{"gene":"ACOT8","run_date":"2026-04-28T17:12:37","timeline":{"discoveries":[{"year":1997,"finding":"ACOT8 (initially named hACTE-III/hTE) was identified as a novel acyl-CoA thioesterase that binds HIV-1 Nef via the central region of Nef (amino acids 109-152), and this direct binding greatly enhances ACOT8 enzymatic activity toward a broad range of fatty acyl-CoAs.","method":"Yeast two-hybrid screen, in vitro binding assay, enzymatic activity assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — direct binding and enzymatic enhancement demonstrated, single lab with two orthogonal methods","pmids":["9299485"],"is_preprint":false},{"year":1997,"finding":"ACOT8 (hTE) interacts with HIV-1 Nef in vitro and is co-immunoprecipitated with Nef in CEM cells; Nef alleles unable to down-regulate CD4 do not interact with ACOT8, and a Nef mutant selected for lack of ACOT8 interaction also fails to down-regulate CD4, suggesting ACOT8 is a cellular mediator of Nef-induced CD4 down-regulation.","method":"Yeast two-hybrid, in vitro binding, co-immunoprecipitation, functional CD4 down-regulation assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — reciprocal co-IP, multiple orthogonal methods, replicated across labs","pmids":["9153233"],"is_preprint":false},{"year":1999,"finding":"ACOT8 (hTE/PTE-1) is a peroxisomal acyl-CoA thioesterase; recombinant ACOT8 shows intrinsic thioesterase activity (6 units/mg) most active on medium-chain acyl-CoAs, and the protein is localized to peroxisomes via a type-1 peroxisomal targeting signal (PTS1).","method":"GFP targeting assay, biochemical fractionation of purified peroxisomes, recombinant protein activity assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — in vitro enzymatic assay with recombinant protein, direct peroxisomal localization demonstrated, replicated by multiple labs","pmids":["10092594"],"is_preprint":false},{"year":2000,"finding":"ACOT8 (hTE) localizes to peroxisomes by immunofluorescence; co-expression of Nef with ACOT8 causes relocalization of Nef to peroxisomes. Point mutations in Nef at residues Asp108, Leu112, Phe121, Pro122, and Asp123 abolish interaction with ACOT8 and also abrogate CD4 down-regulation, defining a surface on Nef critical for both functions.","method":"Nef affinity column purification, peptide microsequence analysis, immunofluorescence, point mutagenesis, CD4 down-regulation assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 — affinity purification, mutagenesis, and functional assay combined; replicated from prior yeast two-hybrid findings","pmids":["10807905"],"is_preprint":false},{"year":2000,"finding":"Mutation of conserved residue D123 in Nef, which is required for Nef oligomerization, abolishes Nef-ACOT8 interaction and impairs Nef-induced CD4 down-regulation, MHC class I down-modulation, and enhancement of viral infectivity, suggesting Nef oligomerization is critical for ACOT8 binding and Nef function.","method":"Mutational analysis, co-immunoprecipitation, CD4/MHC class I functional assays","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 2 — mutagenesis with multiple functional readouts, consistent with prior structural data","pmids":["10799608"],"is_preprint":false},{"year":2000,"finding":"ACOT8 (PTE2, now recognized as a distinct peroxisomal thioesterase) shows intrinsic acyl-CoA thioesterase activity with a pH optimum of 8.5, is targeted to peroxisomes via a PTS1 (SKV), and displays high activity on both medium- and long-chain acyl-CoAs, in contrast to PTE1/ACOT8 which is most active on medium-chain substrates.","method":"Recombinant protein expression, thioesterase activity assay, GFP targeting assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 1 — in vitro enzymatic assay, single lab","pmids":["10944470"],"is_preprint":false},{"year":2004,"finding":"Stable overexpression of ACOT8 (ACTEIII/PTE-1) in human and murine T-cell lines increases peroxisome number and lipid droplet formation in a dose-dependent manner. ACOT8 mutants with reduced enzymatic activity or defective peroxisomal localization do not induce peroxisome proliferation, indicating that ACOT8 catalytic activity within peroxisomes is required for peroxisome biogenesis.","method":"Stable overexpression, immunofluorescence, electron microscopy, catalase quantification, enzymatic activity mutants","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 — loss-of-function mutagenesis with defined cellular phenotype, single lab","pmids":["15194431"],"is_preprint":false},{"year":2005,"finding":"ACOT8 (peroxisomal) preferentially hydrolyzes longer dicarboxylyl-CoA esters (glutaryl-CoA, adipyl-CoA, suberyl-CoA, sebacyl-CoA, and dodecanedioyl-CoA), distinguishing it from ACOT4 which mainly hydrolyzes succinyl-CoA; both enzymes are strongly expressed in kidney and liver and are PPARα target genes, suggesting roles in termination of peroxisomal beta-oxidation of dicarboxylic acids.","method":"Recombinant protein expression, enzyme activity measurements with multiple CoA ester substrates","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — reconstituted in vitro enzymatic assay with substrate specificity profiling","pmids":["16141203"],"is_preprint":false},{"year":2005,"finding":"ACOT8 is identified as an ISG15 conjugation target in IFN-beta-treated HeLa cells, indicating ACOT8 is post-translationally modified by ISG15 during antiviral innate immune responses.","method":"Double-affinity purification of ISG15-modified proteins, mass spectrometry identification, verification of ISG15 modification","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 — MS identification with biochemical verification in IFN-treated cells","pmids":["16009940"],"is_preprint":false},{"year":2006,"finding":"Analysis of the human ACOT gene cluster reveals that ACOT8 is a peroxisomal acyl-CoA thioesterase; the human ACOT gene cluster contains only three full-length thioesterase genes (ACOT1, ACOT2, ACOT4) compared to six in mouse, with ACOT8 being a separate peroxisomal enzyme in the family.","method":"Comparative genomic analysis, expression of recombinant proteins, enzymatic activity assays","journal":"FASEB journal","confidence":"Medium","confidence_rationale":"Tier 1-2 — recombinant protein assays combined with genomic analysis","pmids":["16940157"],"is_preprint":false},{"year":2014,"finding":"ACOT8 knockdown in Huh7 and Hep3B hepatocellular carcinoma cell lines reduces overall thioesterase activity and inhibits anchorage-dependent and -independent cell growth; this growth inhibition is partially rescued by addition of free fatty acid myristic acid, indicating ACOT8 promotes HCC cell growth through its thioesterase activity and free fatty acid generation.","method":"shRNA knockdown, thioesterase activity assay, in vitro tumorigenic assays, fatty acid rescue experiment","journal":"Oncology reports","confidence":"Medium","confidence_rationale":"Tier 2 — KD with defined cellular phenotype and partial mechanistic rescue, single lab","pmids":["24788990"],"is_preprint":false},{"year":2015,"finding":"ACOT8 knockdown by shRNA in primary CD4+ T cells does not impair HIV-1 Nef-mediated CD4 downmodulation, while AP-2 knockdown does; FRET analysis confirmed direct interaction between Nef and ACOT8 in cells, but functional contribution to CD4 downmodulation was not supported.","method":"shRNA knockdown, FRET analysis, CD4 downmodulation assay in HIV-infected primary T cells","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 — direct FRET interaction confirmed, loss-of-function with specific functional readout","pmids":["26423947"],"is_preprint":false},{"year":2022,"finding":"ACOT8 interacts with herpes simplex virus 1 ICP0 protein in both Neuro-2a and 293T cells, as validated by co-immunoprecipitation assay, suggesting ACOT8 is part of the ICP0-host protein interaction network in neuronal cells.","method":"Mass spectrometry-based interactome analysis, co-immunoprecipitation validation","journal":"Frontiers in microbiology","confidence":"Low","confidence_rationale":"Tier 3 — single co-IP validation, no functional consequence for ACOT8 specifically demonstrated","pmids":["35516420"],"is_preprint":false}],"current_model":"ACOT8 is a peroxisomal acyl-CoA thioesterase (localized via a PTS1 signal) that hydrolyzes a broad range of acyl-CoA esters—particularly medium-chain and long-chain dicarboxylyl-CoAs—to generate free fatty acids and CoASH, thereby terminating peroxisomal beta-oxidation; it physically interacts with HIV-1 Nef through a defined surface on Nef's core domain, with this interaction enhancing ACOT8 enzymatic activity and being correlated (though not causally required) with Nef-induced CD4 downmodulation, and ACOT8's catalytic activity within peroxisomes drives peroxisome biogenesis and supports hepatocellular carcinoma cell growth through free fatty acid production."},"narrative":{"teleology":[{"year":1997,"claim":"Identification of ACOT8 as a Nef-binding acyl-CoA thioesterase established it as a potential cellular mediator of HIV-1 pathogenesis and revealed that Nef binding enhances its enzymatic activity.","evidence":"Yeast two-hybrid, in vitro binding, co-immunoprecipitation, enzymatic activity assays in CEM T cells","pmids":["9299485","9153233"],"confidence":"High","gaps":["Whether ACOT8 is causally required for Nef-mediated CD4 downmodulation versus merely correlated","Mechanism by which Nef binding enhances thioesterase activity"]},{"year":1999,"claim":"Demonstration that ACOT8 is a bona fide peroxisomal enzyme targeted via a PTS1 signal resolved its subcellular localization and confirmed intrinsic thioesterase activity with preference for medium-chain acyl-CoAs.","evidence":"GFP targeting assay, peroxisomal fractionation, recombinant protein activity assay","pmids":["10092594"],"confidence":"High","gaps":["Full substrate specificity profile not yet determined","Physiological relevance of peroxisomal localization for Nef interaction unclear"]},{"year":2000,"claim":"Mapping the Nef–ACOT8 interaction surface and showing Nef co-localizes with ACOT8 at peroxisomes defined the structural determinants of their association, while linking these residues to CD4 and MHC-I downmodulation.","evidence":"Nef affinity purification, point mutagenesis of Nef, immunofluorescence, CD4/MHC-I functional assays","pmids":["10807905","10799608"],"confidence":"High","gaps":["Correlation between Nef–ACOT8 binding and CD4 downmodulation does not prove causation","Whether Nef oligomerization requirement is specific to ACOT8 binding or a general folding defect"]},{"year":2004,"claim":"Overexpression studies established that ACOT8 catalytic activity within peroxisomes drives peroxisome biogenesis and lipid droplet formation, revealing a cell-biological function beyond simple fatty acid release.","evidence":"Stable overexpression in T-cell lines, catalytic and localization mutants, electron microscopy, catalase quantification","pmids":["15194431"],"confidence":"Medium","gaps":["Loss-of-function (endogenous KO) confirmation of peroxisome biogenesis role not performed","Mechanism linking CoA hydrolysis to peroxisome proliferation signaling unknown"]},{"year":2005,"claim":"Substrate specificity profiling revealed ACOT8 preferentially hydrolyzes longer-chain dicarboxylyl-CoAs (C5–C12), positioning it as the principal enzyme terminating peroxisomal β-oxidation of dicarboxylic acids, and identifying it as a PPARα target gene.","evidence":"Recombinant protein expression, in vitro activity measurements with panel of CoA ester substrates","pmids":["16141203"],"confidence":"High","gaps":["In vivo flux through dicarboxylic acid β-oxidation pathway upon ACOT8 loss not measured","Contribution of PPARα regulation to ACOT8 expression in disease states not characterized"]},{"year":2005,"claim":"Identification of ACOT8 as an ISG15 conjugation target during interferon-β signaling suggested a regulatory link between innate immunity and peroxisomal lipid metabolism.","evidence":"Double-affinity purification of ISG15-modified proteins, mass spectrometry in IFN-β-treated HeLa cells","pmids":["16009940"],"confidence":"Medium","gaps":["Functional consequence of ISG15 modification on ACOT8 activity or stability unknown","Whether ISGylation alters ACOT8 peroxisomal localization not tested"]},{"year":2014,"claim":"Knockdown of ACOT8 in hepatocellular carcinoma cells reduced growth that was partially rescued by exogenous free fatty acids, establishing that ACOT8 thioesterase activity fuels cancer cell proliferation through fatty acid generation.","evidence":"shRNA knockdown in Huh7/Hep3B, thioesterase activity assay, anchorage-dependent/independent growth assays, myristic acid rescue","pmids":["24788990"],"confidence":"Medium","gaps":["In vivo tumor model validation not performed","Whether specific acyl-CoA substrates or downstream lipid species mediate the growth effect is unresolved"]},{"year":2015,"claim":"Definitive loss-of-function experiments in primary CD4+ T cells showed ACOT8 is dispensable for Nef-mediated CD4 downmodulation despite confirmed direct interaction, resolving the long-standing question of ACOT8's functional role in this process.","evidence":"shRNA knockdown in primary CD4+ T cells, FRET confirmation of Nef–ACOT8 interaction, CD4 downmodulation assay during HIV-1 infection","pmids":["26423947"],"confidence":"Medium","gaps":["Physiological significance of Nef–ACOT8 interaction remains unknown if not CD4 downmodulation","Whether Nef exploits ACOT8 thioesterase activity for viral replication or lipid remodeling not tested"]},{"year":null,"claim":"The physiological consequence of Nef–ACOT8 binding remains unresolved, the mechanism linking ACOT8 catalysis to peroxisome biogenesis is undefined, and the in vivo metabolic and oncogenic roles of ACOT8 lack genetic model validation.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No ACOT8 knockout animal model phenotype reported","Structural basis of ACOT8 substrate selectivity for dicarboxylyl-CoAs not determined","Functional consequence of ISG15 modification on ACOT8 activity unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,2,5,7,10]}],"localization":[{"term_id":"GO:0005777","term_label":"peroxisome","supporting_discovery_ids":[2,3,6]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[2,5,7,10]}],"complexes":[],"partners":["HIV-1 NEF"],"other_free_text":[]},"mechanistic_narrative":"ACOT8 is a peroxisomal acyl-CoA thioesterase that hydrolyzes medium- and long-chain acyl-CoA esters—particularly dicarboxylyl-CoAs—to free fatty acids and CoASH, functioning in the termination of peroxisomal β-oxidation [PMID:10092594, PMID:16141203]. The enzyme is targeted to peroxisomes via a C-terminal PTS1 signal, and its catalytic activity within peroxisomes is required for peroxisome biogenesis and lipid droplet formation [PMID:10092594, PMID:15194431]. ACOT8 directly binds HIV-1 Nef through a defined surface on Nef's core domain, which enhances ACOT8 thioesterase activity, though ACOT8 is dispensable for Nef-mediated CD4 downmodulation [PMID:9153233, PMID:10807905, PMID:26423947]. ACOT8 thioesterase activity and the free fatty acids it generates promote hepatocellular carcinoma cell growth [PMID:24788990]."},"prefetch_data":{"uniprot":{"accession":"O14734","full_name":"Acyl-coenzyme A thioesterase 8","aliases":["Choloyl-coenzyme A thioesterase","HIV-Nef-associated acyl-CoA thioesterase","Peroxisomal acyl-CoA thioesterase 2","PTE-2","Peroxisomal acyl-coenzyme A thioester hydrolase 1","PTE-1","Peroxisomal long-chain acyl-CoA thioesterase 1","Thioesterase II","hACTE-III","hACTEIII","hTE"],"length_aa":319,"mass_kda":35.9,"function":"Catalyzes the hydrolysis of acyl-CoAs into free fatty acids and coenzyme A (CoASH), regulating their respective intracellular levels (PubMed:15194431, PubMed:9153233, PubMed:9299485). Displays no strong substrate specificity with respect to the carboxylic acid moiety of Acyl-CoAs (By similarity). Hydrolyzes medium length (C2 to C20) straight-chain, saturated and unsaturated acyl-CoAS but is inactive towards substrates with longer aliphatic chains (PubMed:9153233, PubMed:9299485). Moreover, it catalyzes the hydrolysis of CoA esters of bile acids, such as choloyl-CoA and chenodeoxycholoyl-CoA and competes with bile acid CoA:amino acid N-acyltransferase (BAAT) (By similarity). Is also able to hydrolyze CoA esters of dicarboxylic acids (By similarity). It is involved in the metabolic regulation of peroxisome proliferation (PubMed:15194431) (Microbial infection) May mediate Nef-induced down-regulation of CD4 cell-surface expression (PubMed:9153233)","subcellular_location":"Peroxisome matrix","url":"https://www.uniprot.org/uniprotkb/O14734/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ACOT8","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ACOT8","total_profiled":1310},"omim":[{"mim_id":"608123","title":"ACYL-CoA THIOESTERASE 8; ACOT8","url":"https://www.omim.org/entry/608123"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Vesicles","reliability":"Supported"},{"location":"Mitochondria","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ACOT8"},"hgnc":{"alias_symbol":["hACTE-III","hTE","PTE-2","NAP1"],"prev_symbol":["PTE1"]},"alphafold":{"accession":"O14734","domains":[{"cath_id":"2.40.160.210","chopping":"27-131_149-313","consensus_level":"medium","plddt":92.2735,"start":27,"end":313}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O14734","model_url":"https://alphafold.ebi.ac.uk/files/AF-O14734-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O14734-F1-predicted_aligned_error_v6.png","plddt_mean":88.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ACOT8","jax_strain_url":"https://www.jax.org/strain/search?query=ACOT8"},"sequence":{"accession":"O14734","fasta_url":"https://rest.uniprot.org/uniprotkb/O14734.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O14734/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O14734"}},"corpus_meta":[{"pmid":"2648569","id":"PMC_2648569","title":"The 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function.","date":"2026","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/41524403","citation_count":0,"is_preprint":false,"source_track":"gene2pubmed"}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":46308,"output_tokens":306,"usd":0.071757},"stage2":{"model":"","input_tokens":0,"output_tokens":0,"usd":0.0},"total_usd":0.2747,"stage1_batch_id":"msgbatch_01TqNM6p6FsoMBT2jzQTwKBr","stage2_batch_id":"msgbatch_01Ya473eco8sTHbvRymQaU8o","note":"batch pricing = 50% of standard","retry_stage1":{"model":"claude-sonnet-4-6","input_tokens":34085,"output_tokens":3102,"usd":0.074393},"retry_stage2":{"model":"claude-opus-4-6","input_tokens":6475,"output_tokens":2133,"usd":0.12855}},"stage1_raw":"Looking at the corpus, I need to identify which papers are about ACOT8 (Acyl-CoA thioesterase 8). Scanning through all 100 abstracts, none of them appear to be about ACOT8. The papers describe:\n\n- NAP-1/IL-8 (interleukin-8, a chemokine)\n- NAP1 (nucleosome assembly protein 1)\n- C-Nap1/CEP250 (centrosomal protein)\n- NAP1 (NF-κB activating kinase-associated protein 1 / TBK1 adaptor)\n- NAP1 (Nck-associated protein 1, WAVE complex component)\n- C. difficile NAP1 strain\n- Various other NAP1 proteins in plants, bacteria, fungi\n\nNone of these are ACOT8 (acyl-CoA thioesterase 8), which is a peroxisomal enzyme that hydrolyzes acyl-CoA thioesters. The corpus appears to have been retrieved on the basis of a symbol collision or retrieval error — none of the papers describe ACOT8 function.\n\n```json\n{\n  \"discoveries\": [],\n  \"current_model\": \"No mechanistic findings in the available literature.\"\n}\n```\n\n--- RETRY (gene2pubmed) ---\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1997,\n      \"finding\": \"ACOT8 (initially named hACTE-III/hTE) was identified as a novel acyl-CoA thioesterase that binds HIV-1 Nef via the central region of Nef (amino acids 109-152), and this direct binding greatly enhances ACOT8 enzymatic activity toward a broad range of fatty acyl-CoAs.\",\n      \"method\": \"Yeast two-hybrid screen, in vitro binding assay, enzymatic activity assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct binding and enzymatic enhancement demonstrated, single lab with two orthogonal methods\",\n      \"pmids\": [\"9299485\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"ACOT8 (hTE) interacts with HIV-1 Nef in vitro and is co-immunoprecipitated with Nef in CEM cells; Nef alleles unable to down-regulate CD4 do not interact with ACOT8, and a Nef mutant selected for lack of ACOT8 interaction also fails to down-regulate CD4, suggesting ACOT8 is a cellular mediator of Nef-induced CD4 down-regulation.\",\n      \"method\": \"Yeast two-hybrid, in vitro binding, co-immunoprecipitation, functional CD4 down-regulation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal co-IP, multiple orthogonal methods, replicated across labs\",\n      \"pmids\": [\"9153233\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"ACOT8 (hTE/PTE-1) is a peroxisomal acyl-CoA thioesterase; recombinant ACOT8 shows intrinsic thioesterase activity (6 units/mg) most active on medium-chain acyl-CoAs, and the protein is localized to peroxisomes via a type-1 peroxisomal targeting signal (PTS1).\",\n      \"method\": \"GFP targeting assay, biochemical fractionation of purified peroxisomes, recombinant protein activity assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro enzymatic assay with recombinant protein, direct peroxisomal localization demonstrated, replicated by multiple labs\",\n      \"pmids\": [\"10092594\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"ACOT8 (hTE) localizes to peroxisomes by immunofluorescence; co-expression of Nef with ACOT8 causes relocalization of Nef to peroxisomes. Point mutations in Nef at residues Asp108, Leu112, Phe121, Pro122, and Asp123 abolish interaction with ACOT8 and also abrogate CD4 down-regulation, defining a surface on Nef critical for both functions.\",\n      \"method\": \"Nef affinity column purification, peptide microsequence analysis, immunofluorescence, point mutagenesis, CD4 down-regulation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — affinity purification, mutagenesis, and functional assay combined; replicated from prior yeast two-hybrid findings\",\n      \"pmids\": [\"10807905\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Mutation of conserved residue D123 in Nef, which is required for Nef oligomerization, abolishes Nef-ACOT8 interaction and impairs Nef-induced CD4 down-regulation, MHC class I down-modulation, and enhancement of viral infectivity, suggesting Nef oligomerization is critical for ACOT8 binding and Nef function.\",\n      \"method\": \"Mutational analysis, co-immunoprecipitation, CD4/MHC class I functional assays\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — mutagenesis with multiple functional readouts, consistent with prior structural data\",\n      \"pmids\": [\"10799608\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"ACOT8 (PTE2, now recognized as a distinct peroxisomal thioesterase) shows intrinsic acyl-CoA thioesterase activity with a pH optimum of 8.5, is targeted to peroxisomes via a PTS1 (SKV), and displays high activity on both medium- and long-chain acyl-CoAs, in contrast to PTE1/ACOT8 which is most active on medium-chain substrates.\",\n      \"method\": \"Recombinant protein expression, thioesterase activity assay, GFP targeting assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 — in vitro enzymatic assay, single lab\",\n      \"pmids\": [\"10944470\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Stable overexpression of ACOT8 (ACTEIII/PTE-1) in human and murine T-cell lines increases peroxisome number and lipid droplet formation in a dose-dependent manner. ACOT8 mutants with reduced enzymatic activity or defective peroxisomal localization do not induce peroxisome proliferation, indicating that ACOT8 catalytic activity within peroxisomes is required for peroxisome biogenesis.\",\n      \"method\": \"Stable overexpression, immunofluorescence, electron microscopy, catalase quantification, enzymatic activity mutants\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function mutagenesis with defined cellular phenotype, single lab\",\n      \"pmids\": [\"15194431\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"ACOT8 (peroxisomal) preferentially hydrolyzes longer dicarboxylyl-CoA esters (glutaryl-CoA, adipyl-CoA, suberyl-CoA, sebacyl-CoA, and dodecanedioyl-CoA), distinguishing it from ACOT4 which mainly hydrolyzes succinyl-CoA; both enzymes are strongly expressed in kidney and liver and are PPARα target genes, suggesting roles in termination of peroxisomal beta-oxidation of dicarboxylic acids.\",\n      \"method\": \"Recombinant protein expression, enzyme activity measurements with multiple CoA ester substrates\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted in vitro enzymatic assay with substrate specificity profiling\",\n      \"pmids\": [\"16141203\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"ACOT8 is identified as an ISG15 conjugation target in IFN-beta-treated HeLa cells, indicating ACOT8 is post-translationally modified by ISG15 during antiviral innate immune responses.\",\n      \"method\": \"Double-affinity purification of ISG15-modified proteins, mass spectrometry identification, verification of ISG15 modification\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — MS identification with biochemical verification in IFN-treated cells\",\n      \"pmids\": [\"16009940\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Analysis of the human ACOT gene cluster reveals that ACOT8 is a peroxisomal acyl-CoA thioesterase; the human ACOT gene cluster contains only three full-length thioesterase genes (ACOT1, ACOT2, ACOT4) compared to six in mouse, with ACOT8 being a separate peroxisomal enzyme in the family.\",\n      \"method\": \"Comparative genomic analysis, expression of recombinant proteins, enzymatic activity assays\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 — recombinant protein assays combined with genomic analysis\",\n      \"pmids\": [\"16940157\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"ACOT8 knockdown in Huh7 and Hep3B hepatocellular carcinoma cell lines reduces overall thioesterase activity and inhibits anchorage-dependent and -independent cell growth; this growth inhibition is partially rescued by addition of free fatty acid myristic acid, indicating ACOT8 promotes HCC cell growth through its thioesterase activity and free fatty acid generation.\",\n      \"method\": \"shRNA knockdown, thioesterase activity assay, in vitro tumorigenic assays, fatty acid rescue experiment\",\n      \"journal\": \"Oncology reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KD with defined cellular phenotype and partial mechanistic rescue, single lab\",\n      \"pmids\": [\"24788990\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"ACOT8 knockdown by shRNA in primary CD4+ T cells does not impair HIV-1 Nef-mediated CD4 downmodulation, while AP-2 knockdown does; FRET analysis confirmed direct interaction between Nef and ACOT8 in cells, but functional contribution to CD4 downmodulation was not supported.\",\n      \"method\": \"shRNA knockdown, FRET analysis, CD4 downmodulation assay in HIV-infected primary T cells\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct FRET interaction confirmed, loss-of-function with specific functional readout\",\n      \"pmids\": [\"26423947\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ACOT8 interacts with herpes simplex virus 1 ICP0 protein in both Neuro-2a and 293T cells, as validated by co-immunoprecipitation assay, suggesting ACOT8 is part of the ICP0-host protein interaction network in neuronal cells.\",\n      \"method\": \"Mass spectrometry-based interactome analysis, co-immunoprecipitation validation\",\n      \"journal\": \"Frontiers in microbiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single co-IP validation, no functional consequence for ACOT8 specifically demonstrated\",\n      \"pmids\": [\"35516420\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ACOT8 is a peroxisomal acyl-CoA thioesterase (localized via a PTS1 signal) that hydrolyzes a broad range of acyl-CoA esters—particularly medium-chain and long-chain dicarboxylyl-CoAs—to generate free fatty acids and CoASH, thereby terminating peroxisomal beta-oxidation; it physically interacts with HIV-1 Nef through a defined surface on Nef's core domain, with this interaction enhancing ACOT8 enzymatic activity and being correlated (though not causally required) with Nef-induced CD4 downmodulation, and ACOT8's catalytic activity within peroxisomes drives peroxisome biogenesis and supports hepatocellular carcinoma cell growth through free fatty acid production.\"\n}\n```","stage2_raw":"\n\n--- RETRY (gene2pubmed) ---\n\n```json\n{\n  \"mechanistic_narrative\": \"ACOT8 is a peroxisomal acyl-CoA thioesterase that hydrolyzes medium- and long-chain acyl-CoA esters—particularly dicarboxylyl-CoAs—to free fatty acids and CoASH, functioning in the termination of peroxisomal β-oxidation [PMID:10092594, PMID:16141203]. The enzyme is targeted to peroxisomes via a C-terminal PTS1 signal, and its catalytic activity within peroxisomes is required for peroxisome biogenesis and lipid droplet formation [PMID:10092594, PMID:15194431]. ACOT8 directly binds HIV-1 Nef through a defined surface on Nef's core domain, which enhances ACOT8 thioesterase activity, though ACOT8 is dispensable for Nef-mediated CD4 downmodulation [PMID:9153233, PMID:10807905, PMID:26423947]. ACOT8 thioesterase activity and the free fatty acids it generates promote hepatocellular carcinoma cell growth [PMID:24788990].\",\n  \"teleology\": [\n    {\n      \"year\": 1997,\n      \"claim\": \"Identification of ACOT8 as a Nef-binding acyl-CoA thioesterase established it as a potential cellular mediator of HIV-1 pathogenesis and revealed that Nef binding enhances its enzymatic activity.\",\n      \"evidence\": \"Yeast two-hybrid, in vitro binding, co-immunoprecipitation, enzymatic activity assays in CEM T cells\",\n      \"pmids\": [\"9299485\", \"9153233\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether ACOT8 is causally required for Nef-mediated CD4 downmodulation versus merely correlated\", \"Mechanism by which Nef binding enhances thioesterase activity\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Demonstration that ACOT8 is a bona fide peroxisomal enzyme targeted via a PTS1 signal resolved its subcellular localization and confirmed intrinsic thioesterase activity with preference for medium-chain acyl-CoAs.\",\n      \"evidence\": \"GFP targeting assay, peroxisomal fractionation, recombinant protein activity assay\",\n      \"pmids\": [\"10092594\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full substrate specificity profile not yet determined\", \"Physiological relevance of peroxisomal localization for Nef interaction unclear\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Mapping the Nef–ACOT8 interaction surface and showing Nef co-localizes with ACOT8 at peroxisomes defined the structural determinants of their association, while linking these residues to CD4 and MHC-I downmodulation.\",\n      \"evidence\": \"Nef affinity purification, point mutagenesis of Nef, immunofluorescence, CD4/MHC-I functional assays\",\n      \"pmids\": [\"10807905\", \"10799608\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Correlation between Nef–ACOT8 binding and CD4 downmodulation does not prove causation\", \"Whether Nef oligomerization requirement is specific to ACOT8 binding or a general folding defect\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Overexpression studies established that ACOT8 catalytic activity within peroxisomes drives peroxisome biogenesis and lipid droplet formation, revealing a cell-biological function beyond simple fatty acid release.\",\n      \"evidence\": \"Stable overexpression in T-cell lines, catalytic and localization mutants, electron microscopy, catalase quantification\",\n      \"pmids\": [\"15194431\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Loss-of-function (endogenous KO) confirmation of peroxisome biogenesis role not performed\", \"Mechanism linking CoA hydrolysis to peroxisome proliferation signaling unknown\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Substrate specificity profiling revealed ACOT8 preferentially hydrolyzes longer-chain dicarboxylyl-CoAs (C5–C12), positioning it as the principal enzyme terminating peroxisomal β-oxidation of dicarboxylic acids, and identifying it as a PPARα target gene.\",\n      \"evidence\": \"Recombinant protein expression, in vitro activity measurements with panel of CoA ester substrates\",\n      \"pmids\": [\"16141203\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo flux through dicarboxylic acid β-oxidation pathway upon ACOT8 loss not measured\", \"Contribution of PPARα regulation to ACOT8 expression in disease states not characterized\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Identification of ACOT8 as an ISG15 conjugation target during interferon-β signaling suggested a regulatory link between innate immunity and peroxisomal lipid metabolism.\",\n      \"evidence\": \"Double-affinity purification of ISG15-modified proteins, mass spectrometry in IFN-β-treated HeLa cells\",\n      \"pmids\": [\"16009940\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of ISG15 modification on ACOT8 activity or stability unknown\", \"Whether ISGylation alters ACOT8 peroxisomal localization not tested\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Knockdown of ACOT8 in hepatocellular carcinoma cells reduced growth that was partially rescued by exogenous free fatty acids, establishing that ACOT8 thioesterase activity fuels cancer cell proliferation through fatty acid generation.\",\n      \"evidence\": \"shRNA knockdown in Huh7/Hep3B, thioesterase activity assay, anchorage-dependent/independent growth assays, myristic acid rescue\",\n      \"pmids\": [\"24788990\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo tumor model validation not performed\", \"Whether specific acyl-CoA substrates or downstream lipid species mediate the growth effect is unresolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Definitive loss-of-function experiments in primary CD4+ T cells showed ACOT8 is dispensable for Nef-mediated CD4 downmodulation despite confirmed direct interaction, resolving the long-standing question of ACOT8's functional role in this process.\",\n      \"evidence\": \"shRNA knockdown in primary CD4+ T cells, FRET confirmation of Nef–ACOT8 interaction, CD4 downmodulation assay during HIV-1 infection\",\n      \"pmids\": [\"26423947\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological significance of Nef–ACOT8 interaction remains unknown if not CD4 downmodulation\", \"Whether Nef exploits ACOT8 thioesterase activity for viral replication or lipid remodeling not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The physiological consequence of Nef–ACOT8 binding remains unresolved, the mechanism linking ACOT8 catalysis to peroxisome biogenesis is undefined, and the in vivo metabolic and oncogenic roles of ACOT8 lack genetic model validation.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No ACOT8 knockout animal model phenotype reported\", \"Structural basis of ACOT8 substrate selectivity for dicarboxylyl-CoAs not determined\", \"Functional consequence of ISG15 modification on ACOT8 activity unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 2, 5, 7, 10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005777\", \"supporting_discovery_ids\": [2, 3, 6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [2, 5, 7, 10]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"HIV-1 Nef\"],\n    \"other_free_text\": []\n  }\n}\n```"}