as possible and finds that 2-HG is only a weak inhibitor of PHD2. The claim presents inhibition across all three enzyme groups more definitively than the source does. (LLM, conf=0.85)

  cites [155] Tarhonskaya, H. et al. Non-enzymatic chemistry enables 2-hydroxyglutarate-mediated activation of 2-oxoglutarate oxygenases. Nat. Commun. 5, 3423 (2014). sourceExperimental — accuracy not yet measured
• Partly supported

  The Introduction (page unavailable) says D-2-HG inhibits α-KG-dependent dioxygenases, including JmjC histone demethylases and TET DNA hydroxylases. Our copy does not support the additional claims that succinate inhibits these enzymes or that PHDs are among the inhibited enzymes; searches for succinate and PHDs/prolyl hydroxylases found no relevant passage. (LLM, conf=0.88)

  cites [156] Wang, P. et al. Oncometabolite d-2-hydroxyglutarate inhibits ALKBH DNA repair enzymes and sensitizes IDH mutant cells to alkylating agents. Cell Rep. 13, 2353–2361 (2015). sourceExperimental — accuracy not yet measured

In the paper

“HIF-1 binds to hypoxia response elements (HREs) in target genes and increases the expression of numerous glycolytic enzymes and the glucose transporters (GLUT)1 and GLUT3.”

In the paper

“Analogous to tumours, LPS-induced succinate was shown to both directly and indirectly (via ROS) inhibit PHD activity in macrophages resulting in stabilization of HIF-1α2.”

What the sources say

• Not checked yetcites [2] Tannahill, G. M. et al. Succinate is an inflammatory signal that induces IL-1β through HIF-1α. Nature 496, 238–242 (2013). source

In the paper

“An additional mechanism by which succinate accumulates tumors involves the mitochondrial chaperone, tumor necrosis factor receptor-associated protein 1 (TRAP1) which is highly expressed in many tumors22. TRAP1 decreases SDH activity and succinate accumulates as a result.”

What the sources say

• Not checked yetcites [22] Epstein, A. C. R. et al. C. elegans EGL-9 and mammalian homologs define a family of dioxygenases that regulate HIF by prolyl hydroxylation. Cell 107, 43–54 (2001). source

In the paper

“In the presence of oxygen, conserved proline residues in the HIF-1α subunit are hydroxylated by PHD 1, 2 and 3 16. Hydroxylation provides a recognition site for the binding of Von Hippel-Lindau (VHL) E3 ubiquitin ligase, which ubiquitinates HIF-1α and subsequently targets it for proteasomal degradation17.”

What the sources say

• Not checked yetcites [16] Peruzzotti-Jametti, L. et al. Macrophage-derived extracellular succinate licenses neural stem cells to suppress chronic neuroinflammation. Cell Stem Cell 22, 355–368.e13 (2018). source
• Not checked yetcites [17] Bhuniya, D. et al. Discovery of a potent and selective small molecule hGPR91 antagonist. Bioorg. Med. Chem. Lett. 21, 3596–3602 (2011). source

In the paper

“SUCNR1 is highly expressed in mouse kidney, liver, spleen, small intestine3, and on dendritic cells (DCs) 4 and ligand binding induces Gi and Gq signalling cascades3.”

What the sources say

• Not checked yetcites [3] He, W. et al. Citric acid cycle intermediates as ligands for orphan G-protein-coupled receptors. Nature 429, 188–193 (2004). source
• Not checked yetcites [4] Chouchani, E. T. et al. A unifying mechanism for mitochondrial superoxide production during ischemia–reperfusion injury. Cell. Metab. 23, 254–263 (2016). source

In the paper

“Extracellular succinate addition also acts in synergy with TLR ligands to increase TNFα and IL-1β expression4 and increases the capacity of DCs to act as antigen presenting cells.”

What the sources say

• Not checked yetcites [4] Chouchani, E. T. et al. A unifying mechanism for mitochondrial superoxide production during ischemia–reperfusion injury. Cell. Metab. 23, 254–263 (2016). source

In the paper

“Specifically, succinate is elevated in plasma after acute exercise and in marathon runners175.”

What the sources say

• Not checked yetcites [175] Sivanand, S. et al. Nuclear acetyl-CoA production by ACLY promotes homologous recombination. Mol. Cell 67, 252–265.e56 (2017). source

In the paper

“succinate has been shown to act through several pathways to exert its inflammatory effects: through direct generation of mitochondrial ROS (mtROS), by activation of hypoxia-inducible factor-1alpha (HIF-1α; discussed below), and by through ligation of the G-protein coupled receptor succinate receptor 1 (SUCNR1).”

In the paper

“In a mouse model of multiple sclerosis (MS) transplantation of neural stem cells (NSCs) reduced succinate levels in the cerebrospinal fluid and thereby decreased infiltration of damaging macrophages and microglial cells10.”

What the sources say

• Not checked yetcites [10] Kim, S. et al. Global metabolite profiling of synovial fluid for the specific diagnosis of rheumatoid arthritis from other inflammatory arthritis. PLoS One 9, e97501 (2014). source

In the paper

“He and colleagues made an important discovery when they found that the Krebs cycle-derived metabolites, succinate and α-KG, acted as ligands for the orphan G-protein coupled receptors GPR91 (now known as SUCNR1) and GPR99 (now known as OXRG1), respectively3.”

What the sources say

• Not checked yetcites [3] He, W. et al. Citric acid cycle intermediates as ligands for orphan G-protein-coupled receptors. Nature 429, 188–193 (2004). source

In the paper

“This degradation is prevented in conditions of limited oxygen, allowing for HIF-1α translocation to the nucleus, dimerization with HIF-1β and binding of target genes13.”

What the sources say

• Not checked yetcites [13] van Diepen, J. A. et al. SUCNR1-mediated chemotaxis of macrophages aggravates obesity-induced inflammation and diabetes. Diabetologia 60, 1304–1313 (2017). source

In the paper

“The authors demonstrated that succinate acted as an important hypertensive agent, modulating the renin-angiotensin system via SUCNR1 signalling, independent of its role in bioenergetics3.”

What the sources say

• Not checked yetcites [3] He, W. et al. Citric acid cycle intermediates as ligands for orphan G-protein-coupled receptors. Nature 429, 188–193 (2004). source

In the paper

“ROS also impair the activity of Factor Inhibiting HIF (FIH), another member of the α-KGDD family25, which hydroxylates an asparagine residue in the carboxy terminal of HIF-1α resulting in a decrease in transcriptional activity.”

What the sources say

• Not checked yetcites [25] Frede, S., Stockmann, C., Freitag, P. & Fandrey, J. Bacterial lipopolysaccharide induces HIF-1 activation in human monocytes via p44/42 MAPK and NF-κB. Biochem. J. 396, 517–527 (2006). source

In the paper

“Recent data indicate that succinate is a pro-inflammatory metabolite that accumulates in LPS/IFN-γ-treated macrophages1,2.”

What the sources say

• Not checked yetcites [1] Jha, A. K. et al. Network integration of parallel metabolic and transcriptional data reveals metabolic modules that regulate macrophage polarization. Immunity 42, 419–430 (2015). source
• Not checked yetcites [2] Tannahill, G. M. et al. Succinate is an inflammatory signal that induces IL-1β through HIF-1α. Nature 496, 238–242 (2013). source

In the paper

“Mechanistically, ligation of SUCNR1 on the surface of NSCs upregulates the expression of the dicarboxylate co-transporter Slc13a3/5, which correlates with increased uptake by the NSCs thereby scavenging succinate away from pro-inflammatory immune cells.”

What the sources say

• Not checked yetcites [10] Kim, S. et al. Global metabolite profiling of synovial fluid for the specific diagnosis of rheumatoid arthritis from other inflammatory arthritis. PLoS One 9, e97501 (2014). source

In the paper

“ROS-can stabilize HIF-1α by inducing non-enzymatic decarboxylation of α-KG24 and by oxidizing iron (Fe2+) to Fe3+, two required PHD co-factors25.”

What the sources say

• Not checked yetcites [24] Pearce, E. L. & Pearce, E. J. Metabolic pathways in immune cell activation and quiescence. Immunity 38, 633–643 (2013). source
• Not checked yetcites [25] Frede, S., Stockmann, C., Freitag, P. & Fandrey, J. Bacterial lipopolysaccharide induces HIF-1 activation in human monocytes via p44/42 MAPK and NF-κB. Biochem. J. 396, 517–527 (2006). source

In the paper

“In the absence of SUCNR1 a reduction in absolute numbers of macrophages, but not inflammatory signalling, was observed and this resulted in an improvement in adipose tissue inflammation and improved glucose tolerance in mice following high-fat diet feeding.”

In the paper

“The PHDs generate succinate from α-KG, and importantly succinate (acting via product inhibition) will inhibit the PHDs and stabilize HIF-1α21.”

What the sources say

• Not checked yetcites [21] Semenza, G. L. Regulation of oxygen homeostasis by hypoxia-inducible factor 1. Physiology (Bethesda) 24, 97–106 (2009).

In the paper

“Following LPS treatment both intracellular succinate levels and the cell surface expression of SUCNR1 are increased.”

What the sources say

• Not checked yetcites [5] Rubic, T. et al. Triggering the succinate receptor GPR91 on dendritic cells enhances immunity. Nat. Immunol. 9, 1261–1269 (2008). source

In the paper

“This modification is caused by the accumulation of succinyl-CoA, which can result from SDH inhibition and succinate accumulation38.”

What the sources say

• Not checked yetcites [38] Jin, Z., Wei, W., Yang, M., Du, Y. & Wan, Y. Mitochondrial complex I activity suppresses inflammation and enhances bone resorption by shifting macrophage-osteoclast polarization. Cell. Metab. 20, 483–498 (2014). source

In the paper

“These data suggest that complex I of the ETC is an important site of ROS production in macrophages and such ROS production may depend on RET.”

In the paper

“These data demonstrate that succinate can have profound impacts on cellular function acting both intracellularly via ROS and HIF-1α, succinylation and histone and DNA modification and extracellularly via SUCNR1.”

In the paper

“Training with β-glucan was shown to be protective against Staphylococcus aureus infection and this effect was abrogated in HIF-1α-deficient mice.”

What the sources say

• Not checked yetcites [37] El-Khoury, R. et al. Engineering the alternative oxidase gene to better understand and counteract mitochondrial defects: state of the art and perspectives. Br. J. Pharmacol. 171, 2243–2249 (2014). source

In the paper

“The authors demonstrate that SIRT5 desuccinylates and activates PKM2 and this limits IL-1β production.”

What the sources say

• Not checked yetcites [46] Zhang, Z. et al. Identification of lysine succinylation as a new post-translational modification. Nat. Chem. Biol. 7, 58–63 (2011). source

In the paper

“DI was first employed as an experimental tool and was shown to potently induce Nrf2 and several Nrf2 target genes in control and LPS-activated BMDMs59.”

What the sources say

• Not checked yetcites [59] Okabe, M., Lies, D., Kanamasa, S. & Park, E. Y. Biotechnological production of itaconic acid and its biosynthesis in Aspergillus terreus. Appl. Microbiol. Biotechnol. 84, 597–606 (2009). source

In the paper

“Lampropoulou and colleagues (2016) suggested that mechanistically the ability of itaconate to modulate inflammation arose from its ability to competitively inhibit SDH and succinate oxidation50.”

What the sources say

• Not checked yetcites [50] Xie, Z. et al. Lysine succinylation and lysine malonylation in histones. Mol. Cell. Proteomics 11, 100–107 (2012). source

In the paper

“This requires both succinate oxidation by the enzyme succinate dehydrogenase (SDH) and an increase in mitochondrial membrane potential.”

What the sources say

• Not checked yetcites [2] Tannahill, G. M. et al. Succinate is an inflammatory signal that induces IL-1β through HIF-1α. Nature 496, 238–242 (2013). source
• Not checked yetcites [30] Guzy, R. D., Sharma, B., Bell, E., Chandel, N. S. & Schumacker, P. T. Loss of the SdhB, but not the SdhA, subunit of complex II triggers reactive oxygen species-dependent hypoxia-inducible factor activation and tumorigenesis. Mol. Cell. Biol. 28, 718–731 (2008). source

In the paper

“Since 2016, several key studies have uncovered a role for itaconate as a crucial anti-inflammatory metabolite that negatively regulates the inflammatory response and cytokine production50,59–61, as shown in Figure 3.”

What the sources say

• Not checked yetcites [50] Xie, Z. et al. Lysine succinylation and lysine malonylation in histones. Mol. Cell. Proteomics 11, 100–107 (2012). source
• Not checked yetcites [59] Okabe, M., Lies, D., Kanamasa, S. & Park, E. Y. Biotechnological production of itaconic acid and its biosynthesis in Aspergillus terreus. Appl. Microbiol. Biotechnol. 84, 597–606 (2009). source
• Not checked yetcites [60] Lee, C. G., Jenkins, N. A., Gilbert, D. J., Copeland, N. G. & O’Brien, W. E. Cloning and analysis of gene regulation of a novel LPS-inducible cDNA. Immunogenetics 41, 263–270 (1995). source
• Not checked yetcites [61] Shin, J. H. et al. 1H NMR-based metabolomic profiling in mice infected with Mycobacterium tuberculosis. J. Proteome Res. 10, 2238–2247 (2011). source

In the paper

“Furthermore, Irg1-deficient BMDMs, whereby genetic deletion of Irg1 completely abolished itaconate synthesis, exhibited a significant increase in the production of IL-12, IL-6, NO, and under conditions that activate the NLRP3 inflammasome, increased IL-1β and IL-1850.”

What the sources say

• Not checked yetcites [50] Xie, Z. et al. Lysine succinylation and lysine malonylation in histones. Mol. Cell. Proteomics 11, 100–107 (2012). source

In the paper

“LPS-induced HIF-1α not only promotes glycolysis but is also directly pro-inflammatory.”

In the paper

“The sustained induction of IL-1β in response to LPS was shown to require HIF-1α and to occur under normoxia.”

What the sources say

• Not checked yetcites [2] Tannahill, G. M. et al. Succinate is an inflammatory signal that induces IL-1β through HIF-1α. Nature 496, 238–242 (2013). source

In the paper

“SirT5, which was previously thought to function primarily as a deacetylase has been shown to have potent desuccinylase activity 44.”

What the sources say

• Not checked yetcites [44] Cheng, S. C. et al. mTOR- and HIF-1α-mediated aerobic glycolysis as metabolic basis for trained immunity. Science 345, 1250684 (2014). source

In the paper

“Limiting succinate oxidation with the pro-drug dimethylmalonate (DMM), which releases malonate that inhibits SDH function, profoundly represses LPS-induced HIF-1α, IL-1β and ROS and boosts IL-10 and IL-1RA.”

In the paper

“Western blot analysis of whole cell lysates revealed that this modification is evolutionarily conserved and that substrates are numerous39 and include proteins involved in cellular metabolism38.”

What the sources say

• Not checked yetcites [38] Jin, Z., Wei, W., Yang, M., Du, Y. & Wan, Y. Mitochondrial complex I activity suppresses inflammation and enhances bone resorption by shifting macrophage-osteoclast polarization. Cell. Metab. 20, 483–498 (2014). source
• Not checked yetcites [39] Murphy, M. P. How mitochondria produce reactive oxygen species. Biochem. J. 417, 1–13 (2009). source

In the paper

“It is also important to note that itaconate is an α,β-unsaturated carbonyl compound, making it a potential Michael acceptor that could undergo nucleophilic attack by the thiolate ion of protein cysteine residues, as such the methyl esterification of the proximal carboxyl group conjugated to the alkene would be predicted to increase the electrophilicity of itaconate63.”

What the sources say

• Not checked yetcites [63] Michelucci, A. et al. Immune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production. Proc. Natl. Acad. Sci. USA. 110, 7820–7825 (2013). source

In the paper

“Interestingly, in addition to potentiating cytokine production in response to LPS, training with β-glucan induced epigenetic upregulation of genes involved in glycolysis such as HIF-1α, Hexokinase (HK) and pyruvate kinase and increased succinate levels37.”

What the sources say

• Not checked yetcites [37] El-Khoury, R. et al. Engineering the alternative oxidase gene to better understand and counteract mitochondrial defects: state of the art and perspectives. Br. J. Pharmacol. 171, 2243–2249 (2014). source

In the paper

“The loss of HIF-1α in macrophages decreased TNF-α, IL-1β and IL-1α production, but did not affect production of the anti-inflammatory cytokines IL-4 or IL-10 29.”

What the sources say

• Not checked yetcites [29] Mu, X. et al. Oncometabolite succinate promotes angiogenesis by upregulating VEGF expression through GPR91-mediated STAT3 and ERK activation. Oncotarget 8, 13174–13185 (2017). source

In the paper

“inhibition of IκBξ by DI was shown to be mediated by activation of the transcription factor ATF3 and occur at the level of Nfkbiz translation, as assessed by eIF2α phosphorylation, in a Nrf2-independent manner60.”

What the sources say

• Not checked yetcites [60] Lee, C. G., Jenkins, N. A., Gilbert, D. J., Copeland, N. G. & O’Brien, W. E. Cloning and analysis of gene regulation of a novel LPS-inducible cDNA. Immunogenetics 41, 263–270 (1995). source

In the paper

“Supplementation of ROS in Irg1-deficient BMDMs increased A20 expression and abolished the break of endotoxin tolerance67.”

What the sources say

• Not checked yetcites [67] Bambouskova, M. et al. Electrophilic properties of itaconate and derivatives regulate the IκBξ–ATF3 inflammatory axis. Nature 556, 501–504 (2018). source

In the paper

“DI is reported to selectively inhibit LPS-induced IL-6 while TNF-α levels remain unaffected”

What the sources say

• Not checked yetcites [60] Lee, C. G., Jenkins, N. A., Gilbert, D. J., Copeland, N. G. & O’Brien, W. E. Cloning and analysis of gene regulation of a novel LPS-inducible cDNA. Immunogenetics 41, 263–270 (1995). source

In the paper

“4-OI was also shown to be protective in an LPS lethality model in vivo, prolonging survival, improving body temperature regulation and decreasing pro-inflammatory cytokine production59.”

What the sources say

• Not checked yetcites [59] Okabe, M., Lies, D., Kanamasa, S. & Park, E. Y. Biotechnological production of itaconic acid and its biosynthesis in Aspergillus terreus. Appl. Microbiol. Biotechnol. 84, 597–606 (2009). source

In the paper

“Intriguingly, endogenous fumarate was also found to succinate GAPDH in both mouse and human macrophages, suggesting that elevated fumarate levels may act as an endogenous anti-inflammatory signal to limit inflammation, however, the precise role of fumarate accumulation remains an open question to be explored.”

In the paper

“The authors proposed that fumarate accumulation acted to inhibit the KDM5 family of histone demethylases, which subsequently increased the levels of H3K4me3, a marker of active gene transcription, at the promoters of both Tnf and Il6, thus providing the first link between Krebs cycle rewiring and epigenetic regulation in an inflammatory context97.”

What the sources say

• Not checked yetcites [97] Rustin, P. et al. Inborn errors of the Krebs cycle: a group of unusual mitochondrial diseases in human. Biochim. Biophys. Acta 1361, 185–197 (1997). source

In the paper

“Later, it was also shown that fumarate binds glutathione (forming succinic-glutathione (succinicGSH)), and thereby depletes this antioxidant molecule leading to unscheduled oxidative stress83,84.”

What the sources say

• Not checked yetcites [83] Shi, H. Z., Wang, D., Sun, X. N. & Sheng, L. MicroRNA-378 acts as a prognosis marker and inhibits cell migration, invasion and epithelial-mesenchymal transition in human glioma by targeting IRG1. Eur. Rev. Med. Pharmacol. Sci. 22, 3837–3846 (2018).
• Not checked yetcites [84] Pan, J. et al. Immune responsive gene 1, a novel oncogene, increases the growth and tumorigenicity of glioma. Oncol. Rep. 32, 1957–1966 (2014). source

In the paper

“This was associated with a decrease in the microRNA miR-378, which targets Irg1 as well as poorer overall survival and clinicopathological parameters.”

What the sources say

• Not checked yetcites [75] Li, Y. et al. Immune responsive gene 1 (IRG1) promotes endotoxin tolerance by increasing A20 expression in macrophages through reactive oxygen species. J. Biol. Chem. 288, 16225–16234 (2013). source

In the paper

“However, in 2002 it was shown that mutations of FH are the cause of Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC), a cancer predisposition syndrome characterised by benign tumours of the smooth muscle of skin and uterus, and a very aggressive form of renal cancer78.”

What the sources say

• Not checked yetcites [78] Cheon, Y. P., Xu, X., Bagchi, M. K. & Bagchi, I. C. Immune-responsive gene 1 is a novel target of progesterone receptor and plays a critical role during implantation in the mouse. Endocrinology 144, 5623–5630 (2003). source

In the paper

“This suggestion arose from the observation that the cell-permeable fumaric esters, DMF and MMF, modify and irreversibly inhibit GAPDH enzymatic activity and aerobic glycolysis in peripheral blood mononuclear cells (PBMCs) from mice and MS patients treated with DMF99.”

What the sources say

• Not checked yetcites [99] Blatnik, M., Thorpe, S. R. & Baynes, J. W. Succination of proteins by fumarate: mechanism of inactivation of glyceraldehyde-3-phosphate dehydrogenase in diabetes. Ann. NY Acad. Sci. 1126, 272–275 (2008). source

In the paper

“suggesting there are two mechanisms for itaconate-induced Nrf2 activation; directly via KEAP1 2,3-dicarboxypropylation and indirectly via ROS production (which would then modify KEAP1)75.”

In the paper

“Mechanistically, DMF blocked the association of PKCθ with the costimulatory receptor CD28 and T cell activation.”

What the sources say

• Not checked yetcites [49] He, D. et al. Global proteome analyses of lysine acetylation and succinylation reveal the widespread involvement of both modification in metabolism in the embryo of germinating rice seed. J. Proteome Res. 15, 879–890 (2016). source

In the paper

“As Asl cleaves argininosuccinate into arginine and fumarate, the authors proposed that this metabolic pathway accounted for the elevated fumarate levels observed in macrophages1.”

What the sources say

• Not checked yetcites [1] Jha, A. K. et al. Network integration of parallel metabolic and transcriptional data reveals metabolic modules that regulate macrophage polarization. Immunity 42, 419–430 (2015). source

In the paper

“Blewett and colleagues (2016) demonstrated that dimethyl fumarate (DMF), a potent electrophile which is currently used to treat psoriasis and relapse-remitting MS, but not MMF inhibited the activation of human and mouse T cells 49.”

What the sources say

• Not checked yetcites [49] He, D. et al. Global proteome analyses of lysine acetylation and succinylation reveal the widespread involvement of both modification in metabolism in the embryo of germinating rice seed. J. Proteome Res. 15, 879–890 (2016). source

In the paper

“More recently, Kornberg and colleagues (2018) suggested that a potential consequence of elevated fumarate levels is to negatively regulate glycolysis via succination of the active site cysteine residue (C152) in GAPDH99,100.”

What the sources say

• Not checked yetcites [99] Blatnik, M., Thorpe, S. R. & Baynes, J. W. Succination of proteins by fumarate: mechanism of inactivation of glyceraldehyde-3-phosphate dehydrogenase in diabetes. Ann. NY Acad. Sci. 1126, 272–275 (2008). source
• Not checked yetcites [100] Adam, J. et al. Renal cyst formation in Fh1-deficient mice is independent of the Hif/Phd pathway: roles for fumarate in KEAP1 succination and Nrf2 signaling. Cancer Cell 20, 524–537 (2011). source

In the paper

“The effect of itaconate on ROS production is consistent with a previous study in zebrafish macrophages, which demonstrated that IRG1 was essential for OXPHOS-driven mtROS production and bactericidal killing172.”

What the sources say

• Not checked yetcites [172] Lee, J. V. et al. Akt-dependent metabolic reprogramming regulates tumor cell histone acetylation. Cell. Metab. 20, 306–319 (2014). source

In the paper

“Overexpression of miR-378 suppressed glioma tumour growth both in vitro and in vivo, the epithelial-mesenchymal transition (EMT) and metastasis75.”

What the sources say

• Not checked yetcites [75] Li, Y. et al. Immune responsive gene 1 (IRG1) promotes endotoxin tolerance by increasing A20 expression in macrophages through reactive oxygen species. J. Biol. Chem. 288, 16225–16234 (2013). source

In the paper

“Inhibition of GOT1 by aminooxyacetic acid (AOAA), which decreases D-2-HG levels, promoted expression Foxp3 and the differentiation of TH17 cells to iTregs143.”

What the sources say

• Not checked yetcites [143] Yan, H. et al. IDH1 and IDH2 mutations in gliomas. N. Engl. J. Med. 360, 765–773 (2009). source

In the paper

“The cause of these so-called 2-hydroxyglutaric acidurias (2HGAs) was attributed to germline mutations in L-2-HG dehydrogenase (L2HGDH) and D-2-HG dehydrogenase (D2HGDH), the mitochondrial enzymes responsible for the conversion of 2-HG to α-KG and thus its breakdown107-109.”

What the sources say

• Not checked yetcites [107] Bardella, C. et al. Aberrant succination of proteins in fumarate hydratase-deficient mice and HLRCC patients is a robust biomarker of mutation status. J. Pathol. 225, 4–11 (2011). source
• Not checked yetcites [108] Laukka, T. et al. Fumarate and succinate regulate expression of hypoxia-inducible genes via TET enzymes. J. Biol. Chem. 291, 4256–4265 (2016). source
• Not checked yetcites [109] Salminen, A., Kauppinen, A. & Kaarniranta, K. 2-Oxoglutarate-dependent dioxygenases are sensors of energy metabolism, oxygen availability, and iron homeostasis: potential role in the regulation of aging process. Cell. Mol. Life Sci. 72, 3897–3914 (2015). source

In the paper

“Overall, these lines of evidence provide a potential model for how fumarate accumulation promotes genomic alterations that could give rise to cancer formation in HLRCC patients, cooperating with the other above-described oncogenic signals it elicits.”

In the paper

“Like TH17 cells, CD8+ T cells are highly dependent on the activation of HIF-1α and glycolysis, which is responsible for mediating trafficking into hypoxic tumour environments and inflamed tissue147,148.”

What the sources say

• Not checked yetcites [147] Turcan, S. et al. IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype. Nature 483, 479–483 (2012). source
• Not checked yetcites [148] Wang, P. et al. Mutations in isocitrate dehydrogenase 1 and 2 occur frequently in intrahepatic cholangiocarcinomas and share hypermethylation targets with glioblastomas. Oncogene 32, 3091–3100 (2013). source

In the paper

“Here, via its reverse activity, it generates fumarate that inhibits histone lysine demethylase KDM2B, which in turn facilitates the binding of proteins involved in DNA repair177.”

What the sources say

• Not checked yetcites [177] Valls-Lacalle, L. et al. Selective inhibition of succinate dehydrogenase in reperfused myocardium with intracoronary malonate reduces infarct size. Sci. Rep. 8, 2442 (2018). source

In the paper

“In the case of D2HGA, about 50% of patients present with D2HGDH mutations, while the remaining half possess mutations in the Krebs cycle enzyme isocitrate dehydrogenase 2 (IDH2), which converts isocitrate to α-KG110.”

What the sources say

• Not checked yetcites [110] Isaacs, J. S. et al. HIF overexpression correlates with biallelic loss of fumarate hydratase in renal cancer: novel role of fumarate in regulation of HIF stability. Cancer Cell. 8, 143–153 (2005). source

In the paper

“T-helper 17 (TH17) cells, derived from naïve CD4+ T cells, are one such subset that rely heavily on a switch from OXPHOS to glycolysis, a process that requires the activation of HIF-1α and induction of RORγt143,146.”

What the sources say

• Not checked yetcites [143] Yan, H. et al. IDH1 and IDH2 mutations in gliomas. N. Engl. J. Med. 360, 765–773 (2009). source
• Not checked yetcites [146] Noushmehr, H. et al. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell. 17, 510–522 (2010). source

In the paper

“Consistent with an important role of senescence bypass for the development of tumorigenesis, recent data in HLRCC patients showed that CDKN2A (also known as P16), a key player in senescence, is hypermethylated and suppressed in tumours85.”

What the sources say

• Not checked yetcites [85] Frezza, C. Mitochondrial metabolites: undercover signalling molecules. Interface Focus 7, 20160100 (2017). source

In the paper

“The elevated levels of D-2-HG was associated with increased DNA methylation levels at the Foxp3 locus, the master transcription factor driving iTreg differentiation, resulting in its repression143.”

What the sources say

• Not checked yetcites [143] Yan, H. et al. IDH1 and IDH2 mutations in gliomas. N. Engl. J. Med. 360, 765–773 (2009). source

In the paper

“Furthermore, TH17 cell differentiation could be initiated by exogenous addition of D-2-HG to naïve CD4+ T cells or by genetic silencing of TET1 and TET2, established targets of 2-HG143-145.”

What the sources say

• Not checked yetcites [143] Yan, H. et al. IDH1 and IDH2 mutations in gliomas. N. Engl. J. Med. 360, 765–773 (2009). source
• Not checked yetcites [144] Chowdhury, R. et al. The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep. 12, 463 (2011). source
• Not checked yetcites [145] Xu, W. et al. Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate-dependent dioxygenases. Cancer Cell. 19, 17–30 (2011). source

In the paper

“Upon DNA damage, FH localises in the nucleus, where it is phosphorylated by the catalytic subunit of DNA-PK (DNA-PKcs)177.”

What the sources say

• Not checked yetcites [177] Valls-Lacalle, L. et al. Selective inhibition of succinate dehydrogenase in reperfused myocardium with intracoronary malonate reduces infarct size. Sci. Rep. 8, 2442 (2018). source

In the paper

“In support of this unexpected function of fumarate, it was recently shown that the aberrant accumulation of this metabolite in HLRCC correlates with increased endogenous damage, lower DNA repair efficiency and increased sensitivity to poly-ADP ribose polymerase (PARP) inhibitors178.”

What the sources say

• Not checked yetcites [178] Kohlhauer, M. et al. Metabolomic profiling in acute ST-segment-elevation myocardial infarction identifies succinate as an early marker of human ischemia-reperfusion injury. J. Am. Heart Assoc. 7, e007546 (2018). source

In the paper

“Although the IC50 of D-2-HG toward KDM family members is in the low micromolar range (24-106 μM), it can also inhibit FIH and PHD2, with IC50 values of 1.5 and 7.3 mM, respectively121.”

What the sources say

• Not checked yetcites [121] Duran, M., Kamerling, J. P., Bakker, H. D., van Gennip, A. H. & Wadman, S. K. l-2-Hydroxyglutaric aciduria: an inborn error of metabolism? J. Inherit. Metab. Dis. 3, 109–112 (1980). source

In the paper

“Mechanistically, HIF-1α stabilisation induced LDHA expression and activity, which promiscuously converted glutamine-derived α-KG to L-2-HG149.”

What the sources say

• Not checked yetcites [149] Flavahan, W. A. et al. Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature 529, 110–114 (2016). source

In the paper

“D-2-HG produced by mIDH1/2 has been shown to drive a CpG island methylator phenotype (G-CIMP) in both glioma and ICC tumours to promote tumorigenesis, and has also been found to occupy the active site of histone demethylases thereby increasing histone methylation in primary gliomas121,123-125.”

What the sources say

• Not checked yetcites [121] Duran, M., Kamerling, J. P., Bakker, H. D., van Gennip, A. H. & Wadman, S. K. l-2-Hydroxyglutaric aciduria: an inborn error of metabolism? J. Inherit. Metab. Dis. 3, 109–112 (1980). source
• Not checked yetcites [123] Rzem, R. et al. A gene encoding a putative FAD-dependent l-2-hydroxyglutarate dehydrogenase is mutated in l-2-hydroxyglutaric aciduria. Proc. Natl. Acad. Sci. USA 101, 16849–16854 (2004). source
• Not checked yetcites [124] Struys, E. A. et al. Mutations in the d-2-hydroxyglutarate dehydrogenase gene cause D-2-hydroxyglutaric aciduria. Am. J. Hum. Genet. 76, 358–360 (2005). source
• Not checked yetcites [125] Topçu, M. et al. l-2-Hydroxyglutaric aciduria: identification of a mutant gene C14orf160, localized on chromosome 14q22.1. Hum. Mol. Genet. 13, 2803–2811 (2004). source

In the paper

“The authors demonstrate that this is independent of IDH1 and 2 and primarily mediated by LDHA and malate dehydrogenase (MDH) via “promiscuous” reduction of αKG and this is enhanced by acidic pH52.”

What the sources say

• Not checked yetcites [52] Wang, Y. et al. KAT2A coupled with the α-KGDH complex acts as a histone H3 succinyltransferase. Nature 552, 273–277 (2017). source

In the paper

“This metabolic rewiring resulted in a decrease in a common dipeptide found in the brain N-acetyl-aspartyl-glutamate (NAAG), and NAAG levels were found to be significantly lower in IDH-mutant human glioma tissue134.”

What the sources say

• Not checked yetcites [134] Figueroa, M. E. et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell. 18, 553–567 (2010). source

In the paper

“As such, these findings directly link mIDH-derived D-2-HG accumulation to DNA damage, genetic instability and carcinogenesis.”

In the paper

“Indeed, D-2-HG accumulation in IDH-mutant glioma has been found to inhibit PHD hydroxylase and stabilise HIF-1α126 and HIF-1αstabilisation has been shown to occur in IDH1-mutant brain tissue127.”

What the sources say

• Not checked yetcites [126] Kranendijk, M. et al. IDH2 mutations in patients with d-2-hydroxyglutaric aciduria. Science 330, 336 (2010). source

In the paper

“Genomic studies have established that somatic mutations in IDH1 and IDH2 are perhaps the first genetic events to occur during tumorigenesis in human glioma and AML, and appear to initiate pathogenesis by a common mechanism103,115-117.”

What the sources say

• Not checked yetcites [103] Linehan, W. M. et al. Comprehensive molecular characterization of papillary renal-cell carcinoma. N. Engl. J. Med. 374, 135–145 (2016). source
• Not checked yetcites [115] Yogev, O. et al. Fumarase: a mitochondrial metabolic enzyme and a cytosolic/nuclear component of the DNA damage response. PLoS Biol. 8, e1000328 (2010). source
• Not checked yetcites [116] Jiang, Y. et al. Local generation of fumarate promotes DNA repair through inhibition of histone H3 demethylation. Nat. Cell Biol. 17, 1158–1168 (2015). source
• Not checked yetcites [117] Sulkowski, P. L. et al. Krebs-cycle-deficient hereditary cancer syndromes are defined by defects in homologous-recombination DNA repair. Nat. Genet. 50, 1086–1092 (2018). source

In the paper

“Under acidic conditions αKG is protonated and this promotes binding to LDHA and L-2HG production.”

What the sources say

• Not checked yetcites [52] Wang, Y. et al. KAT2A coupled with the α-KGDH complex acts as a histone H3 succinyltransferase. Nature 552, 273–277 (2017). source

In the paper

“Indeed, IDH-mutant cells display reduced DNA repair kinetics, accumulate DNA double stranded breaks (DSBs) and are sensitized to alkylating agents131,174.”

What the sources say

• Not checked yetcites [131] MacIver, N. J., Michalek, R. D. & Rathmell, J. C. Metabolic regulation of T lymphocytes. Annu. Rev. Immunol. 31, 259–283 (2013). source
• Not checked yetcites [174] Mi, W. et al. YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer. Nat. Commun. 8, 1088 (2017). source

In the paper

“the concentrations at which it accumulates under pathogenic conditions suggests HIF-1α stabilisation and impaired collagen biogenesis may contribute to tumorigenicity126-130.”

What the sources say

• Not checked yetcites [126] Kranendijk, M. et al. IDH2 mutations in patients with d-2-hydroxyglutaric aciduria. Science 330, 336 (2010). source
• Not checked yetcites [127] Nota, B. et al. Deficiency in SLC25A1, encoding the mitochondrial citrate carrier, causes combined d-2- and l-2-hydroxyglutaric aciduria. Am. J. Hum. Genet. 92, 627–631 (2013). source
• Not checked yetcites [128] Dang, L. & Su, S. M. Isocitrate dehydrogenase mutation and R-2-hydroxyglutarate: from basic discovery to therapeutics development. Annu. Rev. Biochem. 86, 305–331 (2017). source
• Not checked yetcites [129] Mardis, E. R. et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N. Engl. J. Med. 361, 1058–1066 (2009). source
• Not checked yetcites [130] Parsons, D. W. et al. An integrated genomic analysis of human glioblastoma multiforme. Science 321, 1807–1812 (2008). source

In the paper

“This increase occurred under normoxic conditions and was dependent on HIF-1α stabilisation149.”

What the sources say

• Not checked yetcites [149] Flavahan, W. A. et al. Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature 529, 110–114 (2016). source

In the paper

“Functionally, L-2HG is both sufficient to try histone methylation, in particular histone 3 lysine 9 (H3K9me3), and can also promote HIF-1α stabilization in normoxia and therefore may assist with hypoxic adaptation.”

What the sources say

• Not checked yetcites [51] Du, J. et al. Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase. Science 334, 806–809 (2011). source

In the paper

“Remarkably, almost all IDH1/2 mutations occur in a few unique locations in the active site of the enzymes, which results in the acquirement of a neomorphic enzymatic activity converting α-KG to the oncometabolite D-2-HG118-120.”

What the sources say

• Not checked yetcites [118] Johnson, T. I., Costa, A. S. H., Ferguson, A. N. & Frezza, C. Fumarate hydratase loss promotes mitotic entry in the presence of DNA damage after ionising radiation. Cell Death Dis. 9, 913 (2018). source
• Not checked yetcites [119] Ye, D., Guan, K. L. & Xiong, Y. Metabolism, activity, and targeting of d- and l-2-Hydroxyglutarates. Trends Cancer 4, 151–165 (2018). source
• Not checked yetcites [120] Chalmers, R. A. et al. d-2-hydroxyglutaric aciduria: case report and biochemical studies. J. Inherit. Metab. Dis. 3, 11–15 (1980). source

In the paper

“The authors demonstrate that ACLY is required to enhance histone acetylation levels and induce the expression of cell cycle regulating genes in response to IL-2.”

What the sources say

• Not checked yetcites [57] Meiser, J. et al. Pro-inflammatory macrophages sustain pyruvate oxidation through pyruvate dehydrogenase for the synthesis of itaconate and to enable cytokine expression. J. Biol. Chem. 291, 3932–3946 (2016). source

In the paper

“Citrate, a component of the TCA cycle has been shown to act as a source of acetyl-CoA to drive histone acetylation and this process can have profound impacts on both tumor and immune cell function.”

What the sources say

• Not checked yetcites [53] Gibson, G. E. et al. α-ketoglutarate dehydrogenase complex–dependent succinylation of proteins in neurons and neuronal cell lines. J. Neurochem. 134, 86–96 (2015). source

In the paper

“D-2-HG has also been found to bind the DNA methyltransferase DNMT1, which subsequently represses receptor-interacting protein kinase 3 (RIP3).”

What the sources say

• Not checked yetcites [140] Watanabe, T., Nobusawa, S., Kleihues, P. & Ohgaki, H. IDH1 mutations are early events in the development of astrocytomas and oligodendrogliomas. Am. J. Pathol. 174, 1149–1153 (2009). source
• Not checked yetcites [141] Dang, L. et al. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 462, 739–744 (2009). source

In the paper

“Mechanistically LDHA-deficient T cells showed decreased acetyl-CoA levels and decreased histone H3 acetylation at the lysine 9 residue (H3K9Ac), a histone mark associated with active transcription, on the Ifng promoter.”

What the sources say

• Not checked yetcites [55] Cordes, T. et al. Immunoresponsive gene 1 and itaconate inhibit succinate dehydrogenase to modulate intracellular succinate levels. J. Biol. Chem. 291, 14274–14284 (2016). source

In the paper

“One of the earliest studies to identify a role for ACL in histone acetylation demonstrated a requirement for this gene in response to growth factor stimulation and during differentiation, for example the differentiation of murine 3T3- L1 pre-adipocytes into adipocytes.”

What the sources say

• Not checked yetcites [54] Wang, F. et al. SIRT5 desuccinylates and activates pyruvate kinase M2 to block macrophage IL-1β production and to prevent dss-induced colitis in mice. Cell Rep. 19, 2331–2344 (2017). source

In the paper

“Finally, D-2HG also impairs necroptosis and the small GTPase Cdc42, leading to suppression of mixed lineage kinase 3 (MLK3)-mediated apoptosis140,141.”

What the sources say

• Not checked yetcites [140] Watanabe, T., Nobusawa, S., Kleihues, P. & Ohgaki, H. IDH1 mutations are early events in the development of astrocytomas and oligodendrogliomas. Am. J. Pathol. 174, 1149–1153 (2009). source
• Not checked yetcites [141] Dang, L. et al. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 462, 739–744 (2009). source

In the paper

“Furthermore, artificial acetyl-CoA reduction, through inhibition of ACLY, decreased IFN-γ expression and acetate supplementation, which augmented acetyl-CoA production, corrected H3K9Ac marks and IFN-γ expression in LDHA-deficient T cells.”

What the sources say

• Not checked yetcites [55] Cordes, T. et al. Immunoresponsive gene 1 and itaconate inhibit succinate dehydrogenase to modulate intracellular succinate levels. J. Biol. Chem. 291, 14274–14284 (2016). source

In the paper

“It has been demonstrated in mammalian cells that histone acetylation is dependent on ACL, the enzyme that converts citrate into acetyl-CoA, a required co-factor for acetylation,54 with ACL silencing decreasing the degree of histone acetylation.”

What the sources say

• Not checked yetcites [54] Wang, F. et al. SIRT5 desuccinylates and activates pyruvate kinase M2 to block macrophage IL-1β production and to prevent dss-induced colitis in mice. Cell Rep. 19, 2331–2344 (2017). source

In the paper

“ACLY deficiency results in impaired BRCA1 recruitment to sites of DSBs and suppression of homologous recombination.”

What the sources say

• Not checked yetcites [59] Okabe, M., Lies, D., Kanamasa, S. & Park, E. Y. Biotechnological production of itaconic acid and its biosynthesis in Aspergillus terreus. Appl. Microbiol. Biotechnol. 84, 597–606 (2009). source

In the paper

“ACLY is phosphorylated downstream of AKT activation, following DNA damage and this facilitates histone acetylation at double strand break (DSB) sites, enabling breast cancer early onset 1 (BRCA1) recruitment and DNA repair by homologous recombination.”

What the sources say

• Not checked yetcites [59] Okabe, M., Lies, D., Kanamasa, S. & Park, E. Y. Biotechnological production of itaconic acid and its biosynthesis in Aspergillus terreus. Appl. Microbiol. Biotechnol. 84, 597–606 (2009). source

In the paper

“The production of succinate is also enhanced during inflammation13, acting as a signal from mitochondria to the cytosol to activate pro-inflammatory gene expression while also generating ROS as a further pro-inflammatory redox signal28.”

What the sources say

• Not checked yetcites [13] van Diepen, J. A. et al. SUCNR1-mediated chemotaxis of macrophages aggravates obesity-induced inflammation and diabetes. Diabetologia 60, 1304–1313 (2017). source
• Not checked yetcites [28] Rasola, A., Neckers, L. & Picard, D. Mitochondrial oxidative phosphorylation TRAP(1)ped in tumor cells. Trends Cell Biol. 24, 455–463 (2014). source