{"gene":"ACAA1","run_date":"2026-06-09T22:02:37","timeline":{"discoveries":[{"year":2019,"finding":"miR-15a directly targets the 3'UTR of ACAA1 mRNA (validated by dual-luciferase reporter assay in chicken DF1 cells), reducing ACAA1 expression and thereby decreasing fatty acid β-oxidation, which indirectly promotes intramuscular preadipocyte differentiation in chickens.","method":"Dual-luciferase 3'UTR reporter assay, miR-15a mimic transfection in preadipocytes and DF1 cells, qPCR","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — dual-luciferase reporter validates direct 3'UTR targeting, combined with expression knockdown in preadipocytes; single lab, two orthogonal methods","pmids":["31434294"],"is_preprint":false},{"year":2021,"finding":"ACAA1 catalyzes the cleavage of 3-ketoacyl-CoA to acetyl-CoA and acyl-CoA in peroxisomal fatty acid β-oxidation; its deficiency in sheep preadipocytes increases lipid accumulation and triglyceride content and upregulates adipogenic markers PPARγ and C/EBPα, while overexpression inhibits adipogenesis, placing ACAA1 as a negative regulator of adipocyte differentiation via adipogenic transcription factor control.","method":"siRNA knockdown and overexpression in sheep preadipocytes, Oil Red O staining, triglyceride assay, qRT-PCR for PPARγ and C/EBPα","journal":"Frontiers in genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — bidirectional genetic manipulation (KD and OE) with defined cellular phenotype and molecular readouts; single lab, two orthogonal perturbations","pmids":["34234807"],"is_preprint":false},{"year":2021,"finding":"A missense variant p.N299S in ACAA1 disrupts its enzymatic (thiolase) activity, impairs lysosomal function, aggravates amyloid-β pathology and neuronal loss, and causes cognitive impairment in a murine model, identifying peroxisome-mediated lysosomal dysfunction as a mechanistic contributor to early-onset Alzheimer's disease.","method":"Whole-genome sequencing for variant identification, in vitro enzymatic activity assays, in vivo mouse model with Aβ pathology and cognitive testing, loss-of-function cellular assays","journal":"Signal transduction and targeted therapy","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — enzymatic activity assay with disease variant + in vivo model with multiple phenotypic readouts (lysosomal function, Aβ pathology, neuronal loss, cognition); multiple orthogonal methods in one study","pmids":["34465723"],"is_preprint":false},{"year":2023,"finding":"ACAA1 physically interacts with CDK4; inhibition of ACAA1 blocks RB1 phosphorylation, causing G1-S cell-cycle arrest in triple-negative breast cancer cells and potentiating response to CDK4/6 inhibitor abemaciclib.","method":"Co-immunoprecipitation (ACAA1–CDK4 interaction), RB1 phosphorylation immunoblot, cell-cycle analysis, ACAA1 inhibition/knockdown in TNBC cell lines and preclinical mouse models","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP demonstrates ACAA1–CDK4 binding, supported by downstream RB1 phosphorylation readout and in vivo xenograft data; single lab with multiple orthogonal methods","pmids":["37129951"],"is_preprint":false},{"year":2020,"finding":"Oncogenic KRAS downregulates ACAA1 mRNA expression through the MAPK signaling pathway, as demonstrated by siRNA knockdown of mutant KRASG13D and MAPK inhibitor (sorafenib) treatment both increasing ACAA1 expression in H1944 NSCLC cells.","method":"siRNA knockdown of KRASG13D, MAPK pathway inhibitor sorafenib treatment, qPCR measurement of ACAA1 mRNA in H1944 cells","journal":"Frontiers in oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two orthogonal perturbations (genetic KD and pharmacological inhibition) converge on the same ACAA1 mRNA readout; single lab","pmids":["33194642"],"is_preprint":false},{"year":2025,"finding":"In pancreatic ductal adenocarcinoma (PDAC) cells, ACAA1 knockdown reduces oxygen consumption rate by up to 60% and decreases ATP production by up to 70%, lowers ATP-dependent mTOR activity, and induces autophagy (elevated LC3-II), leading to tumor growth retardation in xenograft models and extended survival in KPC mice; this effect is cancer-cell-specific and does not affect normal cell oxygen consumption.","method":"ACAA1 knockout/knockdown in PDAC cells and normal cells, Seahorse oxygen consumption assay, ATP measurement, LC3-II immunoblot, mouse xenograft model, KPC genetic mouse model survival analysis","journal":"Molecular metabolism","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (metabolic flux, ATP, autophagy markers, in vivo xenograft, genetic mouse model) in a single study with cancer-specific selectivity demonstrated","pmids":["40848971"],"is_preprint":false},{"year":2026,"finding":"The molecular glue CLEO4-88 binds solely to the CTLH E3 ligase subunit GID4 and induces an allosteric conformational change that promotes ternary complex formation with ACAA1; this ternary complex formation inhibits ACAA1 thiolase enzymatic activity in vitro and in cellulo, without recruiting ACAA1 to the CTLH holoenzyme for ubiquitination.","method":"Biochemical ternary complex assay, cryo-EM/atomic structure of ternary complex, in vitro thiolase activity assay, cellular target engagement assays","journal":"Nature chemical biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic structure of ternary complex plus biochemical reconstitution of thiolase inhibition and mechanistic characterization of allosteric mechanism; multiple orthogonal methods in one study","pmids":["41957281"],"is_preprint":false},{"year":2025,"finding":"ACAA1 overexpression activates the PI3K/AKT pathway, leading to nuclear translocation of Nrf2; this ACAA1/PI3K/AKT/Nrf2 axis suppresses ferroptosis by regulating redox homeostasis and lipid peroxidation, promoting endometrial cancer cell proliferation, migration, and tumor growth in vivo.","method":"ACAA1 overexpression in EC cell lines, PI3K/AKT phosphorylation immunoblot, Nrf2 nuclear translocation assay, ferroptosis assays (lipid peroxidation, cell viability), xenograft mouse model","journal":"Free radical biology & medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (overexpression, pathway phosphorylation, nuclear translocation, ferroptosis readouts, in vivo xenograft); single lab","pmids":["41052583"],"is_preprint":false},{"year":2025,"finding":"ACAA1 overexpression in renal tubular epithelial cells alleviates arachidonic acid accumulation and reduces accumulation of AA-containing polyunsaturated phospholipids in cell membranes (independently of ACSL4), thereby decreasing membrane peroxidative damage, ferroptosis susceptibility, and calcium oxalate crystal adhesion. Transcription factor ATF1 is identified as an upstream transcriptional activator of ACAA1.","method":"ACAA1 overexpression in RTEC cells, targeted peroxidomics (arachidonic acid quantification), phospholipid profiling, crystal adhesion assay, ferroptosis assays, ACSL4 immunoblot, transcription factor array, ATF1 overexpression rescue experiment","journal":"Journal of pharmaceutical analysis","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal biochemical and cellular methods (lipidomics, phospholipid profiling, crystal adhesion, ferroptosis) in a single lab study","pmids":["42181662"],"is_preprint":false},{"year":2026,"finding":"Benzo[a]pyrene (BaP) binds to PPARα and represses transcription of ACAA1, impairing peroxisomal fatty acid degradation and leading to hepatic lipid accumulation (steatosis); BaP-induced NAFLD is mediated via the PPARα/ACAA1 axis.","method":"In vivo mouse model and in vitro hepatocyte experiments with BaP exposure, network toxicology, bioinformatics, PPARα binding analysis, ACAA1 expression measurement, lipid accumulation assays","journal":"Chemico-biological interactions","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo and in vitro experimental validation of PPARα/ACAA1 axis combined with network toxicology; single lab with multiple approaches","pmids":["41539557"],"is_preprint":false}],"current_model":"ACAA1 is a peroxisomal thiolase that catalyzes the cleavage of 3-ketoacyl-CoA into acetyl-CoA and acyl-CoA as the terminal step of peroxisomal fatty acid β-oxidation; its activity is regulated transcriptionally by PPARα and ATF1, post-translationally inhibited by the molecular glue CLEO4-88 acting via GID4-induced allosteric inhibition, and suppressed by oncogenic KRAS through MAPK signaling. Beyond lipid catabolism, ACAA1 physically interacts with CDK4 to modulate RB1 phosphorylation and cell-cycle progression, activates the PI3K/AKT/Nrf2 axis to suppress ferroptosis, and in PDAC cells supplies acyl-carnitines to mitochondria to sustain ATP production and mTOR activity, such that its loss triggers autophagy-mediated tumor growth inhibition; a disease-linked variant p.N299S disrupts its enzymatic activity, impairs lysosomal function, and drives Alzheimer's disease pathology in vivo."},"narrative":{"mechanistic_narrative":"ACAA1 is a peroxisomal thiolase that catalyzes the terminal cleavage of 3-ketoacyl-CoA into acetyl-CoA and acyl-CoA in peroxisomal fatty acid β-oxidation, positioning it as a control point for cellular lipid catabolism [PMID:34234807]. Its expression is set transcriptionally by PPARα, whose repression by benzo[a]pyrene impairs peroxisomal fatty acid degradation and drives hepatic steatosis [PMID:41539557], and by ATF1, while oncogenic KRAS suppresses ACAA1 mRNA through MAPK signaling [PMID:33194642, PMID:42181662]. Post-translationally, ACAA1 thiolase activity is inhibited by the molecular glue CLEO4-88, which binds the CTLH E3 ligase subunit GID4 and induces an allosteric conformational change promoting a GID4–ACAA1 ternary complex that blocks catalysis without driving ubiquitination [PMID:41957281]. Through its catabolic activity ACAA1 acts as a negative regulator of adipocyte differentiation, with its loss increasing lipid accumulation and adipogenic transcription factors PPARγ and C/EBPα [PMID:34234807]. Beyond lipid metabolism, ACAA1 has been linked to cancer cell biology: it physically interacts with CDK4 to support RB1 phosphorylation and G1-S progression [PMID:37129951], supplies substrate flux that sustains mitochondrial ATP production and mTOR activity in PDAC cells such that its loss induces autophagy and tumor growth arrest [PMID:40848971], and activates a PI3K/AKT/Nrf2 axis that suppresses ferroptosis [PMID:41052583, PMID:42181662]. A missense variant, p.N299S, disrupts ACAA1 thiolase activity, impairs lysosomal function, and aggravates amyloid-β pathology and cognitive impairment in a murine model of early-onset Alzheimer's disease [PMID:34465723].","teleology":[{"year":2019,"claim":"Established a post-transcriptional control point for ACAA1, showing that miR-15a directly represses it to redirect fatty acid handling toward preadipocyte differentiation.","evidence":"Dual-luciferase 3'UTR reporter and miR-15a mimic transfection in chicken preadipocytes/DF1 cells","pmids":["31434294"],"confidence":"Medium","gaps":["Performed in chicken cells; human relevance not tested","Link between reduced β-oxidation and adipogenesis is indirect","No measurement of thiolase activity itself"]},{"year":2020,"claim":"Connected oncogenic signaling to ACAA1, showing that mutant KRAS suppresses ACAA1 mRNA via the MAPK pathway in lung cancer cells.","evidence":"siRNA knockdown of KRASG13D and sorafenib treatment with qPCR readout in H1944 NSCLC cells","pmids":["33194642"],"confidence":"Medium","gaps":["Transcription factor mediating MAPK-dependent repression not identified","Functional consequence of ACAA1 loss in this context not measured","Single cell line"]},{"year":2021,"claim":"Defined ACAA1's enzymatic role and its function as a negative regulator of adipocyte differentiation through bidirectional genetic manipulation.","evidence":"siRNA knockdown and overexpression in sheep preadipocytes with Oil Red O, triglyceride assay, and adipogenic marker qRT-PCR","pmids":["34234807"],"confidence":"Medium","gaps":["Mechanistic link from β-oxidation flux to PPARγ/C/EBPα regulation not resolved","Performed in sheep cells","No direct enzymatic activity assay"]},{"year":2021,"claim":"Linked ACAA1 enzymatic loss-of-function to disease, demonstrating a missense variant that abolishes thiolase activity and drives Alzheimer's pathology via lysosomal dysfunction.","evidence":"Whole-genome sequencing, in vitro enzymatic assays, and an in vivo mouse model with Aβ pathology and cognitive testing","pmids":["34465723"],"confidence":"High","gaps":["Mechanism linking peroxisomal thiolase deficit to lysosomal dysfunction not fully defined","Single variant studied","Penetrance and human genetic spectrum not established"]},{"year":2023,"claim":"Revealed a non-metabolic, cell-cycle role for ACAA1 through a physical interaction with CDK4 controlling RB1 phosphorylation.","evidence":"Co-IP, RB1 phosphorylation immunoblot, cell-cycle analysis, and ACAA1 inhibition in TNBC cells and mouse models","pmids":["37129951"],"confidence":"Medium","gaps":["Co-IP without reciprocal validation or structural mapping of the interaction","Whether the interaction depends on thiolase activity unknown","Direct vs indirect CDK4 binding not resolved"]},{"year":2025,"claim":"Established ACAA1 as a metabolic dependency in PDAC, showing its substrate flux sustains mitochondrial ATP and mTOR activity, with cancer-cell-specific loss inducing autophagy and growth arrest.","evidence":"Knockout/knockdown with Seahorse OCR, ATP measurement, LC3-II immunoblot, xenografts, and KPC mouse survival","pmids":["40848971"],"confidence":"High","gaps":["Molecular basis of cancer-cell selectivity not defined","Mechanism by which a peroxisomal enzyme supplies mitochondrial substrate not fully mapped"]},{"year":2025,"claim":"Identified a pro-tumor signaling output of ACAA1, showing it activates PI3K/AKT/Nrf2 to suppress ferroptosis in endometrial cancer.","evidence":"Overexpression in EC cell lines with pathway phosphorylation, Nrf2 translocation, ferroptosis assays, and xenografts","pmids":["41052583"],"confidence":"Medium","gaps":["How a metabolic enzyme triggers PI3K/AKT activation is unresolved","Relies on overexpression","Direct vs indirect pathway engagement unclear"]},{"year":2025,"claim":"Defined ATF1 as an upstream transcriptional activator of ACAA1 and showed ACAA1 limits arachidonic acid-driven membrane peroxidation independently of ACSL4.","evidence":"Overexpression in renal tubular epithelial cells with peroxidomics, phospholipid profiling, ferroptosis/crystal adhesion assays, and ATF1 rescue","pmids":["42181662"],"confidence":"Medium","gaps":["Direct ATF1 binding to the ACAA1 promoter not demonstrated","Generality of the ACSL4-independent mechanism across tissues unknown"]},{"year":2026,"claim":"Demonstrated PPARα-dependent transcriptional control of ACAA1 in vivo, showing benzo[a]pyrene represses PPARα/ACAA1 to cause hepatic steatosis.","evidence":"In vivo and in vitro BaP exposure with PPARα binding analysis, ACAA1 expression, and lipid accumulation assays plus network toxicology","pmids":["41539557"],"confidence":"Medium","gaps":["Partly bioinformatic; direct PPARα occupancy at the ACAA1 locus not fully defined","Contribution of ACAA1 loss vs broader PPARα targets to steatosis not isolated"]},{"year":2026,"claim":"Defined a pharmacological mechanism to silence ACAA1 enzymatic activity, showing a molecular glue acts through GID4 to allosterically inhibit thiolase activity without degradation.","evidence":"Biochemical ternary complex assay, cryo-EM/atomic structure, in vitro thiolase activity assay, and cellular target engagement","pmids":["41957281"],"confidence":"High","gaps":["Therapeutic context and selectivity in disease models not established here","Whether GID4 has any endogenous role in regulating ACAA1 unknown"]},{"year":null,"claim":"How ACAA1's peroxisomal thiolase activity mechanistically connects to its reported non-catabolic functions (CDK4 binding, PI3K/AKT/Nrf2 activation, mitochondrial ATP supply) remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural or genetic test of whether catalytic activity is required for the cell-cycle and signaling roles","No unified model reconciling lipid catabolism with the cancer signaling outputs"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[1,2,6]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[3]}],"localization":[],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[1,9]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[3]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[5]}],"complexes":[],"partners":["CDK4","GID4"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P09110","full_name":"3-ketoacyl-CoA thiolase, peroxisomal","aliases":["Acetyl-CoA C-myristoyltransferase","Acetyl-CoA acyltransferase","Beta-ketothiolase","Peroxisomal 3-oxoacyl-CoA thiolase"],"length_aa":424,"mass_kda":44.3,"function":"Responsible for the thiolytic cleavage of straight chain 3-keto fatty acyl-CoAs (3-oxoacyl-CoAs) (PubMed:11734571, PubMed:2882519). Plays an important role in fatty acid peroxisomal beta-oxidation (PubMed:11734571, PubMed:2882519). Catalyzes the cleavage of short, medium, long, and very long straight chain 3-oxoacyl-CoAs (PubMed:11734571, PubMed:2882519)","subcellular_location":"Peroxisome","url":"https://www.uniprot.org/uniprotkb/P09110/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ACAA1","classification":"Not Classified","n_dependent_lines":11,"n_total_lines":1208,"dependency_fraction":0.009105960264900662},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ACAA1","total_profiled":1310},"omim":[{"mim_id":"617774","title":"LON PEPTIDASE 2, PEROXISOMAL; LONP2","url":"https://www.omim.org/entry/617774"},{"mim_id":"611017","title":"TRYPSIN DOMAIN-CONTAINING PROTEIN 1; TYSND1","url":"https://www.omim.org/entry/611017"},{"mim_id":"609751","title":"ACYL-CoA OXIDASE 1, PALMITOYL; ACOX1","url":"https://www.omim.org/entry/609751"},{"mim_id":"604770","title":"ACETYL-CoA ACYLTRANSFERASE 2; ACAA2","url":"https://www.omim.org/entry/604770"},{"mim_id":"604054","title":"ACETYL-CoA ACYLTRANSFERASE 1; ACAA1","url":"https://www.omim.org/entry/604054"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Peroxisomes","reliability":"Supported"}],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"kidney","ntpm":198.3},{"tissue":"liver","ntpm":616.3}],"url":"https://www.proteinatlas.org/search/ACAA1"},"hgnc":{"alias_symbol":["Lnc-Myd88"],"prev_symbol":[]},"alphafold":{"accession":"P09110","domains":[{"cath_id":"3.40.47.10","chopping":"37-156_172-418","consensus_level":"medium","plddt":98.3323,"start":37,"end":418}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P09110","model_url":"https://alphafold.ebi.ac.uk/files/AF-P09110-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P09110-F1-predicted_aligned_error_v6.png","plddt_mean":93.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ACAA1","jax_strain_url":"https://www.jax.org/strain/search?query=ACAA1"},"sequence":{"accession":"P09110","fasta_url":"https://rest.uniprot.org/uniprotkb/P09110.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P09110/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P09110"}},"corpus_meta":[{"pmid":"31434294","id":"PMC_31434294","title":"MicroRNA-15a Regulates the Differentiation of Intramuscular Preadipocytes by Targeting ACAA1, ACOX1 and SCP2 in Chickens.","date":"2019","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/31434294","citation_count":39,"is_preprint":false},{"pmid":"34234807","id":"PMC_34234807","title":"Effect of the ACAA1 Gene on Preadipocyte Differentiation in Sheep.","date":"2021","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/34234807","citation_count":38,"is_preprint":false},{"pmid":"34465723","id":"PMC_34465723","title":"A novel missense variant in ACAA1 contributes to early-onset Alzheimer's disease, impairs lysosomal function, and facilitates amyloid-β pathology and cognitive decline.","date":"2021","source":"Signal transduction and targeted therapy","url":"https://pubmed.ncbi.nlm.nih.gov/34465723","citation_count":35,"is_preprint":false},{"pmid":"37129951","id":"PMC_37129951","title":"Inhibition of ACAA1 Restrains Proliferation and Potentiates the Response to CDK4/6 Inhibitors in Triple-Negative Breast Cancer.","date":"2023","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/37129951","citation_count":26,"is_preprint":false},{"pmid":"32265992","id":"PMC_32265992","title":"HSD17B4, ACAA1, and PXMP4 in Peroxisome Pathway Are Down-Regulated and Have Clinical Significance in Non-small Cell Lung Cancer.","date":"2020","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/32265992","citation_count":19,"is_preprint":false},{"pmid":"22151743","id":"PMC_22151743","title":"Effects of endotoxin exposure on childhood asthma risk are modified by a genetic polymorphism in ACAA1.","date":"2011","source":"BMC medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/22151743","citation_count":17,"is_preprint":false},{"pmid":"33194642","id":"PMC_33194642","title":"ACAA1 Is a Predictive Factor of Survival and Is Correlated With T Cell Infiltration in Non-Small Cell Lung Cancer.","date":"2020","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/33194642","citation_count":15,"is_preprint":false},{"pmid":"40848971","id":"PMC_40848971","title":"ACAA1 knockout increases the survival rate of KPC mice by activating autophagy.","date":"2025","source":"Molecular metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/40848971","citation_count":1,"is_preprint":false},{"pmid":"41539557","id":"PMC_41539557","title":"Polycyclic aromatic hydrocarbons-induced suppression of the PPARα/ACAA1 axis drives hepatic steatosis: Integrating epidemiology, network toxicology, and experimental validation.","date":"2026","source":"Chemico-biological interactions","url":"https://pubmed.ncbi.nlm.nih.gov/41539557","citation_count":1,"is_preprint":false},{"pmid":"41957281","id":"PMC_41957281","title":"The molecular glue CLEO4-88 inhibits the ACAA1 thiolase by induced binding to GID4.","date":"2026","source":"Nature chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/41957281","citation_count":1,"is_preprint":false},{"pmid":"41052583","id":"PMC_41052583","title":"Turning off the ferroptosis switch: ACAA1-Driven PI3K/AKT/Nrf2 signaling as a novel driver of endometrial cancer progression.","date":"2025","source":"Free radical biology & medicine","url":"https://pubmed.ncbi.nlm.nih.gov/41052583","citation_count":0,"is_preprint":false},{"pmid":"42181662","id":"PMC_42181662","title":"ACAA1 mediates arachidonic acid dysregulation and membrane phospholipid remodeling to promote crystal-cell adhesion and ferroptosis susceptibility in calcium oxalate kidney stone.","date":"2025","source":"Journal of pharmaceutical analysis","url":"https://pubmed.ncbi.nlm.nih.gov/42181662","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8850,"output_tokens":2955,"usd":0.035437,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10453,"output_tokens":3557,"usd":0.070595,"stage2_stop_reason":"end_turn"},"total_usd":0.106032,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2019,\n      \"finding\": \"miR-15a directly targets the 3'UTR of ACAA1 mRNA (validated by dual-luciferase reporter assay in chicken DF1 cells), reducing ACAA1 expression and thereby decreasing fatty acid β-oxidation, which indirectly promotes intramuscular preadipocyte differentiation in chickens.\",\n      \"method\": \"Dual-luciferase 3'UTR reporter assay, miR-15a mimic transfection in preadipocytes and DF1 cells, qPCR\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — dual-luciferase reporter validates direct 3'UTR targeting, combined with expression knockdown in preadipocytes; single lab, two orthogonal methods\",\n      \"pmids\": [\"31434294\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ACAA1 catalyzes the cleavage of 3-ketoacyl-CoA to acetyl-CoA and acyl-CoA in peroxisomal fatty acid β-oxidation; its deficiency in sheep preadipocytes increases lipid accumulation and triglyceride content and upregulates adipogenic markers PPARγ and C/EBPα, while overexpression inhibits adipogenesis, placing ACAA1 as a negative regulator of adipocyte differentiation via adipogenic transcription factor control.\",\n      \"method\": \"siRNA knockdown and overexpression in sheep preadipocytes, Oil Red O staining, triglyceride assay, qRT-PCR for PPARγ and C/EBPα\",\n      \"journal\": \"Frontiers in genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — bidirectional genetic manipulation (KD and OE) with defined cellular phenotype and molecular readouts; single lab, two orthogonal perturbations\",\n      \"pmids\": [\"34234807\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"A missense variant p.N299S in ACAA1 disrupts its enzymatic (thiolase) activity, impairs lysosomal function, aggravates amyloid-β pathology and neuronal loss, and causes cognitive impairment in a murine model, identifying peroxisome-mediated lysosomal dysfunction as a mechanistic contributor to early-onset Alzheimer's disease.\",\n      \"method\": \"Whole-genome sequencing for variant identification, in vitro enzymatic activity assays, in vivo mouse model with Aβ pathology and cognitive testing, loss-of-function cellular assays\",\n      \"journal\": \"Signal transduction and targeted therapy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — enzymatic activity assay with disease variant + in vivo model with multiple phenotypic readouts (lysosomal function, Aβ pathology, neuronal loss, cognition); multiple orthogonal methods in one study\",\n      \"pmids\": [\"34465723\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ACAA1 physically interacts with CDK4; inhibition of ACAA1 blocks RB1 phosphorylation, causing G1-S cell-cycle arrest in triple-negative breast cancer cells and potentiating response to CDK4/6 inhibitor abemaciclib.\",\n      \"method\": \"Co-immunoprecipitation (ACAA1–CDK4 interaction), RB1 phosphorylation immunoblot, cell-cycle analysis, ACAA1 inhibition/knockdown in TNBC cell lines and preclinical mouse models\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP demonstrates ACAA1–CDK4 binding, supported by downstream RB1 phosphorylation readout and in vivo xenograft data; single lab with multiple orthogonal methods\",\n      \"pmids\": [\"37129951\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Oncogenic KRAS downregulates ACAA1 mRNA expression through the MAPK signaling pathway, as demonstrated by siRNA knockdown of mutant KRASG13D and MAPK inhibitor (sorafenib) treatment both increasing ACAA1 expression in H1944 NSCLC cells.\",\n      \"method\": \"siRNA knockdown of KRASG13D, MAPK pathway inhibitor sorafenib treatment, qPCR measurement of ACAA1 mRNA in H1944 cells\",\n      \"journal\": \"Frontiers in oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two orthogonal perturbations (genetic KD and pharmacological inhibition) converge on the same ACAA1 mRNA readout; single lab\",\n      \"pmids\": [\"33194642\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In pancreatic ductal adenocarcinoma (PDAC) cells, ACAA1 knockdown reduces oxygen consumption rate by up to 60% and decreases ATP production by up to 70%, lowers ATP-dependent mTOR activity, and induces autophagy (elevated LC3-II), leading to tumor growth retardation in xenograft models and extended survival in KPC mice; this effect is cancer-cell-specific and does not affect normal cell oxygen consumption.\",\n      \"method\": \"ACAA1 knockout/knockdown in PDAC cells and normal cells, Seahorse oxygen consumption assay, ATP measurement, LC3-II immunoblot, mouse xenograft model, KPC genetic mouse model survival analysis\",\n      \"journal\": \"Molecular metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (metabolic flux, ATP, autophagy markers, in vivo xenograft, genetic mouse model) in a single study with cancer-specific selectivity demonstrated\",\n      \"pmids\": [\"40848971\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"The molecular glue CLEO4-88 binds solely to the CTLH E3 ligase subunit GID4 and induces an allosteric conformational change that promotes ternary complex formation with ACAA1; this ternary complex formation inhibits ACAA1 thiolase enzymatic activity in vitro and in cellulo, without recruiting ACAA1 to the CTLH holoenzyme for ubiquitination.\",\n      \"method\": \"Biochemical ternary complex assay, cryo-EM/atomic structure of ternary complex, in vitro thiolase activity assay, cellular target engagement assays\",\n      \"journal\": \"Nature chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic structure of ternary complex plus biochemical reconstitution of thiolase inhibition and mechanistic characterization of allosteric mechanism; multiple orthogonal methods in one study\",\n      \"pmids\": [\"41957281\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ACAA1 overexpression activates the PI3K/AKT pathway, leading to nuclear translocation of Nrf2; this ACAA1/PI3K/AKT/Nrf2 axis suppresses ferroptosis by regulating redox homeostasis and lipid peroxidation, promoting endometrial cancer cell proliferation, migration, and tumor growth in vivo.\",\n      \"method\": \"ACAA1 overexpression in EC cell lines, PI3K/AKT phosphorylation immunoblot, Nrf2 nuclear translocation assay, ferroptosis assays (lipid peroxidation, cell viability), xenograft mouse model\",\n      \"journal\": \"Free radical biology & medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (overexpression, pathway phosphorylation, nuclear translocation, ferroptosis readouts, in vivo xenograft); single lab\",\n      \"pmids\": [\"41052583\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ACAA1 overexpression in renal tubular epithelial cells alleviates arachidonic acid accumulation and reduces accumulation of AA-containing polyunsaturated phospholipids in cell membranes (independently of ACSL4), thereby decreasing membrane peroxidative damage, ferroptosis susceptibility, and calcium oxalate crystal adhesion. Transcription factor ATF1 is identified as an upstream transcriptional activator of ACAA1.\",\n      \"method\": \"ACAA1 overexpression in RTEC cells, targeted peroxidomics (arachidonic acid quantification), phospholipid profiling, crystal adhesion assay, ferroptosis assays, ACSL4 immunoblot, transcription factor array, ATF1 overexpression rescue experiment\",\n      \"journal\": \"Journal of pharmaceutical analysis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal biochemical and cellular methods (lipidomics, phospholipid profiling, crystal adhesion, ferroptosis) in a single lab study\",\n      \"pmids\": [\"42181662\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Benzo[a]pyrene (BaP) binds to PPARα and represses transcription of ACAA1, impairing peroxisomal fatty acid degradation and leading to hepatic lipid accumulation (steatosis); BaP-induced NAFLD is mediated via the PPARα/ACAA1 axis.\",\n      \"method\": \"In vivo mouse model and in vitro hepatocyte experiments with BaP exposure, network toxicology, bioinformatics, PPARα binding analysis, ACAA1 expression measurement, lipid accumulation assays\",\n      \"journal\": \"Chemico-biological interactions\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo and in vitro experimental validation of PPARα/ACAA1 axis combined with network toxicology; single lab with multiple approaches\",\n      \"pmids\": [\"41539557\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ACAA1 is a peroxisomal thiolase that catalyzes the cleavage of 3-ketoacyl-CoA into acetyl-CoA and acyl-CoA as the terminal step of peroxisomal fatty acid β-oxidation; its activity is regulated transcriptionally by PPARα and ATF1, post-translationally inhibited by the molecular glue CLEO4-88 acting via GID4-induced allosteric inhibition, and suppressed by oncogenic KRAS through MAPK signaling. Beyond lipid catabolism, ACAA1 physically interacts with CDK4 to modulate RB1 phosphorylation and cell-cycle progression, activates the PI3K/AKT/Nrf2 axis to suppress ferroptosis, and in PDAC cells supplies acyl-carnitines to mitochondria to sustain ATP production and mTOR activity, such that its loss triggers autophagy-mediated tumor growth inhibition; a disease-linked variant p.N299S disrupts its enzymatic activity, impairs lysosomal function, and drives Alzheimer's disease pathology in vivo.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ACAA1 is a peroxisomal thiolase that catalyzes the terminal cleavage of 3-ketoacyl-CoA into acetyl-CoA and acyl-CoA in peroxisomal fatty acid β-oxidation, positioning it as a control point for cellular lipid catabolism [#1]. Its expression is set transcriptionally by PPARα, whose repression by benzo[a]pyrene impairs peroxisomal fatty acid degradation and drives hepatic steatosis [#9], and by ATF1, while oncogenic KRAS suppresses ACAA1 mRNA through MAPK signaling [#4, #8]. Post-translationally, ACAA1 thiolase activity is inhibited by the molecular glue CLEO4-88, which binds the CTLH E3 ligase subunit GID4 and induces an allosteric conformational change promoting a GID4–ACAA1 ternary complex that blocks catalysis without driving ubiquitination [#6]. Through its catabolic activity ACAA1 acts as a negative regulator of adipocyte differentiation, with its loss increasing lipid accumulation and adipogenic transcription factors PPARγ and C/EBPα [#1]. Beyond lipid metabolism, ACAA1 has been linked to cancer cell biology: it physically interacts with CDK4 to support RB1 phosphorylation and G1-S progression [#3], supplies substrate flux that sustains mitochondrial ATP production and mTOR activity in PDAC cells such that its loss induces autophagy and tumor growth arrest [#5], and activates a PI3K/AKT/Nrf2 axis that suppresses ferroptosis [#7, #8]. A missense variant, p.N299S, disrupts ACAA1 thiolase activity, impairs lysosomal function, and aggravates amyloid-β pathology and cognitive impairment in a murine model of early-onset Alzheimer's disease [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"Established a post-transcriptional control point for ACAA1, showing that miR-15a directly represses it to redirect fatty acid handling toward preadipocyte differentiation.\",\n      \"evidence\": \"Dual-luciferase 3'UTR reporter and miR-15a mimic transfection in chicken preadipocytes/DF1 cells\",\n      \"pmids\": [\"31434294\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Performed in chicken cells; human relevance not tested\", \"Link between reduced β-oxidation and adipogenesis is indirect\", \"No measurement of thiolase activity itself\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Connected oncogenic signaling to ACAA1, showing that mutant KRAS suppresses ACAA1 mRNA via the MAPK pathway in lung cancer cells.\",\n      \"evidence\": \"siRNA knockdown of KRASG13D and sorafenib treatment with qPCR readout in H1944 NSCLC cells\",\n      \"pmids\": [\"33194642\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Transcription factor mediating MAPK-dependent repression not identified\", \"Functional consequence of ACAA1 loss in this context not measured\", \"Single cell line\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined ACAA1's enzymatic role and its function as a negative regulator of adipocyte differentiation through bidirectional genetic manipulation.\",\n      \"evidence\": \"siRNA knockdown and overexpression in sheep preadipocytes with Oil Red O, triglyceride assay, and adipogenic marker qRT-PCR\",\n      \"pmids\": [\"34234807\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic link from β-oxidation flux to PPARγ/C/EBPα regulation not resolved\", \"Performed in sheep cells\", \"No direct enzymatic activity assay\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Linked ACAA1 enzymatic loss-of-function to disease, demonstrating a missense variant that abolishes thiolase activity and drives Alzheimer's pathology via lysosomal dysfunction.\",\n      \"evidence\": \"Whole-genome sequencing, in vitro enzymatic assays, and an in vivo mouse model with Aβ pathology and cognitive testing\",\n      \"pmids\": [\"34465723\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking peroxisomal thiolase deficit to lysosomal dysfunction not fully defined\", \"Single variant studied\", \"Penetrance and human genetic spectrum not established\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Revealed a non-metabolic, cell-cycle role for ACAA1 through a physical interaction with CDK4 controlling RB1 phosphorylation.\",\n      \"evidence\": \"Co-IP, RB1 phosphorylation immunoblot, cell-cycle analysis, and ACAA1 inhibition in TNBC cells and mouse models\",\n      \"pmids\": [\"37129951\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Co-IP without reciprocal validation or structural mapping of the interaction\", \"Whether the interaction depends on thiolase activity unknown\", \"Direct vs indirect CDK4 binding not resolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established ACAA1 as a metabolic dependency in PDAC, showing its substrate flux sustains mitochondrial ATP and mTOR activity, with cancer-cell-specific loss inducing autophagy and growth arrest.\",\n      \"evidence\": \"Knockout/knockdown with Seahorse OCR, ATP measurement, LC3-II immunoblot, xenografts, and KPC mouse survival\",\n      \"pmids\": [\"40848971\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of cancer-cell selectivity not defined\", \"Mechanism by which a peroxisomal enzyme supplies mitochondrial substrate not fully mapped\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified a pro-tumor signaling output of ACAA1, showing it activates PI3K/AKT/Nrf2 to suppress ferroptosis in endometrial cancer.\",\n      \"evidence\": \"Overexpression in EC cell lines with pathway phosphorylation, Nrf2 translocation, ferroptosis assays, and xenografts\",\n      \"pmids\": [\"41052583\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How a metabolic enzyme triggers PI3K/AKT activation is unresolved\", \"Relies on overexpression\", \"Direct vs indirect pathway engagement unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined ATF1 as an upstream transcriptional activator of ACAA1 and showed ACAA1 limits arachidonic acid-driven membrane peroxidation independently of ACSL4.\",\n      \"evidence\": \"Overexpression in renal tubular epithelial cells with peroxidomics, phospholipid profiling, ferroptosis/crystal adhesion assays, and ATF1 rescue\",\n      \"pmids\": [\"42181662\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct ATF1 binding to the ACAA1 promoter not demonstrated\", \"Generality of the ACSL4-independent mechanism across tissues unknown\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Demonstrated PPARα-dependent transcriptional control of ACAA1 in vivo, showing benzo[a]pyrene represses PPARα/ACAA1 to cause hepatic steatosis.\",\n      \"evidence\": \"In vivo and in vitro BaP exposure with PPARα binding analysis, ACAA1 expression, and lipid accumulation assays plus network toxicology\",\n      \"pmids\": [\"41539557\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Partly bioinformatic; direct PPARα occupancy at the ACAA1 locus not fully defined\", \"Contribution of ACAA1 loss vs broader PPARα targets to steatosis not isolated\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined a pharmacological mechanism to silence ACAA1 enzymatic activity, showing a molecular glue acts through GID4 to allosterically inhibit thiolase activity without degradation.\",\n      \"evidence\": \"Biochemical ternary complex assay, cryo-EM/atomic structure, in vitro thiolase activity assay, and cellular target engagement\",\n      \"pmids\": [\"41957281\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Therapeutic context and selectivity in disease models not established here\", \"Whether GID4 has any endogenous role in regulating ACAA1 unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ACAA1's peroxisomal thiolase activity mechanistically connects to its reported non-catabolic functions (CDK4 binding, PI3K/AKT/Nrf2 activation, mitochondrial ATP supply) remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural or genetic test of whether catalytic activity is required for the cell-cycle and signaling roles\", \"No unified model reconciling lipid catabolism with the cancer signaling outputs\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [1, 2, 6]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [1, 9]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"CDK4\", \"GID4\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}