{"gene":"ACOT12","run_date":"2026-04-28T17:12:37","timeline":{"discoveries":[{"year":2013,"finding":"ACOT12 is the major cytoplasmic enzyme that hydrolyzes the thioester bond of acetyl-CoA in the liver. Its activity is inhibited by phosphatidic acid (PA) in a noncompetitive manner, and this inhibition requires the C-terminal START domain, as a mutant lacking the START domain was not inhibited by PA. PA was found to bind to the thioesterase domain but not the START domain, suggesting the START domain is required for allosteric regulation. Additionally, insulin treatment decreased ACOT12 mRNA and protein levels in rat primary hepatocytes, indicating transcriptional regulation by insulin.","method":"In vitro thioesterase activity assays with phospholipid/lipid additions, domain-deletion mutagenesis, lipid-binding assays, primary hepatocyte culture with insulin treatment","journal":"Journal of lipid research","confidence":"High","confidence_rationale":"Tier 1 — in vitro enzymatic assay with mutagenesis and ligand-binding confirmation in a single rigorous study","pmids":["23709691"],"is_preprint":false},{"year":2019,"finding":"ACOT12 suppresses hepatocellular carcinoma (HCC) metastasis by regulating cellular acetyl-CoA levels and histone acetylation. Downregulation of ACOT12 leads to increased acetyl-CoA, which drives epigenetic induction of TWIST2 expression and promotes epithelial-mesenchymal transition (EMT).","method":"Gain- and loss-of-function studies in vitro and in vivo, acetyl-CoA metabolite measurement, histone acetylation assays, TWIST2 expression analysis, EMT marker assessment","journal":"Cell metabolism","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (metabolomics, epigenetic assays, in vivo models) with functional epistasis linking ACOT12 → acetyl-CoA → histone acetylation → TWIST2 → EMT","pmids":["30661930"],"is_preprint":false},{"year":2021,"finding":"ACOT12 deficiency in mice (Acot12-/- KO) leads to accumulation of acetyl-CoA, stimulation of de novo lipogenesis (DNL) and cholesterol biosynthesis in the liver, causing NAFLD. BioID proximity-ligation proteomics identified a direct interaction between ACOT12 and VPS33A, suggesting ACOT12 plays a role in vesicle-mediated cholesterol trafficking and lysosomal degradation of cholesterol in hepatocytes. The PPARα pathway was identified as the most enriched pathway in Acot12-/- livers.","method":"Acot12-/- knockout mice, KEGG pathway analysis, proximity-dependent biotin identification (BioID) interactome, acetyl-CoA quantification, lipid/cholesterol biosynthesis assays","journal":"Experimental & molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 — KO mouse with metabolic phenotype plus BioID interaction data; VPS33A interaction not yet confirmed by reciprocal co-IP","pmids":["34285335"],"is_preprint":false},{"year":2022,"finding":"In cartilage, ACOT12 functions downstream of PPARα to regulate de novo lipogenesis (DNL). Loss of ACOT12 in Acot12-/- mice causes accumulation of acetyl-CoA, stimulation of DNL and MMP activity, and chondrocyte apoptosis leading to cartilage degradation. Restoration of ACOT12 in human OA chondrocytes rescued pathophysiological features of osteoarthritis.","method":"Acot12-/- knockout mice generated by RNA-guided endonuclease, Ppara-/- mice, acetyl-CoA-conjugated chitosan delivery, immunohistochemistry, MMP and apoptosis assays, ACOT12 rescue experiments in human chondrocytes","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — KO mouse phenotype with epistasis (PPARα-ACOT12 axis) confirmed by rescue experiments in human cells, multiple orthogonal methods","pmids":["34987154"],"is_preprint":false},{"year":2022,"finding":"ACOT12 suppresses intrahepatic cholangiocarcinoma (ICC) metastasis; mechanistically, downregulation of ACOT12 promotes ICC metastasis by inducing Slug expression and EMT, linking acetyl-CoA metabolic aberration to ICC progression.","method":"In vitro and in vivo ICC cell line studies, ACOT12 gain/loss-of-function, Slug and EMT marker expression analysis","journal":"Journal of Cancer","confidence":"Medium","confidence_rationale":"Tier 2 — functional in vitro/in vivo data but single lab with limited mechanistic depth","pmids":["35399720"],"is_preprint":false},{"year":2022,"finding":"Exosomal miR-155-5p from glioma stem-like cells (GSCs) directly targets ACOT12 mRNA, reducing its expression in surrounding glioma cells and promoting mesenchymal transition.","method":"Exosome transfer experiments, miR-155-5p overexpression/inhibition, ACOT12 reporter assays, mesenchymal transition marker analysis","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 3 — single lab, miRNA target validation with functional phenotype but limited mechanistic depth on ACOT12 itself","pmids":["35986010"],"is_preprint":false},{"year":2023,"finding":"Loss of both Acot12 and Nudt7 (dKO mice) results in accumulation of acetyl-CoA that upregulates FOXM1 expression, driving chondrocyte senescence and cartilage degradation in osteoarthritis. Scavenging acetyl-CoA with an acetyl-CoA binding protein (ACBP) or silencing FoxM1 suppressed the senescence phenotype.","method":"Acot12/Nudt7 double-knockout mice, microarray, acetyl-CoA quantification, FOXM1 overexpression, siFoxM1 nanoparticle delivery, immunohistochemistry, qRT-PCR, cell apoptosis/proliferation assay","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 — dKO mouse with epistatic pathway (acetyl-CoA → FOXM1 → senescence) and rescue experiments; single lab","pmids":["37908734"],"is_preprint":false},{"year":2025,"finding":"ACOT12 deficiency in kidneys reduces the level of ACBD5 and impairs selective autophagic degradation of peroxisomes (pexophagy), contributing to lipid accumulation and fibrosis independently of PPARα signaling. Restoration of ACOT12 in Acot12-/-Pparα-/- mice significantly reduced lipid accumulation and renal fibrosis.","method":"Acot12-/- and Acot12-/-Pparα-/- knockout mice with UUO renal injury model, fenofibrate treatment, ACBD5 protein quantification, pexophagy markers, rescue experiments","journal":"Experimental & molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 — KO mouse with epistasis experiments and rescue, single lab","pmids":["39939783"],"is_preprint":false}],"current_model":"ACOT12 is a cytoplasmic acyl-CoA thioesterase that hydrolyzes acetyl-CoA into acetate and CoA; its activity is allosterically inhibited by phosphatidic acid via its C-terminal START domain and is transcriptionally downregulated by insulin, thereby controlling cellular acetyl-CoA pools that regulate histone acetylation, de novo lipogenesis, cholesterol trafficking (via VPS33A interaction), pexophagy (via ACBD5), and transcription factor (TWIST2, Slug, FOXM1) expression in liver, cartilage, and kidney biology."},"narrative":{"teleology":[{"year":2013,"claim":"Establishing ACOT12 as the dominant hepatic acetyl-CoA thioesterase and defining its allosteric regulation resolved how acetyl-CoA hydrolysis is controlled in the cytoplasm.","evidence":"In vitro activity assays with phospholipid panels, START-domain deletion mutagenesis, lipid-binding assays, and insulin-treated rat hepatocytes","pmids":["23709691"],"confidence":"High","gaps":["Structural basis for START-domain-mediated allosteric inhibition by phosphatidic acid unresolved","Upstream signaling pathway linking insulin to ACOT12 transcription not mapped","Contribution of other ACOT family members to acetyl-CoA hydrolysis in non-hepatic tissues unknown"]},{"year":2019,"claim":"Demonstrating that ACOT12 loss raises acetyl-CoA to drive histone acetylation and TWIST2-mediated EMT in hepatocellular carcinoma revealed a metabolite–epigenetic axis linking acetyl-CoA homeostasis to metastasis.","evidence":"Gain- and loss-of-function in HCC cells and xenograft models, acetyl-CoA quantification, histone acetylation assays, TWIST2 epistasis","pmids":["30661930"],"confidence":"High","gaps":["Specific histone marks and genomic loci altered by ACOT12 loss not mapped genome-wide","Whether ACOT12 re-expression fully reverses EMT in established tumors not tested"]},{"year":2021,"claim":"Acot12-knockout mice developed NAFLD with elevated de novo lipogenesis and cholesterol biosynthesis, and BioID identified VPS33A as a proximity interactor, linking ACOT12 to vesicle-mediated cholesterol trafficking.","evidence":"Acot12−/− mice, acetyl-CoA and lipid quantification, BioID proximity proteomics in hepatocytes","pmids":["34285335"],"confidence":"Medium","gaps":["VPS33A interaction not confirmed by reciprocal co-immunoprecipitation or functional validation","Whether cholesterol trafficking defect is a direct consequence of ACOT12–VPS33A interaction or secondary to acetyl-CoA accumulation unclear"]},{"year":2022,"claim":"Placing ACOT12 downstream of PPARα in cartilage and showing that its loss causes acetyl-CoA-driven lipogenesis, MMP activation, and chondrocyte apoptosis established ACOT12 as a joint-protective enzyme relevant to osteoarthritis.","evidence":"Acot12−/− and Ppara−/− mice, acetyl-CoA chitosan delivery, rescue with ACOT12 in human OA chondrocytes, immunohistochemistry","pmids":["34987154"],"confidence":"High","gaps":["Direct PPARα binding site on the Acot12 promoter not characterized","Whether other acyl-CoA thioesterases compensate partially in cartilage unknown"]},{"year":2022,"claim":"Extending the ACOT12–EMT axis to cholangiocarcinoma via Slug induction broadened the tumor-suppressive role of ACOT12 beyond HCC.","evidence":"In vitro and in vivo ICC models with ACOT12 manipulation, Slug and EMT marker quantification","pmids":["35399720"],"confidence":"Medium","gaps":["Whether Slug induction depends on the same histone acetylation mechanism as TWIST2 in HCC not tested","Single-lab finding without independent replication"]},{"year":2023,"claim":"Double knockout of Acot12 and Nudt7 revealed that combined acetyl-CoA accumulation upregulates FOXM1 to drive chondrocyte senescence, identifying an additional transcription factor axis in cartilage degeneration.","evidence":"Acot12/Nudt7 dKO mice, microarray, FOXM1 overexpression and siFoxM1 nanoparticle rescue, acetyl-CoA scavenging with ACBP","pmids":["37908734"],"confidence":"Medium","gaps":["Individual contributions of ACOT12 vs. NUDT7 to the FOXM1–senescence axis not fully deconvolved","Mechanism by which acetyl-CoA upregulates FOXM1 expression not defined"]},{"year":2025,"claim":"ACOT12 loss impairs ACBD5-dependent pexophagy in the kidney independently of PPARα, establishing a non-hepatic, non-cartilage role for ACOT12 in organelle quality control and renal fibrosis.","evidence":"Acot12−/− and Acot12−/−Ppara−/− mice with UUO renal injury, ACBD5 quantification, pexophagy markers, ACOT12 rescue","pmids":["39939783"],"confidence":"Medium","gaps":["Mechanism linking ACOT12 to ACBD5 protein levels (transcriptional, translational, or degradative) not determined","Whether the pexophagy defect is cell-autonomous in tubular epithelial cells not formally shown","Single lab; awaits independent replication"]},{"year":null,"claim":"Major open questions include the structural basis of START-domain-mediated allosteric regulation, whether ACOT12's non-enzymatic interactions (VPS33A, ACBD5) are direct or metabolite-mediated, and the relative contribution of acetyl-CoA-dependent histone acetylation versus other downstream metabolic pathways across tissues.","evidence":"","pmids":[],"confidence":"Low","gaps":["No crystal structure of ACOT12 with or without phosphatidic acid available","Quantitative contribution of ACOT12 vs. other acetyl-CoA consuming/producing enzymes to nuclear acetyl-CoA pools unknown","Whether ACOT12 has thioesterase activity toward substrates other than acetyl-CoA in vivo not systematically tested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,1,2,3]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,1,2]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,2,3]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[7]}],"complexes":[],"partners":["VPS33A","ACBD5","NUDT7"],"other_free_text":[]},"mechanistic_narrative":"ACOT12 is the principal cytoplasmic acetyl-CoA thioesterase that hydrolyzes acetyl-CoA to acetate and coenzyme A, thereby governing intracellular acetyl-CoA pools that feed into de novo lipogenesis, cholesterol biosynthesis, histone acetylation, and peroxisome turnover. Its catalytic activity is allosterically inhibited by phosphatidic acid through a mechanism requiring the C-terminal START domain, and its expression is transcriptionally downregulated by insulin and positively regulated by PPARα [PMID:23709691, PMID:34987154]. In hepatocytes, loss of ACOT12 elevates acetyl-CoA, driving histone acetylation–dependent induction of TWIST2 and Slug to promote epithelial–mesenchymal transition and metastasis in hepatocellular carcinoma and cholangiocarcinoma [PMID:30661930, PMID:35399720]; in cartilage, ACOT12 deficiency causes acetyl-CoA accumulation that stimulates lipogenesis, MMP activation, FOXM1-driven chondrocyte senescence, and cartilage degradation consistent with osteoarthritis [PMID:34987154, PMID:37908734]. In the kidney, ACOT12 supports ACBD5-dependent pexophagy independently of PPARα, and its loss leads to peroxisome accumulation, lipid deposition, and renal fibrosis [PMID:39939783]."},"prefetch_data":{"uniprot":{"accession":"Q8WYK0","full_name":"Acetyl-coenzyme A thioesterase","aliases":["Acyl-CoA thioester hydrolase 12","Acyl-coenzyme A thioesterase 12","Acyl-CoA thioesterase 12","Cytoplasmic acetyl-CoA hydrolase 1","CACH-1","hCACH-1","START domain-containing protein 15","StARD15"],"length_aa":555,"mass_kda":62.0,"function":"Catalyzes the hydrolysis of acyl-CoAs into free fatty acids and coenzyme A (CoASH), regulating their respective intracellular levels (PubMed:16951743). Preferentially hydrolyzes acetyl-CoA (PubMed:16951743)","subcellular_location":"Cytoplasm, cytosol","url":"https://www.uniprot.org/uniprotkb/Q8WYK0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ACOT12","classification":"Not Classified","n_dependent_lines":60,"n_total_lines":1208,"dependency_fraction":0.04966887417218543},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ACOT12","total_profiled":1310},"omim":[{"mim_id":"618354","title":"HOUGE-JANSSENS SYNDROME 3; HJS3","url":"https://www.omim.org/entry/618354"},{"mim_id":"614315","title":"ACYL-CoA THIOESTERASE 12; ACOT12","url":"https://www.omim.org/entry/614315"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Cytokinetic bridge","reliability":"Additional"}],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"liver","ntpm":94.1}],"url":"https://www.proteinatlas.org/search/ACOT12"},"hgnc":{"alias_symbol":["Cach","THEAL","STARD15"],"prev_symbol":[]},"alphafold":{"accession":"Q8WYK0","domains":[{"cath_id":"3.10.129.10","chopping":"9-116_123-331","consensus_level":"medium","plddt":92.5087,"start":9,"end":331},{"cath_id":"3.30.530.20","chopping":"344-366_383-545","consensus_level":"high","plddt":87.7186,"start":344,"end":545}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8WYK0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8WYK0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8WYK0-F1-predicted_aligned_error_v6.png","plddt_mean":88.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ACOT12","jax_strain_url":"https://www.jax.org/strain/search?query=ACOT12"},"sequence":{"accession":"Q8WYK0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8WYK0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8WYK0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8WYK0"}},"corpus_meta":[{"pmid":"30661930","id":"PMC_30661930","title":"ACOT12-Dependent Alteration of Acetyl-CoA Drives Hepatocellular Carcinoma Metastasis by Epigenetic Induction of Epithelial-Mesenchymal Transition.","date":"2019","source":"Cell metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/30661930","citation_count":111,"is_preprint":false},{"pmid":"12325082","id":"PMC_12325082","title":"Cree leukoencephalopathy and CACH/VWM disease are allelic at the EIF2B5 locus.","date":"2002","source":"Annals of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/12325082","citation_count":104,"is_preprint":false},{"pmid":"10334484","id":"PMC_10334484","title":"Increased density of oligodendrocytes in childhood ataxia with diffuse central hypomyelination (CACH) syndrome: neuropathological and biochemical study of two cases.","date":"1999","source":"Acta neuropathologica","url":"https://pubmed.ncbi.nlm.nih.gov/10334484","citation_count":70,"is_preprint":false},{"pmid":"16041584","id":"PMC_16041584","title":"Heightened stress response in primary fibroblasts expressing mutant eIF2B genes from CACH/VWM leukodystrophy patients.","date":"2005","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/16041584","citation_count":65,"is_preprint":false},{"pmid":"34987154","id":"PMC_34987154","title":"PPARα-ACOT12 axis is responsible for maintaining cartilage homeostasis through modulating de novo lipogenesis.","date":"2022","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/34987154","citation_count":60,"is_preprint":false},{"pmid":"11468311","id":"PMC_11468311","title":"Fatal infantile leukodystrophy: a severe variant of CACH/VWM syndrome, allelic to chromosome 3q27.","date":"2001","source":"Neurology","url":"https://pubmed.ncbi.nlm.nih.gov/11468311","citation_count":44,"is_preprint":false},{"pmid":"35986010","id":"PMC_35986010","title":"Exosomal miR-155-5p derived from glioma stem-like cells promotes mesenchymal transition via targeting ACOT12.","date":"2022","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/35986010","citation_count":32,"is_preprint":false},{"pmid":"23709691","id":"PMC_23709691","title":"Enzymatic and transcriptional regulation of the cytoplasmic acetyl-CoA hydrolase ACOT12.","date":"2013","source":"Journal of lipid research","url":"https://pubmed.ncbi.nlm.nih.gov/23709691","citation_count":26,"is_preprint":false},{"pmid":"20958979","id":"PMC_20958979","title":"Evaluation of the endoplasmic reticulum-stress response in eIF2B-mutated lymphocytes and lymphoblasts from CACH/VWM patients.","date":"2010","source":"BMC neurology","url":"https://pubmed.ncbi.nlm.nih.gov/20958979","citation_count":16,"is_preprint":false},{"pmid":"23335982","id":"PMC_23335982","title":"A yeast purification system for human translation initiation factors eIF2 and eIF2Bε and their use in the diagnosis of CACH/VWM disease.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23335982","citation_count":12,"is_preprint":false},{"pmid":"34285335","id":"PMC_34285335","title":"Loss of Acot12 contributes to NAFLD independent of lipolysis of adipose tissue.","date":"2021","source":"Experimental & molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34285335","citation_count":11,"is_preprint":false},{"pmid":"37908734","id":"PMC_37908734","title":"Upregulated FOXM1 stimulates chondrocyte senescence in Acot12-/-Nudt7-/- double knockout mice.","date":"2023","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/37908734","citation_count":10,"is_preprint":false},{"pmid":"17878805","id":"PMC_17878805","title":"[CACH/VWM syndrome and leucodystrophies related to EIF2B mutations].","date":"2007","source":"Revue neurologique","url":"https://pubmed.ncbi.nlm.nih.gov/17878805","citation_count":9,"is_preprint":false},{"pmid":"18294360","id":"PMC_18294360","title":"Exon deletion in the non-catalytic domain of eIF2Bepsilon due to a splice site mutation leads to infantile forms of CACH/VWM with severe decrease of eIF2B GEF activity.","date":"2008","source":"Annals of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/18294360","citation_count":9,"is_preprint":false},{"pmid":"35399720","id":"PMC_35399720","title":"ACOT12-mediated acetyl-CoA hydrolysis suppresses intrahepatic cholangiocarcinoma metastasis by inhibiting epithelial-mesenchymal transition.","date":"2022","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/35399720","citation_count":6,"is_preprint":false},{"pmid":"31858748","id":"PMC_31858748","title":"Variation at ACOT12 and CT62 locus represents susceptibility to psoriasis in Han population.","date":"2019","source":"Molecular genetics & genomic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/31858748","citation_count":4,"is_preprint":false},{"pmid":"39939783","id":"PMC_39939783","title":"ACOT12, a novel factor in the pathogenesis of kidney fibrosis, modulates ACBD5.","date":"2025","source":"Experimental & molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/39939783","citation_count":4,"is_preprint":false},{"pmid":"40247960","id":"PMC_40247960","title":"An atypical initial revelation of CACH-vanishing white matter syndrome miming herpetic encephalitis in a 6-year-old child: Case report and brief review.","date":"2025","source":"Radiology case reports","url":"https://pubmed.ncbi.nlm.nih.gov/40247960","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9858,"output_tokens":2243,"usd":0.031609},"stage2":{"model":"claude-opus-4-6","input_tokens":5569,"output_tokens":2293,"usd":0.127755},"total_usd":0.159364,"stage1_batch_id":"msgbatch_01TqNM6p6FsoMBT2jzQTwKBr","stage2_batch_id":"msgbatch_01Ya473eco8sTHbvRymQaU8o","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"ACOT12 is the major cytoplasmic enzyme that hydrolyzes the thioester bond of acetyl-CoA in the liver. Its activity is inhibited by phosphatidic acid (PA) in a noncompetitive manner, and this inhibition requires the C-terminal START domain, as a mutant lacking the START domain was not inhibited by PA. PA was found to bind to the thioesterase domain but not the START domain, suggesting the START domain is required for allosteric regulation. Additionally, insulin treatment decreased ACOT12 mRNA and protein levels in rat primary hepatocytes, indicating transcriptional regulation by insulin.\",\n      \"method\": \"In vitro thioesterase activity assays with phospholipid/lipid additions, domain-deletion mutagenesis, lipid-binding assays, primary hepatocyte culture with insulin treatment\",\n      \"journal\": \"Journal of lipid research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro enzymatic assay with mutagenesis and ligand-binding confirmation in a single rigorous study\",\n      \"pmids\": [\"23709691\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ACOT12 suppresses hepatocellular carcinoma (HCC) metastasis by regulating cellular acetyl-CoA levels and histone acetylation. Downregulation of ACOT12 leads to increased acetyl-CoA, which drives epigenetic induction of TWIST2 expression and promotes epithelial-mesenchymal transition (EMT).\",\n      \"method\": \"Gain- and loss-of-function studies in vitro and in vivo, acetyl-CoA metabolite measurement, histone acetylation assays, TWIST2 expression analysis, EMT marker assessment\",\n      \"journal\": \"Cell metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (metabolomics, epigenetic assays, in vivo models) with functional epistasis linking ACOT12 → acetyl-CoA → histone acetylation → TWIST2 → EMT\",\n      \"pmids\": [\"30661930\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ACOT12 deficiency in mice (Acot12-/- KO) leads to accumulation of acetyl-CoA, stimulation of de novo lipogenesis (DNL) and cholesterol biosynthesis in the liver, causing NAFLD. BioID proximity-ligation proteomics identified a direct interaction between ACOT12 and VPS33A, suggesting ACOT12 plays a role in vesicle-mediated cholesterol trafficking and lysosomal degradation of cholesterol in hepatocytes. The PPARα pathway was identified as the most enriched pathway in Acot12-/- livers.\",\n      \"method\": \"Acot12-/- knockout mice, KEGG pathway analysis, proximity-dependent biotin identification (BioID) interactome, acetyl-CoA quantification, lipid/cholesterol biosynthesis assays\",\n      \"journal\": \"Experimental & molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with metabolic phenotype plus BioID interaction data; VPS33A interaction not yet confirmed by reciprocal co-IP\",\n      \"pmids\": [\"34285335\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In cartilage, ACOT12 functions downstream of PPARα to regulate de novo lipogenesis (DNL). Loss of ACOT12 in Acot12-/- mice causes accumulation of acetyl-CoA, stimulation of DNL and MMP activity, and chondrocyte apoptosis leading to cartilage degradation. Restoration of ACOT12 in human OA chondrocytes rescued pathophysiological features of osteoarthritis.\",\n      \"method\": \"Acot12-/- knockout mice generated by RNA-guided endonuclease, Ppara-/- mice, acetyl-CoA-conjugated chitosan delivery, immunohistochemistry, MMP and apoptosis assays, ACOT12 rescue experiments in human chondrocytes\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse phenotype with epistasis (PPARα-ACOT12 axis) confirmed by rescue experiments in human cells, multiple orthogonal methods\",\n      \"pmids\": [\"34987154\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ACOT12 suppresses intrahepatic cholangiocarcinoma (ICC) metastasis; mechanistically, downregulation of ACOT12 promotes ICC metastasis by inducing Slug expression and EMT, linking acetyl-CoA metabolic aberration to ICC progression.\",\n      \"method\": \"In vitro and in vivo ICC cell line studies, ACOT12 gain/loss-of-function, Slug and EMT marker expression analysis\",\n      \"journal\": \"Journal of Cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — functional in vitro/in vivo data but single lab with limited mechanistic depth\",\n      \"pmids\": [\"35399720\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Exosomal miR-155-5p from glioma stem-like cells (GSCs) directly targets ACOT12 mRNA, reducing its expression in surrounding glioma cells and promoting mesenchymal transition.\",\n      \"method\": \"Exosome transfer experiments, miR-155-5p overexpression/inhibition, ACOT12 reporter assays, mesenchymal transition marker analysis\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single lab, miRNA target validation with functional phenotype but limited mechanistic depth on ACOT12 itself\",\n      \"pmids\": [\"35986010\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Loss of both Acot12 and Nudt7 (dKO mice) results in accumulation of acetyl-CoA that upregulates FOXM1 expression, driving chondrocyte senescence and cartilage degradation in osteoarthritis. Scavenging acetyl-CoA with an acetyl-CoA binding protein (ACBP) or silencing FoxM1 suppressed the senescence phenotype.\",\n      \"method\": \"Acot12/Nudt7 double-knockout mice, microarray, acetyl-CoA quantification, FOXM1 overexpression, siFoxM1 nanoparticle delivery, immunohistochemistry, qRT-PCR, cell apoptosis/proliferation assay\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — dKO mouse with epistatic pathway (acetyl-CoA → FOXM1 → senescence) and rescue experiments; single lab\",\n      \"pmids\": [\"37908734\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ACOT12 deficiency in kidneys reduces the level of ACBD5 and impairs selective autophagic degradation of peroxisomes (pexophagy), contributing to lipid accumulation and fibrosis independently of PPARα signaling. Restoration of ACOT12 in Acot12-/-Pparα-/- mice significantly reduced lipid accumulation and renal fibrosis.\",\n      \"method\": \"Acot12-/- and Acot12-/-Pparα-/- knockout mice with UUO renal injury model, fenofibrate treatment, ACBD5 protein quantification, pexophagy markers, rescue experiments\",\n      \"journal\": \"Experimental & molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with epistasis experiments and rescue, single lab\",\n      \"pmids\": [\"39939783\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ACOT12 is a cytoplasmic acyl-CoA thioesterase that hydrolyzes acetyl-CoA into acetate and CoA; its activity is allosterically inhibited by phosphatidic acid via its C-terminal START domain and is transcriptionally downregulated by insulin, thereby controlling cellular acetyl-CoA pools that regulate histone acetylation, de novo lipogenesis, cholesterol trafficking (via VPS33A interaction), pexophagy (via ACBD5), and transcription factor (TWIST2, Slug, FOXM1) expression in liver, cartilage, and kidney biology.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"ACOT12 is the principal cytoplasmic acetyl-CoA thioesterase that hydrolyzes acetyl-CoA to acetate and coenzyme A, thereby governing intracellular acetyl-CoA pools that feed into de novo lipogenesis, cholesterol biosynthesis, histone acetylation, and peroxisome turnover. Its catalytic activity is allosterically inhibited by phosphatidic acid through a mechanism requiring the C-terminal START domain, and its expression is transcriptionally downregulated by insulin and positively regulated by PPARα [PMID:23709691, PMID:34987154]. In hepatocytes, loss of ACOT12 elevates acetyl-CoA, driving histone acetylation–dependent induction of TWIST2 and Slug to promote epithelial–mesenchymal transition and metastasis in hepatocellular carcinoma and cholangiocarcinoma [PMID:30661930, PMID:35399720]; in cartilage, ACOT12 deficiency causes acetyl-CoA accumulation that stimulates lipogenesis, MMP activation, FOXM1-driven chondrocyte senescence, and cartilage degradation consistent with osteoarthritis [PMID:34987154, PMID:37908734]. In the kidney, ACOT12 supports ACBD5-dependent pexophagy independently of PPARα, and its loss leads to peroxisome accumulation, lipid deposition, and renal fibrosis [PMID:39939783].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Establishing ACOT12 as the dominant hepatic acetyl-CoA thioesterase and defining its allosteric regulation resolved how acetyl-CoA hydrolysis is controlled in the cytoplasm.\",\n      \"evidence\": \"In vitro activity assays with phospholipid panels, START-domain deletion mutagenesis, lipid-binding assays, and insulin-treated rat hepatocytes\",\n      \"pmids\": [\"23709691\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis for START-domain-mediated allosteric inhibition by phosphatidic acid unresolved\",\n        \"Upstream signaling pathway linking insulin to ACOT12 transcription not mapped\",\n        \"Contribution of other ACOT family members to acetyl-CoA hydrolysis in non-hepatic tissues unknown\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrating that ACOT12 loss raises acetyl-CoA to drive histone acetylation and TWIST2-mediated EMT in hepatocellular carcinoma revealed a metabolite–epigenetic axis linking acetyl-CoA homeostasis to metastasis.\",\n      \"evidence\": \"Gain- and loss-of-function in HCC cells and xenograft models, acetyl-CoA quantification, histone acetylation assays, TWIST2 epistasis\",\n      \"pmids\": [\"30661930\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Specific histone marks and genomic loci altered by ACOT12 loss not mapped genome-wide\",\n        \"Whether ACOT12 re-expression fully reverses EMT in established tumors not tested\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Acot12-knockout mice developed NAFLD with elevated de novo lipogenesis and cholesterol biosynthesis, and BioID identified VPS33A as a proximity interactor, linking ACOT12 to vesicle-mediated cholesterol trafficking.\",\n      \"evidence\": \"Acot12−/− mice, acetyl-CoA and lipid quantification, BioID proximity proteomics in hepatocytes\",\n      \"pmids\": [\"34285335\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"VPS33A interaction not confirmed by reciprocal co-immunoprecipitation or functional validation\",\n        \"Whether cholesterol trafficking defect is a direct consequence of ACOT12–VPS33A interaction or secondary to acetyl-CoA accumulation unclear\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Placing ACOT12 downstream of PPARα in cartilage and showing that its loss causes acetyl-CoA-driven lipogenesis, MMP activation, and chondrocyte apoptosis established ACOT12 as a joint-protective enzyme relevant to osteoarthritis.\",\n      \"evidence\": \"Acot12−/− and Ppara−/− mice, acetyl-CoA chitosan delivery, rescue with ACOT12 in human OA chondrocytes, immunohistochemistry\",\n      \"pmids\": [\"34987154\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct PPARα binding site on the Acot12 promoter not characterized\",\n        \"Whether other acyl-CoA thioesterases compensate partially in cartilage unknown\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Extending the ACOT12–EMT axis to cholangiocarcinoma via Slug induction broadened the tumor-suppressive role of ACOT12 beyond HCC.\",\n      \"evidence\": \"In vitro and in vivo ICC models with ACOT12 manipulation, Slug and EMT marker quantification\",\n      \"pmids\": [\"35399720\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether Slug induction depends on the same histone acetylation mechanism as TWIST2 in HCC not tested\",\n        \"Single-lab finding without independent replication\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Double knockout of Acot12 and Nudt7 revealed that combined acetyl-CoA accumulation upregulates FOXM1 to drive chondrocyte senescence, identifying an additional transcription factor axis in cartilage degeneration.\",\n      \"evidence\": \"Acot12/Nudt7 dKO mice, microarray, FOXM1 overexpression and siFoxM1 nanoparticle rescue, acetyl-CoA scavenging with ACBP\",\n      \"pmids\": [\"37908734\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Individual contributions of ACOT12 vs. NUDT7 to the FOXM1–senescence axis not fully deconvolved\",\n        \"Mechanism by which acetyl-CoA upregulates FOXM1 expression not defined\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"ACOT12 loss impairs ACBD5-dependent pexophagy in the kidney independently of PPARα, establishing a non-hepatic, non-cartilage role for ACOT12 in organelle quality control and renal fibrosis.\",\n      \"evidence\": \"Acot12−/− and Acot12−/−Ppara−/− mice with UUO renal injury, ACBD5 quantification, pexophagy markers, ACOT12 rescue\",\n      \"pmids\": [\"39939783\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism linking ACOT12 to ACBD5 protein levels (transcriptional, translational, or degradative) not determined\",\n        \"Whether the pexophagy defect is cell-autonomous in tubular epithelial cells not formally shown\",\n        \"Single lab; awaits independent replication\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Major open questions include the structural basis of START-domain-mediated allosteric regulation, whether ACOT12's non-enzymatic interactions (VPS33A, ACBD5) are direct or metabolite-mediated, and the relative contribution of acetyl-CoA-dependent histone acetylation versus other downstream metabolic pathways across tissues.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No crystal structure of ACOT12 with or without phosphatidic acid available\",\n        \"Quantitative contribution of ACOT12 vs. other acetyl-CoA consuming/producing enzymes to nuclear acetyl-CoA pools unknown\",\n        \"Whether ACOT12 has thioesterase activity toward substrates other than acetyl-CoA in vivo not systematically tested\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 1, 2, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 2, 3]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"VPS33A\",\n      \"ACBD5\",\n      \"NUDT7\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}