{"gene":"MDH1","run_date":"2026-06-10T02:59:50","timeline":{"discoveries":[{"year":2016,"finding":"PRMT4/CARM1 methylates MDH1 at arginine 248 (R248), inhibiting its enzymatic activity by disrupting MDH1 dimerization. This methylation negatively regulates the unconventional glutamine metabolic pathway in pancreatic ductal adenocarcinoma cells that supports NADPH production. Re-expression of wild-type MDH1, but not its methylation-mimetic mutant, restored cell growth and clonogenic activity.","method":"In vitro methylation assay, site-directed mutagenesis (R248 methylation-mimetic mutant), Co-IP for dimerization, knockdown/re-expression rescue experiments, metabolic flux assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods including in vitro methylation assay, mutagenesis of active site, dimerization disruption assay, and functional rescue experiments in a single rigorous study","pmids":["27840030"],"is_preprint":false},{"year":2022,"finding":"HDAC6 binds MDH1 and mediates its deacetylation at lysine residues K121 and K298. The acetylation-mimetic mutant of MDH1 (but not the acetylation-resistant mutant) protected neurons from oxidative injury. HDAC6 inhibition failed to alleviate brain damage after ICH when MDH1 was knocked down, placing MDH1 downstream of HDAC6 in the oxidative stress response.","method":"Co-IP (HDAC6-MDH1 interaction), site-directed mutagenesis (K121 and K298 acetylation-mimetic and acetylation-resistant mutants), HDAC6 KO mice, MDH1 knockdown, NADPH/NADP+ and ROS assays","journal":"Cellular and molecular life sciences : CMLS","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, site-directed mutagenesis, KO mice, and MDH1 KD rescue experiments with multiple orthogonal functional readouts in one study","pmids":["35678904"],"is_preprint":false},{"year":2019,"finding":"MDH1 is required for maintenance of the levels of the autophagy-initiating kinase ULK1, and MDH1 activity increases upon induction of autophagy. MDH1 knockdown identified it as a regulator of early autophagosome formation stages in PDAC cells.","method":"Genome-wide siRNA screen with autophagy readout, siRNA knockdown validation, ULK1 protein level measurement","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — siRNA screen with validation, two orthogonal readouts (ULK1 levels and autophagosome formation), but no direct biochemical interaction assay between MDH1 and ULK1","pmids":["30765601"],"is_preprint":false},{"year":2019,"finding":"MDH1 deficiency (homozygous missense variant in the NAD+-binding domain) leads to severely diminished MDH1 protein expression and disrupts the malate-aspartate shuttle, resulting in elevated glycerol-3-phosphate (a compensatory mechanism via the glycerol-P-shuttle), increased aspartate, and decreased fumarate in MDH1 knockout HEK293 cells.","method":"CRISPR/Cas9 MDH1 knockout HEK293 cells, untargeted metabolomics on dried blood spots and KO cells","journal":"Human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR KO with metabolomics in cells and patient samples, single lab, two orthogonal approaches (patient DBS and KO cells)","pmids":["31538237"],"is_preprint":false},{"year":2020,"finding":"STAT3 transactivates MDH1 to sustain malate-aspartate NADH shuttle activity required for fetal liver hematopoietic stem cell (HSC) self-renewal and differentiation. MDH1 mediates the metabolic program of FL-HSCs supporting HSC maintenance.","method":"Transgenic SoNar NADH/NAD+ sensor mice, transcriptional reporter assays for STAT3-MDH1, functional HSC assays (self-renewal, differentiation)","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct metabolic sensor imaging in vivo combined with STAT3-MDH1 transactivation and HSC functional assays, single lab","pmids":["32396938"],"is_preprint":false},{"year":2020,"finding":"Oxidative damage (trioxidation) accumulates at Cys137 of MDH1 in aged murine brain, located at the protein active zone. This modification significantly reduces MDH1 enzymatic activity, dysregulating TCA cycle bioenergetics in the aging brain.","method":"LC-MS/MS proteomics, quantitative MRM-MS, 3D structural modeling of MDH1, enzymatic kinetic analysis of MDH1 from old vs. young mouse brain","journal":"Journal of proteome research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mass spectrometry identification of modification site plus enzymatic kinetic validation, single lab, two orthogonal methods","pmids":["32175745"],"is_preprint":false},{"year":2024,"finding":"Deacetylation of MDH1 at K118 reduces MDH1 enzymatic activity and promotes NETosis (neutrophil extracellular trap formation), aggravating acute liver failure. This deacetylated MDH1 also promotes PANoptosis through endoplasmic reticulum stress signaling (upregulating BIP, ATF6, XBP1, CHOP), which is blocked by the ER stress inhibitor 4-PBA.","method":"Site-directed mutagenesis (K118 acetylation-mimetic and deacetylation mutants), adeno-associated virus in vivo delivery, immunoprecipitation, ER stress inhibitor rescue (4-PBA), LPS/D-gal ALF mouse model","journal":"Cellular & molecular biology letters / Cell death discovery / iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (mutagenesis, AAV in vivo, pharmacological rescue) across related papers from same lab, single group","pmids":["38172700","38851781","38660411"],"is_preprint":false},{"year":2024,"finding":"Deacetylation of MDH1 at K118 promotes NETosis by upregulating OPA1 (mitochondrial dynamin) and enhancing autophagy (increased LC3B-II and Beclin1, decreased p62). The HDAC6 inhibitor ACY1215 reverses these effects.","method":"Western blotting for OPA1 and autophagy markers, Mito-Tracker Red staining, LC3 fluorescence staining, LPS/D-gal ALF mouse model, IDH1/MDH1 deacetylation mutant transfection","journal":"International immunopharmacology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — multiple orthogonal cell biological methods, pharmacological rescue, in vivo validation, single lab","pmids":["39353390"],"is_preprint":false},{"year":2024,"finding":"IDH1/MDH1 deacetylation activates the cGAS-STING signaling pathway via NETs formation, promoting pro-inflammatory cytokine production and aggravating ALF. DNase 1 degraded NETs formed by IDH1/MDH1 deacetylation and attenuated hepatic tissue injury.","method":"Western blotting and immunofluorescence for NETs and cGAS-STING pathway proteins, DNase 1 treatment, HDAC6i (ACY1215) treatment, LPS/D-gal ALF mouse model, exogenous NET treatment of HepG2 cells","journal":"International immunopharmacology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — multiple orthogonal methods in vitro and in vivo, pharmacological and enzymatic rescue, single lab","pmids":["40388861"],"is_preprint":false},{"year":2025,"finding":"Hydroxysafflor yellow A (HSYA) covalently activates MDH1 through Cys residue 137, promoting MDH1 bioenergetic enzymatic activity and restoring mitochondrial energy metabolism homeostasis in myocardial ischemia/reperfusion injury. Disruption of MDH1 or the C137 binding site abolished cardioprotective effects of HSYA.","method":"rdTOP-ABPP (reducing dimethyl labeling with tandem orthogonal proteolysis-activity-based protein profiling) combined with LC-MS/MS, cellular thermal shift assay for drug-target binding, enzymatic activity profiling, siRNA knockdown, MIRI mouse model","journal":"Phytomedicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — chemoproteomic identification of binding site plus thermal shift assay plus enzymatic activity and siRNA rescue, single lab, multiple orthogonal methods","pmids":["40513321"],"is_preprint":false},{"year":2025,"finding":"M2 macrophage-derived exosomes transfer MDH1 protein into lung adenocarcinoma (LUAD) cells, upregulating MDH1 levels and activating the Hippo/YAP signaling pathway to enhance LUAD cell growth and metastasis. YAP depletion abrogates M2-exos-induced malignant phenotypes.","method":"Exosome isolation and co-culture, xenograft tumor models, CCK-8/EdU/colony formation/wound-healing/transwell assays, Western blotting, siRNA knockdown of MDH1 and YAP","journal":"Pathology, research and practice","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, exosome transfer shown but mechanism linking MDH1 to YAP activation not biochemically elucidated beyond correlation","pmids":["40090126"],"is_preprint":false},{"year":2025,"finding":"Yeast mitochondrial MDH1 (ortholog) and citrate synthase (CIT1) form a dynamic metabolon that channels oxaloacetate. The MDH1-CIT1 complex dissociates when aerobic respiration is suppressed (Crabtree effect) and reassociates when respiratory activity is enhanced by acetate. Complex assembly is regulated by mitochondrial matrix pH (within physiological range 6.0–7.0), redox state, and metabolite levels (malate, fumarate, citrate).","method":"In vitro reconstitution of MDH1-CIT1 complex, pharmacological TCA cycle and ETC inhibition, affinity binding assays at varying pH and metabolite concentrations, yeast genetic manipulation","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — in vitro reconstitution of metabolon with functional validation and multiple pharmacological perturbations, single lab, preprint not yet peer-reviewed","pmids":["bio_10.1101_2025.06.16.659985"],"is_preprint":true},{"year":2025,"finding":"Conditional deletion of Mdh1 in erythroid cells did not cause anemia, demonstrating that MDH1-mediated malate-aspartate shuttle activity is not required for erythropoiesis, in contrast to aspartate aminotransferases GOT1/GOT2.","method":"Conditional Mdh1 knockout mouse (erythroid-specific), complete blood count and erythroid progenitor analysis","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean conditional KO with defined cellular phenotype (negative result); single lab, preprint","pmids":["bio_10.1101_2025.09.16.675844"],"is_preprint":true},{"year":1996,"finding":"Human MDH1 cDNA encodes a 334 amino acid cytosolic malate dehydrogenase with 96% identity to murine cytosolic MDH. The gene maps to chromosomal location 2p15 by fluorescence in situ hybridization, and is most highly expressed in heart and skeletal muscle.","method":"cDNA cloning, Northern blot analysis, fluorescence in situ hybridization (FISH)","journal":"Genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Strong — molecular cloning with chromosomal localization by FISH and tissue expression profiling, foundational characterization replicated by subsequent studies","pmids":["8786100"],"is_preprint":false}],"current_model":"MDH1 is a cytosolic NAD(H)-dependent malate dehydrogenase that catalyzes the reversible oxidation of malate to oxaloacetate, functioning as a core component of the malate-aspartate shuttle and TCA cycle; its activity is regulated by post-translational modifications including CARM1-mediated arginine methylation at R248 (which disrupts dimerization and inhibits activity), HDAC6-mediated deacetylation at K121/K298 and K118 (which impairs redox homeostasis and promotes cell death pathways including NETosis, PANoptosis, and ER stress), and oxidative trioxidation at Cys137 (which reduces enzymatic activity in aging brain); MDH1 forms a dynamic metabolon with citrate synthase regulated by mitochondrial pH and metabolite levels, supports NADPH production in a glutamine metabolic pathway critical for pancreatic cancer, maintains fetal liver hematopoietic stem cell self-renewal downstream of STAT3, and regulates autophagosome formation by sustaining ULK1 levels."},"narrative":{"mechanistic_narrative":"MDH1 is a cytosolic NAD(H)-dependent malate dehydrogenase that catalyzes the reversible interconversion of malate and oxaloacetate as a core component of the malate-aspartate shuttle, coupling cytosolic and mitochondrial redox state [PMID:8786100, PMID:31538237]. Loss of MDH1 disrupts this shuttle, elevating glycerol-3-phosphate (a compensatory glycerol-phosphate shuttle response), aspartate, and lowering fumarate, with a homozygous missense variant in its NAD+-binding domain causing severely diminished protein expression [PMID:31538237]. Its enzymatic output is tuned by multiple post-translational modifications: CARM1/PRMT4 methylates Arg248 to block dimerization and inhibit activity, restraining a glutamine-driven NADPH-generating pathway in pancreatic cancer [PMID:27840030]; HDAC6-mediated deacetylation at K121/K298 and at K118 lowers activity and impairs NADPH/redox homeostasis, driving oxidative neuronal injury and, in liver, NETosis, ER-stress-dependent PANoptosis, and cGAS-STING inflammatory signaling [PMID:35678904, PMID:38172700, PMID:38851781, PMID:38660411, PMID:40388861]; and oxidative trioxidation at the active-zone residue Cys137 reduces activity in aged brain [PMID:32175745]. Beyond core metabolism, MDH1 sustains levels of the autophagy-initiating kinase ULK1 to promote autophagosome formation [PMID:30765601] and acts downstream of STAT3, which transactivates MDH1 to maintain malate-aspartate shuttle flux required for fetal liver hematopoietic stem cell self-renewal [PMID:32396938]. In yeast, the mitochondrial ortholog forms a pH- and metabolite-regulated metabolon with citrate synthase that channels oxaloacetate [PMID:bio_10.1101_2025.06.16.659985].","teleology":[{"year":1996,"claim":"Establishing the molecular identity of human MDH1 was the prerequisite for all mechanistic work, defining it as a cytosolic malate dehydrogenase, its gene locus, and its tissue distribution.","evidence":"cDNA cloning, Northern blot, and FISH mapping to 2p15","pmids":["8786100"],"confidence":"Medium","gaps":["No catalytic or structural mechanism addressed","Physiological role inferred from expression, not function"]},{"year":2016,"claim":"Resolved how MDH1 activity is post-translationally restrained, showing CARM1 methylation of R248 disrupts dimerization to inhibit the enzyme and a glutamine-derived NADPH pathway supporting pancreatic cancer growth.","evidence":"In vitro methylation, methylation-mimetic mutagenesis, dimerization Co-IP, and metabolic rescue in PDAC cells","pmids":["27840030"],"confidence":"High","gaps":["Demethylase not identified","Extent of regulation outside PDAC unknown"]},{"year":2019,"claim":"Identified a non-canonical role for MDH1 in autophagy, linking it to maintenance of ULK1 levels and early autophagosome formation.","evidence":"Genome-wide siRNA screen with knockdown validation and ULK1 protein measurement in PDAC cells","pmids":["30765601"],"confidence":"Medium","gaps":["No direct MDH1-ULK1 biochemical interaction shown","Mechanism connecting MDH1 to ULK1 stability unresolved"]},{"year":2019,"claim":"Demonstrated the metabolic consequence of MDH1 loss, defining its role in the malate-aspartate shuttle through a disease-associated NAD+-binding-domain variant.","evidence":"CRISPR MDH1 KO HEK293 cells and untargeted metabolomics on patient dried blood spots","pmids":["31538237"],"confidence":"Medium","gaps":["Clinical phenotype-to-metabolite causality not fully resolved","Single patient/cell-line context"]},{"year":2020,"claim":"Placed MDH1 in developmental hematopoiesis as a STAT3-induced effector sustaining malate-aspartate shuttle flux for fetal liver HSC self-renewal.","evidence":"In vivo SoNar NADH/NAD+ sensor mice, STAT3-MDH1 transactivation reporters, and HSC functional assays","pmids":["32396938"],"confidence":"Medium","gaps":["Direct STAT3 binding to the MDH1 promoter not detailed","Relevance to adult HSC unaddressed"]},{"year":2020,"claim":"Showed MDH1 activity declines with age via oxidative modification, identifying trioxidation of active-zone Cys137 as a mechanism dysregulating brain bioenergetics.","evidence":"LC-MS/MS, MRM-MS, structural modeling, and enzymatic kinetics of MDH1 from old vs young mouse brain","pmids":["32175745"],"confidence":"Medium","gaps":["Causal link to neurodegenerative phenotype not established","Reversibility of trioxidation unknown"]},{"year":2022,"claim":"Defined HDAC6 as an upstream regulator of MDH1, with deacetylation at K121/K298 controlling NADPH/redox homeostasis and neuronal survival after hemorrhage.","evidence":"Reciprocal Co-IP, acetylation-site mutants, HDAC6 KO mice, and MDH1 knockdown rescue with NADPH/ROS readouts","pmids":["35678904"],"confidence":"High","gaps":["Acetyltransferase counterpart not identified","Quantitative stoichiometry of site occupancy unknown"]},{"year":2024,"claim":"Extended MDH1 deacetylation signaling to acute liver failure, linking K118 deacetylation to NETosis, ER-stress-driven PANoptosis, mitochondrial dynamics/autophagy, and cGAS-STING inflammation.","evidence":"K118 acetylation mutants, AAV delivery, ER stress and HDAC6 inhibitor rescue, DNase 1 NET degradation, and LPS/D-gal ALF mouse model","pmids":["38172700","38851781","38660411","39353390","40388861"],"confidence":"Medium","gaps":["Direct enzymatic basis linking MDH1 activity loss to downstream effectors not fully dissected","Findings concentrated in a single lab's ALF model"]},{"year":2025,"claim":"Demonstrated MDH1 can be pharmacologically activated, with covalent engagement of Cys137 by HSYA restoring enzymatic activity and mitochondrial energetics in cardiac ischemia/reperfusion.","evidence":"rdTOP-ABPP chemoproteomics, cellular thermal shift assay, enzymatic profiling, and siRNA rescue in a MIRI mouse model","pmids":["40513321"],"confidence":"Medium","gaps":["Specificity of HSYA for MDH1 over other Cys-containing targets not fully bounded","Translational dosing unaddressed"]},{"year":2025,"claim":"Provided structural-functional insight into MDH1 organization, showing the ortholog forms a metabolite- and pH-regulated metabolon with citrate synthase that channels oxaloacetate.","evidence":"In vitro reconstitution and affinity assays under varying pH/metabolite conditions in yeast (preprint)","pmids":["bio_10.1101_2025.06.16.659985"],"confidence":"Medium","gaps":["Demonstrated in yeast mitochondrial ortholog, not human cytosolic MDH1","Preprint, not peer-reviewed"]},{"year":2025,"claim":"Tested the in vivo requirement for MDH1 in erythropoiesis, finding the malate-aspartate shuttle via MDH1 dispensable for red cell development unlike GOT1/GOT2.","evidence":"Erythroid-specific conditional Mdh1 knockout mouse with blood and progenitor analysis (preprint)","pmids":["bio_10.1101_2025.09.16.675844"],"confidence":"Medium","gaps":["Negative result; compensatory pathways not mapped","Preprint, not peer-reviewed"]},{"year":null,"claim":"How the converging post-translational modifications (methylation, acetylation, oxidation) are integrated to set MDH1 activity in any single physiological context, and the identities of the writer enzymes opposing HDAC6 deacetylation, remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No acetyltransferase or demethylase identified for MDH1","Cross-talk among R248 methylation, K118/K121/K298 acetylation, and C137 oxidation not jointly studied","Human structural model of the metabolon lacking"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016491","term_label":"oxidoreductase activity","supporting_discovery_ids":[13,3,0,5,9]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[13,3]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[13,3,0]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[2]}],"complexes":["MDH1-citrate synthase (CIT1) metabolon"],"partners":["CARM1","HDAC6","CIT1","STAT3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P40925","full_name":"Malate dehydrogenase, cytoplasmic","aliases":["Aromatic alpha-keto acid reductase","KAR","Cytosolic malate dehydrogenase"],"length_aa":334,"mass_kda":36.4,"function":"Catalyzes the reduction of aromatic alpha-keto acids in the presence of NADH (PubMed:2449162, PubMed:3052244). Plays essential roles in the malate-aspartate shuttle and the tricarboxylic acid cycle, important in mitochondrial NADH supply for oxidative phosphorylation (PubMed:31538237). Catalyzes the reduction of 2-oxoglutarate to 2-hydroxyglutarate, leading to elevated reactive oxygen species (ROS) (PubMed:34012073)","subcellular_location":"Cytoplasm, cytosol","url":"https://www.uniprot.org/uniprotkb/P40925/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/MDH1","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000014641","cell_line_id":"CID001703","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"nucleoplasm","grade":3}],"interactors":[{"gene":"INPPL1","stoichiometry":0.2},{"gene":"LMNA","stoichiometry":0.2},{"gene":"LMNB1","stoichiometry":0.2},{"gene":"NFKBIA","stoichiometry":0.2},{"gene":"SAR1B","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001703","total_profiled":1310},"omim":[{"mim_id":"618959","title":"DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 88; DEE88","url":"https://www.omim.org/entry/618959"},{"mim_id":"308350","title":"DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 1; DEE1","url":"https://www.omim.org/entry/308350"},{"mim_id":"191110","title":"TUBULIN, ALPHA-4A; TUBA4A","url":"https://www.omim.org/entry/191110"},{"mim_id":"171500","title":"ACID PHOSPHATASE 1, SOLUBLE; ACP1","url":"https://www.omim.org/entry/171500"},{"mim_id":"154200","title":"MALATE DEHYDROGENASE 1; MDH1","url":"https://www.omim.org/entry/154200"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Centrosome","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"heart muscle","ntpm":1262.4},{"tissue":"tongue","ntpm":1722.1}],"url":"https://www.proteinatlas.org/search/MDH1"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"P40925","domains":[{"cath_id":"3.40.50.720","chopping":"1-71","consensus_level":"medium","plddt":97.5559,"start":1,"end":71},{"cath_id":"3.90.110.10","chopping":"155-321","consensus_level":"high","plddt":97.6468,"start":155,"end":321}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P40925","model_url":"https://alphafold.ebi.ac.uk/files/AF-P40925-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P40925-F1-predicted_aligned_error_v6.png","plddt_mean":96.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=MDH1","jax_strain_url":"https://www.jax.org/strain/search?query=MDH1"},"sequence":{"accession":"P40925","fasta_url":"https://rest.uniprot.org/uniprotkb/P40925.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P40925/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P40925"}},"corpus_meta":[{"pmid":"27840030","id":"PMC_27840030","title":"Arginine Methylation of MDH1 by CARM1 Inhibits Glutamine Metabolism and Suppresses Pancreatic Cancer.","date":"2016","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/27840030","citation_count":176,"is_preprint":false},{"pmid":"15565635","id":"PMC_15565635","title":"Developmental regulation and cellular distribution of human cytosolic malate dehydrogenase (MDH1).","date":"2005","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15565635","citation_count":59,"is_preprint":false},{"pmid":"31538237","id":"PMC_31538237","title":"MDH1 deficiency is a metabolic disorder of the malate-aspartate shuttle associated with early onset severe encephalopathy.","date":"2019","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31538237","citation_count":49,"is_preprint":false},{"pmid":"35678904","id":"PMC_35678904","title":"Upregulation of MDH1 acetylation by HDAC6 inhibition protects against oxidative stress-derived neuronal apoptosis following 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MGG","url":"https://pubmed.ncbi.nlm.nih.gov/9870696","citation_count":7,"is_preprint":false},{"pmid":"40513321","id":"PMC_40513321","title":"Hydroxysafflor yellow A ameliorates myocardial ischemia/reperfusion injury by promoting MDH1-mediated mitochondrial metabolic homeostasis.","date":"2025","source":"Phytomedicine : international journal of phytotherapy and phytopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/40513321","citation_count":6,"is_preprint":false},{"pmid":"40090126","id":"PMC_40090126","title":"M2 macrophages-derived exosomal MDH1 drives lung adenocarcinoma progression via the Hippo/YAP signaling.","date":"2025","source":"Pathology, research and practice","url":"https://pubmed.ncbi.nlm.nih.gov/40090126","citation_count":5,"is_preprint":false},{"pmid":"38484665","id":"PMC_38484665","title":"A novel HDAC6 inhibitor attenuate APAP-induced liver injury by regulating MDH1-mediated oxidative stress.","date":"2024","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/38484665","citation_count":5,"is_preprint":false},{"pmid":"40948768","id":"PMC_40948768","title":"Panoramic view of MDH1: driving cancer progression and shaping the tumor immune microenvironment.","date":"2025","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/40948768","citation_count":4,"is_preprint":false},{"pmid":"39818404","id":"PMC_39818404","title":"Unveiling the role of MDH1 in breast cancer drug resistance through single-cell sequencing and schottenol intervention.","date":"2025","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/39818404","citation_count":4,"is_preprint":false},{"pmid":"24963377","id":"PMC_24963377","title":"Fin whale MDH-1 and MPI allozyme variation is not reflected in the corresponding DNA sequences.","date":"2014","source":"Ecology and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/24963377","citation_count":4,"is_preprint":false},{"pmid":"20011630","id":"PMC_20011630","title":"Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.","date":"2009","source":"Molecular vision","url":"https://pubmed.ncbi.nlm.nih.gov/20011630","citation_count":3,"is_preprint":false},{"pmid":"40388861","id":"PMC_40388861","title":"IDH1/MDH1 deacetylation activates the cGAS-STING pathway by promoting NETosis in acute liver failure.","date":"2025","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/40388861","citation_count":1,"is_preprint":false},{"pmid":"38094447","id":"PMC_38094447","title":"Retracted: MDH1 and MDH2 Promote Cell Viability of Primary AT2 Cells by Increasing Glucose Uptake.","date":"2023","source":"Computational and mathematical methods in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38094447","citation_count":0,"is_preprint":false},{"pmid":"16837566","id":"PMC_16837566","title":"Genetic analysis of 4 new mutants at the unstable k2 Mdh1-n y20 chromosomal region in soybean.","date":"2006","source":"The Journal of heredity","url":"https://pubmed.ncbi.nlm.nih.gov/16837566","citation_count":0,"is_preprint":false},{"pmid":"11357367","id":"PMC_11357367","title":"[Expression of Mdh1 locus alleles in apozygotic progenies of sugar beet (Beta vulgaris L.)].","date":"2001","source":"Genetika","url":"https://pubmed.ncbi.nlm.nih.gov/11357367","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.06.16.659985","title":"Dynamic assembly of malate dehydrogenase-citrate synthase multienzyme complex in the mitochondria","date":"2025-06-20","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.16.659985","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.09.16.675844","title":"Aspartate transaminases are required for blood development","date":"2025-09-19","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.16.675844","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":18461,"output_tokens":3864,"usd":0.056671,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11635,"output_tokens":3633,"usd":0.0745,"stage2_stop_reason":"end_turn"},"total_usd":0.131171,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2016,\n      \"finding\": \"PRMT4/CARM1 methylates MDH1 at arginine 248 (R248), inhibiting its enzymatic activity by disrupting MDH1 dimerization. This methylation negatively regulates the unconventional glutamine metabolic pathway in pancreatic ductal adenocarcinoma cells that supports NADPH production. Re-expression of wild-type MDH1, but not its methylation-mimetic mutant, restored cell growth and clonogenic activity.\",\n      \"method\": \"In vitro methylation assay, site-directed mutagenesis (R248 methylation-mimetic mutant), Co-IP for dimerization, knockdown/re-expression rescue experiments, metabolic flux assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods including in vitro methylation assay, mutagenesis of active site, dimerization disruption assay, and functional rescue experiments in a single rigorous study\",\n      \"pmids\": [\"27840030\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"HDAC6 binds MDH1 and mediates its deacetylation at lysine residues K121 and K298. The acetylation-mimetic mutant of MDH1 (but not the acetylation-resistant mutant) protected neurons from oxidative injury. HDAC6 inhibition failed to alleviate brain damage after ICH when MDH1 was knocked down, placing MDH1 downstream of HDAC6 in the oxidative stress response.\",\n      \"method\": \"Co-IP (HDAC6-MDH1 interaction), site-directed mutagenesis (K121 and K298 acetylation-mimetic and acetylation-resistant mutants), HDAC6 KO mice, MDH1 knockdown, NADPH/NADP+ and ROS assays\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, site-directed mutagenesis, KO mice, and MDH1 KD rescue experiments with multiple orthogonal functional readouts in one study\",\n      \"pmids\": [\"35678904\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"MDH1 is required for maintenance of the levels of the autophagy-initiating kinase ULK1, and MDH1 activity increases upon induction of autophagy. MDH1 knockdown identified it as a regulator of early autophagosome formation stages in PDAC cells.\",\n      \"method\": \"Genome-wide siRNA screen with autophagy readout, siRNA knockdown validation, ULK1 protein level measurement\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — siRNA screen with validation, two orthogonal readouts (ULK1 levels and autophagosome formation), but no direct biochemical interaction assay between MDH1 and ULK1\",\n      \"pmids\": [\"30765601\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"MDH1 deficiency (homozygous missense variant in the NAD+-binding domain) leads to severely diminished MDH1 protein expression and disrupts the malate-aspartate shuttle, resulting in elevated glycerol-3-phosphate (a compensatory mechanism via the glycerol-P-shuttle), increased aspartate, and decreased fumarate in MDH1 knockout HEK293 cells.\",\n      \"method\": \"CRISPR/Cas9 MDH1 knockout HEK293 cells, untargeted metabolomics on dried blood spots and KO cells\",\n      \"journal\": \"Human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR KO with metabolomics in cells and patient samples, single lab, two orthogonal approaches (patient DBS and KO cells)\",\n      \"pmids\": [\"31538237\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"STAT3 transactivates MDH1 to sustain malate-aspartate NADH shuttle activity required for fetal liver hematopoietic stem cell (HSC) self-renewal and differentiation. MDH1 mediates the metabolic program of FL-HSCs supporting HSC maintenance.\",\n      \"method\": \"Transgenic SoNar NADH/NAD+ sensor mice, transcriptional reporter assays for STAT3-MDH1, functional HSC assays (self-renewal, differentiation)\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct metabolic sensor imaging in vivo combined with STAT3-MDH1 transactivation and HSC functional assays, single lab\",\n      \"pmids\": [\"32396938\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Oxidative damage (trioxidation) accumulates at Cys137 of MDH1 in aged murine brain, located at the protein active zone. This modification significantly reduces MDH1 enzymatic activity, dysregulating TCA cycle bioenergetics in the aging brain.\",\n      \"method\": \"LC-MS/MS proteomics, quantitative MRM-MS, 3D structural modeling of MDH1, enzymatic kinetic analysis of MDH1 from old vs. young mouse brain\",\n      \"journal\": \"Journal of proteome research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mass spectrometry identification of modification site plus enzymatic kinetic validation, single lab, two orthogonal methods\",\n      \"pmids\": [\"32175745\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Deacetylation of MDH1 at K118 reduces MDH1 enzymatic activity and promotes NETosis (neutrophil extracellular trap formation), aggravating acute liver failure. This deacetylated MDH1 also promotes PANoptosis through endoplasmic reticulum stress signaling (upregulating BIP, ATF6, XBP1, CHOP), which is blocked by the ER stress inhibitor 4-PBA.\",\n      \"method\": \"Site-directed mutagenesis (K118 acetylation-mimetic and deacetylation mutants), adeno-associated virus in vivo delivery, immunoprecipitation, ER stress inhibitor rescue (4-PBA), LPS/D-gal ALF mouse model\",\n      \"journal\": \"Cellular & molecular biology letters / Cell death discovery / iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (mutagenesis, AAV in vivo, pharmacological rescue) across related papers from same lab, single group\",\n      \"pmids\": [\"38172700\", \"38851781\", \"38660411\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Deacetylation of MDH1 at K118 promotes NETosis by upregulating OPA1 (mitochondrial dynamin) and enhancing autophagy (increased LC3B-II and Beclin1, decreased p62). The HDAC6 inhibitor ACY1215 reverses these effects.\",\n      \"method\": \"Western blotting for OPA1 and autophagy markers, Mito-Tracker Red staining, LC3 fluorescence staining, LPS/D-gal ALF mouse model, IDH1/MDH1 deacetylation mutant transfection\",\n      \"journal\": \"International immunopharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — multiple orthogonal cell biological methods, pharmacological rescue, in vivo validation, single lab\",\n      \"pmids\": [\"39353390\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"IDH1/MDH1 deacetylation activates the cGAS-STING signaling pathway via NETs formation, promoting pro-inflammatory cytokine production and aggravating ALF. DNase 1 degraded NETs formed by IDH1/MDH1 deacetylation and attenuated hepatic tissue injury.\",\n      \"method\": \"Western blotting and immunofluorescence for NETs and cGAS-STING pathway proteins, DNase 1 treatment, HDAC6i (ACY1215) treatment, LPS/D-gal ALF mouse model, exogenous NET treatment of HepG2 cells\",\n      \"journal\": \"International immunopharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — multiple orthogonal methods in vitro and in vivo, pharmacological and enzymatic rescue, single lab\",\n      \"pmids\": [\"40388861\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Hydroxysafflor yellow A (HSYA) covalently activates MDH1 through Cys residue 137, promoting MDH1 bioenergetic enzymatic activity and restoring mitochondrial energy metabolism homeostasis in myocardial ischemia/reperfusion injury. Disruption of MDH1 or the C137 binding site abolished cardioprotective effects of HSYA.\",\n      \"method\": \"rdTOP-ABPP (reducing dimethyl labeling with tandem orthogonal proteolysis-activity-based protein profiling) combined with LC-MS/MS, cellular thermal shift assay for drug-target binding, enzymatic activity profiling, siRNA knockdown, MIRI mouse model\",\n      \"journal\": \"Phytomedicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — chemoproteomic identification of binding site plus thermal shift assay plus enzymatic activity and siRNA rescue, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"40513321\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"M2 macrophage-derived exosomes transfer MDH1 protein into lung adenocarcinoma (LUAD) cells, upregulating MDH1 levels and activating the Hippo/YAP signaling pathway to enhance LUAD cell growth and metastasis. YAP depletion abrogates M2-exos-induced malignant phenotypes.\",\n      \"method\": \"Exosome isolation and co-culture, xenograft tumor models, CCK-8/EdU/colony formation/wound-healing/transwell assays, Western blotting, siRNA knockdown of MDH1 and YAP\",\n      \"journal\": \"Pathology, research and practice\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, exosome transfer shown but mechanism linking MDH1 to YAP activation not biochemically elucidated beyond correlation\",\n      \"pmids\": [\"40090126\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Yeast mitochondrial MDH1 (ortholog) and citrate synthase (CIT1) form a dynamic metabolon that channels oxaloacetate. The MDH1-CIT1 complex dissociates when aerobic respiration is suppressed (Crabtree effect) and reassociates when respiratory activity is enhanced by acetate. Complex assembly is regulated by mitochondrial matrix pH (within physiological range 6.0–7.0), redox state, and metabolite levels (malate, fumarate, citrate).\",\n      \"method\": \"In vitro reconstitution of MDH1-CIT1 complex, pharmacological TCA cycle and ETC inhibition, affinity binding assays at varying pH and metabolite concentrations, yeast genetic manipulation\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro reconstitution of metabolon with functional validation and multiple pharmacological perturbations, single lab, preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.06.16.659985\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Conditional deletion of Mdh1 in erythroid cells did not cause anemia, demonstrating that MDH1-mediated malate-aspartate shuttle activity is not required for erythropoiesis, in contrast to aspartate aminotransferases GOT1/GOT2.\",\n      \"method\": \"Conditional Mdh1 knockout mouse (erythroid-specific), complete blood count and erythroid progenitor analysis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean conditional KO with defined cellular phenotype (negative result); single lab, preprint\",\n      \"pmids\": [\"bio_10.1101_2025.09.16.675844\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Human MDH1 cDNA encodes a 334 amino acid cytosolic malate dehydrogenase with 96% identity to murine cytosolic MDH. The gene maps to chromosomal location 2p15 by fluorescence in situ hybridization, and is most highly expressed in heart and skeletal muscle.\",\n      \"method\": \"cDNA cloning, Northern blot analysis, fluorescence in situ hybridization (FISH)\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Strong — molecular cloning with chromosomal localization by FISH and tissue expression profiling, foundational characterization replicated by subsequent studies\",\n      \"pmids\": [\"8786100\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"MDH1 is a cytosolic NAD(H)-dependent malate dehydrogenase that catalyzes the reversible oxidation of malate to oxaloacetate, functioning as a core component of the malate-aspartate shuttle and TCA cycle; its activity is regulated by post-translational modifications including CARM1-mediated arginine methylation at R248 (which disrupts dimerization and inhibits activity), HDAC6-mediated deacetylation at K121/K298 and K118 (which impairs redox homeostasis and promotes cell death pathways including NETosis, PANoptosis, and ER stress), and oxidative trioxidation at Cys137 (which reduces enzymatic activity in aging brain); MDH1 forms a dynamic metabolon with citrate synthase regulated by mitochondrial pH and metabolite levels, supports NADPH production in a glutamine metabolic pathway critical for pancreatic cancer, maintains fetal liver hematopoietic stem cell self-renewal downstream of STAT3, and regulates autophagosome formation by sustaining ULK1 levels.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"MDH1 is a cytosolic NAD(H)-dependent malate dehydrogenase that catalyzes the reversible interconversion of malate and oxaloacetate as a core component of the malate-aspartate shuttle, coupling cytosolic and mitochondrial redox state [#13, #3]. Loss of MDH1 disrupts this shuttle, elevating glycerol-3-phosphate (a compensatory glycerol-phosphate shuttle response), aspartate, and lowering fumarate, with a homozygous missense variant in its NAD+-binding domain causing severely diminished protein expression [#3]. Its enzymatic output is tuned by multiple post-translational modifications: CARM1/PRMT4 methylates Arg248 to block dimerization and inhibit activity, restraining a glutamine-driven NADPH-generating pathway in pancreatic cancer [#0]; HDAC6-mediated deacetylation at K121/K298 and at K118 lowers activity and impairs NADPH/redox homeostasis, driving oxidative neuronal injury and, in liver, NETosis, ER-stress-dependent PANoptosis, and cGAS-STING inflammatory signaling [#1, #6, #8]; and oxidative trioxidation at the active-zone residue Cys137 reduces activity in aged brain [#5]. Beyond core metabolism, MDH1 sustains levels of the autophagy-initiating kinase ULK1 to promote autophagosome formation [#2] and acts downstream of STAT3, which transactivates MDH1 to maintain malate-aspartate shuttle flux required for fetal liver hematopoietic stem cell self-renewal [#4]. In yeast, the mitochondrial ortholog forms a pH- and metabolite-regulated metabolon with citrate synthase that channels oxaloacetate [#11].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Establishing the molecular identity of human MDH1 was the prerequisite for all mechanistic work, defining it as a cytosolic malate dehydrogenase, its gene locus, and its tissue distribution.\",\n      \"evidence\": \"cDNA cloning, Northern blot, and FISH mapping to 2p15\",\n      \"pmids\": [\"8786100\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No catalytic or structural mechanism addressed\", \"Physiological role inferred from expression, not function\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Resolved how MDH1 activity is post-translationally restrained, showing CARM1 methylation of R248 disrupts dimerization to inhibit the enzyme and a glutamine-derived NADPH pathway supporting pancreatic cancer growth.\",\n      \"evidence\": \"In vitro methylation, methylation-mimetic mutagenesis, dimerization Co-IP, and metabolic rescue in PDAC cells\",\n      \"pmids\": [\"27840030\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Demethylase not identified\", \"Extent of regulation outside PDAC unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified a non-canonical role for MDH1 in autophagy, linking it to maintenance of ULK1 levels and early autophagosome formation.\",\n      \"evidence\": \"Genome-wide siRNA screen with knockdown validation and ULK1 protein measurement in PDAC cells\",\n      \"pmids\": [\"30765601\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct MDH1-ULK1 biochemical interaction shown\", \"Mechanism connecting MDH1 to ULK1 stability unresolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrated the metabolic consequence of MDH1 loss, defining its role in the malate-aspartate shuttle through a disease-associated NAD+-binding-domain variant.\",\n      \"evidence\": \"CRISPR MDH1 KO HEK293 cells and untargeted metabolomics on patient dried blood spots\",\n      \"pmids\": [\"31538237\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Clinical phenotype-to-metabolite causality not fully resolved\", \"Single patient/cell-line context\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Placed MDH1 in developmental hematopoiesis as a STAT3-induced effector sustaining malate-aspartate shuttle flux for fetal liver HSC self-renewal.\",\n      \"evidence\": \"In vivo SoNar NADH/NAD+ sensor mice, STAT3-MDH1 transactivation reporters, and HSC functional assays\",\n      \"pmids\": [\"32396938\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct STAT3 binding to the MDH1 promoter not detailed\", \"Relevance to adult HSC unaddressed\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Showed MDH1 activity declines with age via oxidative modification, identifying trioxidation of active-zone Cys137 as a mechanism dysregulating brain bioenergetics.\",\n      \"evidence\": \"LC-MS/MS, MRM-MS, structural modeling, and enzymatic kinetics of MDH1 from old vs young mouse brain\",\n      \"pmids\": [\"32175745\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causal link to neurodegenerative phenotype not established\", \"Reversibility of trioxidation unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined HDAC6 as an upstream regulator of MDH1, with deacetylation at K121/K298 controlling NADPH/redox homeostasis and neuronal survival after hemorrhage.\",\n      \"evidence\": \"Reciprocal Co-IP, acetylation-site mutants, HDAC6 KO mice, and MDH1 knockdown rescue with NADPH/ROS readouts\",\n      \"pmids\": [\"35678904\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Acetyltransferase counterpart not identified\", \"Quantitative stoichiometry of site occupancy unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended MDH1 deacetylation signaling to acute liver failure, linking K118 deacetylation to NETosis, ER-stress-driven PANoptosis, mitochondrial dynamics/autophagy, and cGAS-STING inflammation.\",\n      \"evidence\": \"K118 acetylation mutants, AAV delivery, ER stress and HDAC6 inhibitor rescue, DNase 1 NET degradation, and LPS/D-gal ALF mouse model\",\n      \"pmids\": [\"38172700\", \"38851781\", \"38660411\", \"39353390\", \"40388861\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct enzymatic basis linking MDH1 activity loss to downstream effectors not fully dissected\", \"Findings concentrated in a single lab's ALF model\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated MDH1 can be pharmacologically activated, with covalent engagement of Cys137 by HSYA restoring enzymatic activity and mitochondrial energetics in cardiac ischemia/reperfusion.\",\n      \"evidence\": \"rdTOP-ABPP chemoproteomics, cellular thermal shift assay, enzymatic profiling, and siRNA rescue in a MIRI mouse model\",\n      \"pmids\": [\"40513321\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specificity of HSYA for MDH1 over other Cys-containing targets not fully bounded\", \"Translational dosing unaddressed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Provided structural-functional insight into MDH1 organization, showing the ortholog forms a metabolite- and pH-regulated metabolon with citrate synthase that channels oxaloacetate.\",\n      \"evidence\": \"In vitro reconstitution and affinity assays under varying pH/metabolite conditions in yeast (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.06.16.659985\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Demonstrated in yeast mitochondrial ortholog, not human cytosolic MDH1\", \"Preprint, not peer-reviewed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Tested the in vivo requirement for MDH1 in erythropoiesis, finding the malate-aspartate shuttle via MDH1 dispensable for red cell development unlike GOT1/GOT2.\",\n      \"evidence\": \"Erythroid-specific conditional Mdh1 knockout mouse with blood and progenitor analysis (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.09.16.675844\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Negative result; compensatory pathways not mapped\", \"Preprint, not peer-reviewed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the converging post-translational modifications (methylation, acetylation, oxidation) are integrated to set MDH1 activity in any single physiological context, and the identities of the writer enzymes opposing HDAC6 deacetylation, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No acetyltransferase or demethylase identified for MDH1\", \"Cross-talk among R248 methylation, K118/K121/K298 acetylation, and C137 oxidation not jointly studied\", \"Human structural model of the metabolon lacking\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016491\", \"supporting_discovery_ids\": [13, 3, 0, 5, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [13, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [13, 3, 0]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\"MDH1-citrate synthase (CIT1) metabolon\"],\n    \"partners\": [\"CARM1\", \"HDAC6\", \"CIT1\", \"STAT3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}