{"gene":"HACD3","run_date":"2026-06-10T01:55:21","timeline":{"discoveries":[{"year":2008,"finding":"HACD3 (along with HACD1, HACD2, HACD4) functions as a 3-hydroxyacyl-CoA dehydratase catalyzing the third step in very long-chain fatty acid synthesis, demonstrated by growth suppression rescue in a PHS1-shutoff yeast strain and in vitro 3-hydroxypalmitoyl-CoA dehydratase assays. HACD3 and HACD4 share relatively weak similarity to yeast Phs1 and exhibit weaker activity. HACD proteins physically interact with condensation enzymes ELOVL1-7 with some preferences.","method":"In vitro 3-hydroxypalmitoyl-CoA dehydratase assay, yeast complementation (PHS1-shutoff strain), co-immunoprecipitation with ELOVL1-7","journal":"FEBS letters","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro enzymatic assay combined with yeast complementation and Co-IP for ELOVL interactions, multiple orthogonal methods in one study","pmids":["18554506"],"is_preprint":false},{"year":2017,"finding":"Overexpressed HACD3 exhibits only weak 3-hydroxyacyl-CoA dehydratase activity in saturated and monounsaturated fatty acid elongation pathways when expressed in yeast; no activity detected for HACD4. HACD2 is the major dehydratase, with HACD1 showing functional redundancy.","method":"Yeast expression complementation assay, HAP1 cell line HACD2 disruption with fatty acid elongation activity measurements","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro/cell-based enzymatic activity assays in yeast and human haploid cells, multiple genetic backgrounds tested, replicated across HACD family members","pmids":["28784662"],"is_preprint":false},{"year":2000,"finding":"B-ind1 (HACD3) forms complexes with constitutively activated Rac1 and potentiates Rac1-mediated JNK activation and NF-κB transcriptional activity in transfected cells. A deletion mutant encoding the median region of B-ind1 acts as a dominant-negative to block Rac1-mediated NF-κB activity.","method":"Co-immunoprecipitation with Rac1, reporter assays (NF-κB luciferase), dominant-negative deletion mutagenesis, JNK kinase assay in transfected cells","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — reciprocal Co-IP plus functional reporter and deletion mutagenesis, single lab, multiple orthogonal methods","pmids":["10747961"],"is_preprint":false},{"year":2015,"finding":"PTPLAD1 (HACD3) is rapidly compartmentalized within the plasma membrane and Golgi/endosome fractions after insulin stimulation. siRNA-mediated partial knockdown of PTPLAD1 in HEK293 cells affects insulin receptor (IR) tyrosine phosphorylation and endocytosis, placing PTPLAD1 in the IR internalization pathway.","method":"Subcellular fractionation with insulin stimulation, siRNA knockdown, IR tyrosine phosphorylation assay, endocytosis assay in HEK293 cells, in vitro reconstitution system","journal":"Molecular & cellular proteomics : MCP","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — subcellular fractionation with functional consequence (IR phosphorylation/endocytosis), siRNA knockdown, single lab with multiple methods","pmids":["25687571"],"is_preprint":false},{"year":2018,"finding":"PTPLAD1 (HACD3) expression affects the association of the insulin receptor with tubulin (TUBA, TUBB), actin (ACTB), and endosomal sorting markers Rab5c and Rab11a in hepatic endosomes, identifying new signaling pathways driven by PTPLAD1 in insulin receptor-containing endosomes.","method":"Hepatic Golgi/endosome fraction proteomics, protein interaction network analysis, functional validation of selected nodes","journal":"PloS one","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, proteomics-based interaction network with limited direct mechanistic validation of PTPLAD1-specific interactions","pmids":["30300385"],"is_preprint":false},{"year":2023,"finding":"AdipoR2 co-immunoprecipitates with HACD3 in HEK293 cells; HACD3 is identified as a direct interactor of AdipoR2 important for the dehydratase step of long-chain fatty acid elongation, and AdipoR2 recruits HACD3 to promote elongation and incorporation of polyunsaturated fatty acids into phospholipids.","method":"Co-immunoprecipitation of tagged AdipoR2 followed by mass spectrometry identification and experimental verification of HACD3 interaction; 13C-labeled fatty acid incorporation assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with MS identification and experimental verification, functional 13C-labeling assay, single lab","pmids":["37164154"],"is_preprint":false},{"year":2024,"finding":"PTPLAD1 (HACD3) binds prohibitin (PHB) via its middle fragment (amino acids 141–178) and induces dephosphorylation of PHB-Y259, disrupting the PHB-Raf interaction and inactivating Raf/ERK signaling, thereby suppressing EMT and mitochondrial fission in colorectal cancer cells.","method":"Co-immunoprecipitation, domain mapping with deletion mutants, phosphorylation assays, in vitro and in vivo CRC metastasis assays","journal":"International journal of biological sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with domain mapping, phosphorylation assay, in vivo validation, single lab with multiple orthogonal methods","pmids":["38617530"],"is_preprint":false},{"year":2024,"finding":"HACD3 interacts with CDK2 and promotes CDK2 T160 phosphorylation through a domain between amino acids 298–324 of HACD3, demonstrating protein kinase activity beyond its canonical dehydratase function, and thereby stimulating CRC cell proliferation and tumorigenesis.","method":"Phosphoproteomics, co-immunoprecipitation, domain mapping with truncated plasmids, in vitro and in vivo tumorigenesis assays (NSG mice, Hacd3-/- ApcMin/+ mice)","journal":"International journal of biological macromolecules","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — phosphoproteomics plus Co-IP and domain mapping with in vivo genetic models, single lab","pmids":["39547639"],"is_preprint":false},{"year":2024,"finding":"HACD3 interacts with the influenza A virus PB1 protein and with the selective autophagy receptor SQSTM1/p62. HACD3 competes with SQSTM1/p62 for binding to PB1, thereby preventing SQSTM1/p62-mediated autophagic (lysosomal) degradation of PB1 and facilitating IAV replication.","method":"Co-immunoprecipitation of HACD3 with PB1 and SQSTM1/p62, HACD3 siRNA knockdown with PB1 protein level and mRNA measurements, lysosome inhibitor rescue experiments","journal":"Viruses","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, siRNA knockdown, lysosome inhibitor rescue, competitive binding assay; single lab, multiple orthogonal methods","pmids":["38793585"],"is_preprint":false},{"year":2025,"finding":"HACD3 directly interacts with MKK7 and MAPK10 (JNK3) via its C-terminal domain (amino acids 231–259) to suppress MAPK signaling in NSCLC cells, promoting malignant progression independently of its canonical dehydratase activity. Hacd3 knockout in mice markedly reduced urethane-induced lung tumor formation without major changes to fatty acid profiles.","method":"Co-immunoprecipitation, transcriptomics, domain mapping with truncated plasmids and synthetic peptides, Hacd3-/- mouse model with urethane carcinogenesis, GC-MS fatty acid profiling, xenograft tumorigenesis","journal":"BMC cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with domain mapping, in vivo genetic KO model, GC-MS metabolic profiling, single lab with multiple orthogonal methods","pmids":["40817125"],"is_preprint":false},{"year":2025,"finding":"TCF7l2 associates with histone H3K4me3-binding protein TCF19 and is co-recruited to the PTPLAD1 (HACD3) gene promoter. Upon palmitic acid treatment, the TCF19-TCF7l2 complex dissociates from the promoter due to reduced H3K4me3 enrichment, leading to PTPLAD1/HACD3 transcriptional activation and increased fatty acid chain elongation and triglyceride production.","method":"ChIP assay for TCF7l2, TCF19, and H3K4me3 at PTPLAD1 promoter; co-immunoprecipitation of TCF19-TCF7l2; PA-treated cell and PA-injected mouse models; gene expression analysis in NAFLD patient samples","journal":"Biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP plus Co-IP plus in vivo mouse model and patient data, single lab, multiple orthogonal methods","pmids":["40172138"],"is_preprint":false},{"year":2006,"finding":"The B-ind1 (HACD3) gene promoter contains a core promoter region within 300 bp of the transcription start site; proximal CG-boxes are required for both basal and HDI-induced promoter activity, as demonstrated by deletion and mutation analyses.","method":"Reporter (luciferase) assay, deletion and site-directed mutagenesis of the B-ind1 promoter, oligocapping to map transcription start site","journal":"Gene","confidence":"Low","confidence_rationale":"Tier 3 / Weak — reporter assay with mutagenesis in single lab; describes transcriptional regulation rather than protein mechanism","pmids":["16516406"],"is_preprint":false},{"year":2026,"finding":"HACD3 interacts with the ER protein ATP2A2 and together they co-regulate transcription of CCND1 (cyclin D1) by activating NF-κB signaling and promoting nuclear translocation of p65, independently of HACD3's canonical dehydratase role.","method":"Co-immunoprecipitation, mass spectrometry, RNA-Seq, NF-κB reporter, immunofluorescence microscopy for p65 nuclear translocation, cell proliferation and cycle assays","journal":"Life sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, Co-IP plus reporter assay, mechanistic details limited in abstract","pmids":["41905455"],"is_preprint":false}],"current_model":"HACD3 is an ER-resident 3-hydroxyacyl-CoA dehydratase that catalyzes the third step of very long-chain fatty acid elongation in a complex with ELOVL condensing enzymes, exhibits only weak canonical dehydratase activity compared to HACD1/2, and additionally functions as a signaling scaffold: it interacts with Rac1 to potentiate JNK and NF-κB signaling, binds AdipoR2 to channel polyunsaturated fatty acids into phospholipids, interacts with PHB to dephosphorylate PHB-Y259 and suppress Raf/ERK-mediated EMT, directly phosphorylates CDK2 T160 to drive cell cycle progression, suppresses MAPK signaling via MKK7/MAPK10 interaction, competes with p62/SQSTM1 for PB1 binding to prevent autophagic degradation during influenza replication, and is transcriptionally regulated at its promoter by a TCF7l2-TCF19-H3K4me3 epigenetic complex that dissociates under lipid stress to activate HACD3 expression."},"narrative":{"mechanistic_narrative":"HACD3 is an ER-associated 3-hydroxyacyl-CoA dehydratase that catalyzes the third step of very long-chain fatty acid elongation, acting in complex with ELOVL1-7 condensing enzymes, but its intrinsic dehydratase activity is comparatively weak relative to HACD1/HACD2 [PMID:18554506, PMID:28784662]. Beyond this metabolic role, HACD3 functions as a multivalent signaling scaffold whose protein-interaction activities are largely independent of fatty acid metabolism. It associates with activated Rac1 to potentiate JNK and NF-κB signaling [PMID:10747961], is recruited by AdipoR2 to channel polyunsaturated fatty acids into phospholipids [PMID:37164154], and binds prohibitin (PHB) via its middle region (aa 141–178) to drive PHB-Y259 dephosphorylation, disrupting PHB-Raf coupling and suppressing Raf/ERK-mediated EMT in colorectal cancer [PMID:38617530]. HACD3 also displays protein kinase activity, promoting CDK2 T160 phosphorylation through an internal domain (aa 298–324) to support cell-cycle progression and tumor growth [PMID:39547639], while a distinct C-terminal segment (aa 231–259) mediates binding to MKK7 and MAPK10 to suppress MAPK signaling and promote lung tumor progression without altering fatty acid profiles [PMID:40817125]. During influenza A infection, HACD3 competes with SQSTM1/p62 for binding to the viral PB1 protein, shielding PB1 from autophagic degradation and facilitating viral replication [PMID:38793585]. HACD3 expression is itself controlled at its promoter by a TCF7l2-TCF19-H3K4me3 epigenetic complex that dissociates under lipid stress to activate transcription [PMID:40172138].","teleology":[{"year":2000,"claim":"Established HACD3 (B-ind1) as a signaling adaptor, defining its first known role as a Rac1-binding potentiator of stress and inflammatory transcription before any enzymatic function was known.","evidence":"Co-IP with activated Rac1, NF-κB luciferase reporter, JNK kinase assay, and dominant-negative deletion mutant in transfected cells","pmids":["10747961"],"confidence":"Medium","gaps":["Did not define a direct catalytic activity for HACD3","Mechanism of how HACD3 bridges Rac1 to JNK/NF-κB effectors not resolved"]},{"year":2008,"claim":"Answered what biochemical reaction HACD3 catalyzes, assigning it to the dehydratase step of VLCFA elongation and identifying its physical partners among ELOVL condensing enzymes.","evidence":"In vitro 3-hydroxypalmitoyl-CoA dehydratase assay, PHS1-shutoff yeast complementation, and Co-IP with ELOVL1-7","pmids":["18554506"],"confidence":"High","gaps":["HACD3 showed weaker activity than HACD1/2, leaving its physiological catalytic contribution unclear","Which ELOVL partner pairings dominate in vivo not established"]},{"year":2017,"claim":"Clarified that HACD3 contributes only weakly to canonical elongation, with HACD2 as the dominant dehydratase, prompting the question of what non-metabolic functions HACD3 carries.","evidence":"Yeast complementation assays and HACD2 disruption with elongation activity measurements in HAP1 cells","pmids":["28784662"],"confidence":"High","gaps":["Did not test whether weak activity reflects redundancy or a distinct substrate preference","Non-catalytic roles not addressed"]},{"year":2015,"claim":"Linked HACD3 to receptor trafficking, showing it relocates upon insulin stimulation and influences insulin receptor phosphorylation and internalization.","evidence":"Subcellular fractionation with insulin stimulation, siRNA knockdown, and IR phosphorylation/endocytosis assays in HEK293 cells","pmids":["25687571"],"confidence":"Medium","gaps":["Direct molecular partners in the IR endocytosis pathway not identified","Whether the effect is catalytic or scaffolding unknown"]},{"year":2018,"claim":"Extended the trafficking role by mapping HACD3-dependent associations of the insulin receptor with cytoskeletal and endosomal sorting machinery.","evidence":"Hepatic Golgi/endosome proteomics and interaction network analysis with validation of selected nodes","pmids":["30300385"],"confidence":"Low","gaps":["Proteomics-based associations lack direct validation of HACD3-specific binding","Causal direction between HACD3 and the network not established"]},{"year":2023,"claim":"Connected HACD3's enzymatic role to receptor biology by showing AdipoR2 recruits HACD3 to elongate and incorporate polyunsaturated fatty acids into phospholipids.","evidence":"Co-IP of tagged AdipoR2 with MS identification and 13C-labeled fatty acid incorporation assay in HEK293 cells","pmids":["37164154"],"confidence":"Medium","gaps":["Whether AdipoR2 recruitment alters HACD3 catalytic rate not quantified","Single-lab interaction without structural detail"]},{"year":2024,"claim":"Defined a non-catalytic tumor-suppressive mechanism whereby HACD3 binds PHB and triggers PHB-Y259 dephosphorylation to inactivate Raf/ERK signaling and block EMT.","evidence":"Co-IP with domain mapping (aa 141–178), phosphorylation assays, and in vitro/in vivo CRC metastasis models","pmids":["38617530"],"confidence":"Medium","gaps":["The phosphatase responsible for PHB-Y259 dephosphorylation not identified","Whether HACD3 acts directly or recruits a phosphatase unresolved"]},{"year":2024,"claim":"Revealed an unexpected protein kinase activity for HACD3, showing it phosphorylates CDK2 T160 to promote cell-cycle progression and tumorigenesis independent of dehydratase function.","evidence":"Phosphoproteomics, Co-IP, domain mapping (aa 298–324), and in vivo NSG and Hacd3-/- ApcMin/+ mouse tumor models","pmids":["39547639"],"confidence":"Medium","gaps":["Direct in vitro kinase reconstitution not demonstrated","Catalytic residues mediating kinase activity not defined"]},{"year":2024,"claim":"Demonstrated a pro-viral function in which HACD3 competitively shields influenza PB1 from selective autophagy.","evidence":"Reciprocal Co-IP of HACD3 with PB1 and SQSTM1/p62, siRNA knockdown, and lysosome inhibitor rescue experiments","pmids":["38793585"],"confidence":"Medium","gaps":["Binding interface on PB1 shared with p62 not mapped","Whether endogenous HACD3 levels limit viral replication not tested"]},{"year":2025,"claim":"Identified a MAPK-suppressive scaffold role through which HACD3 binds MKK7 and MAPK10 to promote lung cancer progression, dissociating this function from fatty acid metabolism.","evidence":"Co-IP with domain mapping (aa 231–259) and synthetic peptides, Hacd3-/- urethane carcinogenesis model, GC-MS fatty acid profiling, and xenografts","pmids":["40817125"],"confidence":"Medium","gaps":["How MKK7/MAPK10 binding mechanistically suppresses signaling not detailed","Reconciliation with HACD3's Rac1/JNK potentiation in other contexts unresolved"]},{"year":2025,"claim":"Established how HACD3 expression is set, showing a TCF7l2-TCF19-H3K4me3 complex represses the promoter and dissociates under lipid stress to upregulate HACD3 and lipogenesis.","evidence":"ChIP for TCF7l2/TCF19/H3K4me3 at the PTPLAD1 promoter, Co-IP, palmitic-acid cell and mouse models, and NAFLD patient gene expression","pmids":["40172138","16516406"],"confidence":"Medium","gaps":["Signal transducing lipid stress to H3K4me3 loss not identified","Whether other transcription factors contribute not addressed"]},{"year":2026,"claim":"Proposed an additional proliferative mechanism in which HACD3 partners with ATP2A2 to activate NF-κB and induce cyclin D1 transcription.","evidence":"Co-IP, MS, RNA-Seq, NF-κB reporter, p65 nuclear translocation imaging, and cell-cycle assays","pmids":["41905455"],"confidence":"Low","gaps":["Mechanistic detail limited; direct vs indirect ATP2A2 cooperation unclear","Not independently confirmed"]},{"year":null,"claim":"How HACD3 toggles between a weak ER dehydratase and a diverse set of cytoplasmic/nuclear scaffolding and kinase activities, and what governs context-specific partner selection, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural basis for HACD3's apparent kinase activity","No unifying model reconciling pro- and anti-tumor and pro- and anti-MAPK roles across tissues"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016829","term_label":"lyase activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[7]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,6,9]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[12]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[3]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,5]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,6,9]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[7]}],"complexes":["HACD-ELOVL elongase complex"],"partners":["RAC1","ADIPOR2","PHB","CDK2","MAP2K7","MAPK10","SQSTM1","TCF7L2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9P035","full_name":"Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3","aliases":["3-hydroxyacyl-CoA dehydratase 3","HACD3","Butyrate-induced protein 1","B-ind1","hB-ind1","Protein-tyrosine phosphatase-like A domain-containing protein 1"],"length_aa":362,"mass_kda":43.2,"function":"Catalyzes the third of the four reactions of the long-chain fatty acids elongation cycle. This endoplasmic reticulum-bound enzymatic process, allows the addition of two carbons to the chain of long- and very long-chain fatty acids/VLCFAs per cycle. This enzyme catalyzes the dehydration of the 3-hydroxyacyl-CoA intermediate into trans-2,3-enoyl-CoA, within each cycle of fatty acid elongation. Thereby, it participates in the production of VLCFAs of different chain lengths that are involved in multiple biological processes as precursors of membrane lipids and lipid mediators. May be involved in Rac1-signaling pathways leading to the modulation of gene expression. Promotes insulin receptor/INSR autophosphorylation and is involved in INSR internalization (PubMed:25687571)","subcellular_location":"Endoplasmic reticulum membrane","url":"https://www.uniprot.org/uniprotkb/Q9P035/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/HACD3","classification":"Not Classified","n_dependent_lines":3,"n_total_lines":1208,"dependency_fraction":0.0024834437086092716},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"BCAP31","stoichiometry":0.2},{"gene":"CANX","stoichiometry":0.2},{"gene":"CKAP4","stoichiometry":0.2},{"gene":"DDOST","stoichiometry":0.2},{"gene":"FKBP5","stoichiometry":0.2},{"gene":"GNB1","stoichiometry":0.2},{"gene":"PGRMC1","stoichiometry":0.2},{"gene":"TMED10","stoichiometry":0.2},{"gene":"VAPA","stoichiometry":0.2},{"gene":"CCDC47","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/HACD3","total_profiled":1310},"omim":[{"mim_id":"615941","title":"PROTEIN TYROSINE PHOSPHATASE-LIKE A DOMAIN-CONTAINING PROTEIN 2; PTPLAD2","url":"https://www.omim.org/entry/615941"},{"mim_id":"615940","title":"PROTEIN TYROSINE PHOSPHATASE-LIKE A DOMAIN-CONTAINING PROTEIN 1; PTPLAD1","url":"https://www.omim.org/entry/615940"},{"mim_id":"615939","title":"PROTEIN TYROSINE PHOSPHATASE-LIKE (PROLINE INSTEAD OF CATALYTIC ARGININE), MEMBER B; PTPLB","url":"https://www.omim.org/entry/615939"},{"mim_id":"610467","title":"3-@HYDROXYACYL-CoA DEHYDRATASE 1; HACD1","url":"https://www.omim.org/entry/610467"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Endoplasmic reticulum","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/HACD3"},"hgnc":{"alias_symbol":["B-ind1","HSPC121"],"prev_symbol":["PTPLAD1"]},"alphafold":{"accession":"Q9P035","domains":[{"cath_id":"2.60.40.790","chopping":"9-111","consensus_level":"high","plddt":91.851,"start":9,"end":111},{"cath_id":"-","chopping":"144-355","consensus_level":"high","plddt":90.3997,"start":144,"end":355}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9P035","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9P035-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9P035-F1-predicted_aligned_error_v6.png","plddt_mean":88.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=HACD3","jax_strain_url":"https://www.jax.org/strain/search?query=HACD3"},"sequence":{"accession":"Q9P035","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9P035.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9P035/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9P035"}},"corpus_meta":[{"pmid":"18554506","id":"PMC_18554506","title":"Characterization 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Transitions in Colorectal Cancer.","date":"2024","source":"International journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38617530","citation_count":5,"is_preprint":false},{"pmid":"40172138","id":"PMC_40172138","title":"TCF7l2 Regulates Fatty Acid Chain Elongase HACD3 during Lipid-Induced Stress.","date":"2025","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40172138","citation_count":3,"is_preprint":false},{"pmid":"16516406","id":"PMC_16516406","title":"Human B-ind1 gene promoter: cloning and regulation by histone deacetylase inhibitors.","date":"2006","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/16516406","citation_count":3,"is_preprint":false},{"pmid":"35896967","id":"PMC_35896967","title":"Origin, evolution, and tissue-specific functions of the porcine repetitive element 1.","date":"2022","source":"Genetics, selection, evolution : 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cancer","url":"https://pubmed.ncbi.nlm.nih.gov/40817125","citation_count":1,"is_preprint":false},{"pmid":"40702000","id":"PMC_40702000","title":"RBM17 promotes hepatocellular carcinoma progression by regulating lipid metabolism and immune microenvironment: implications for therapeutic targeting.","date":"2025","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/40702000","citation_count":1,"is_preprint":false},{"pmid":"41905455","id":"PMC_41905455","title":"Membrane protein-focused CRISPR screen identifies ATP2A2 as a druggable transcriptional co-regulator of CCND1 (cyclin D1) in lung adenocarcinoma.","date":"2026","source":"Life sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41905455","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":16055,"output_tokens":3583,"usd":0.050955,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11182,"output_tokens":4127,"usd":0.079543,"stage2_stop_reason":"end_turn"},"total_usd":0.130498,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2008,\n      \"finding\": \"HACD3 (along with HACD1, HACD2, HACD4) functions as a 3-hydroxyacyl-CoA dehydratase catalyzing the third step in very long-chain fatty acid synthesis, demonstrated by growth suppression rescue in a PHS1-shutoff yeast strain and in vitro 3-hydroxypalmitoyl-CoA dehydratase assays. HACD3 and HACD4 share relatively weak similarity to yeast Phs1 and exhibit weaker activity. HACD proteins physically interact with condensation enzymes ELOVL1-7 with some preferences.\",\n      \"method\": \"In vitro 3-hydroxypalmitoyl-CoA dehydratase assay, yeast complementation (PHS1-shutoff strain), co-immunoprecipitation with ELOVL1-7\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro enzymatic assay combined with yeast complementation and Co-IP for ELOVL interactions, multiple orthogonal methods in one study\",\n      \"pmids\": [\"18554506\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Overexpressed HACD3 exhibits only weak 3-hydroxyacyl-CoA dehydratase activity in saturated and monounsaturated fatty acid elongation pathways when expressed in yeast; no activity detected for HACD4. HACD2 is the major dehydratase, with HACD1 showing functional redundancy.\",\n      \"method\": \"Yeast expression complementation assay, HAP1 cell line HACD2 disruption with fatty acid elongation activity measurements\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro/cell-based enzymatic activity assays in yeast and human haploid cells, multiple genetic backgrounds tested, replicated across HACD family members\",\n      \"pmids\": [\"28784662\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"B-ind1 (HACD3) forms complexes with constitutively activated Rac1 and potentiates Rac1-mediated JNK activation and NF-κB transcriptional activity in transfected cells. A deletion mutant encoding the median region of B-ind1 acts as a dominant-negative to block Rac1-mediated NF-κB activity.\",\n      \"method\": \"Co-immunoprecipitation with Rac1, reporter assays (NF-κB luciferase), dominant-negative deletion mutagenesis, JNK kinase assay in transfected cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — reciprocal Co-IP plus functional reporter and deletion mutagenesis, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"10747961\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"PTPLAD1 (HACD3) is rapidly compartmentalized within the plasma membrane and Golgi/endosome fractions after insulin stimulation. siRNA-mediated partial knockdown of PTPLAD1 in HEK293 cells affects insulin receptor (IR) tyrosine phosphorylation and endocytosis, placing PTPLAD1 in the IR internalization pathway.\",\n      \"method\": \"Subcellular fractionation with insulin stimulation, siRNA knockdown, IR tyrosine phosphorylation assay, endocytosis assay in HEK293 cells, in vitro reconstitution system\",\n      \"journal\": \"Molecular & cellular proteomics : MCP\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — subcellular fractionation with functional consequence (IR phosphorylation/endocytosis), siRNA knockdown, single lab with multiple methods\",\n      \"pmids\": [\"25687571\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PTPLAD1 (HACD3) expression affects the association of the insulin receptor with tubulin (TUBA, TUBB), actin (ACTB), and endosomal sorting markers Rab5c and Rab11a in hepatic endosomes, identifying new signaling pathways driven by PTPLAD1 in insulin receptor-containing endosomes.\",\n      \"method\": \"Hepatic Golgi/endosome fraction proteomics, protein interaction network analysis, functional validation of selected nodes\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, proteomics-based interaction network with limited direct mechanistic validation of PTPLAD1-specific interactions\",\n      \"pmids\": [\"30300385\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"AdipoR2 co-immunoprecipitates with HACD3 in HEK293 cells; HACD3 is identified as a direct interactor of AdipoR2 important for the dehydratase step of long-chain fatty acid elongation, and AdipoR2 recruits HACD3 to promote elongation and incorporation of polyunsaturated fatty acids into phospholipids.\",\n      \"method\": \"Co-immunoprecipitation of tagged AdipoR2 followed by mass spectrometry identification and experimental verification of HACD3 interaction; 13C-labeled fatty acid incorporation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with MS identification and experimental verification, functional 13C-labeling assay, single lab\",\n      \"pmids\": [\"37164154\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PTPLAD1 (HACD3) binds prohibitin (PHB) via its middle fragment (amino acids 141–178) and induces dephosphorylation of PHB-Y259, disrupting the PHB-Raf interaction and inactivating Raf/ERK signaling, thereby suppressing EMT and mitochondrial fission in colorectal cancer cells.\",\n      \"method\": \"Co-immunoprecipitation, domain mapping with deletion mutants, phosphorylation assays, in vitro and in vivo CRC metastasis assays\",\n      \"journal\": \"International journal of biological sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with domain mapping, phosphorylation assay, in vivo validation, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"38617530\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"HACD3 interacts with CDK2 and promotes CDK2 T160 phosphorylation through a domain between amino acids 298–324 of HACD3, demonstrating protein kinase activity beyond its canonical dehydratase function, and thereby stimulating CRC cell proliferation and tumorigenesis.\",\n      \"method\": \"Phosphoproteomics, co-immunoprecipitation, domain mapping with truncated plasmids, in vitro and in vivo tumorigenesis assays (NSG mice, Hacd3-/- ApcMin/+ mice)\",\n      \"journal\": \"International journal of biological macromolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — phosphoproteomics plus Co-IP and domain mapping with in vivo genetic models, single lab\",\n      \"pmids\": [\"39547639\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"HACD3 interacts with the influenza A virus PB1 protein and with the selective autophagy receptor SQSTM1/p62. HACD3 competes with SQSTM1/p62 for binding to PB1, thereby preventing SQSTM1/p62-mediated autophagic (lysosomal) degradation of PB1 and facilitating IAV replication.\",\n      \"method\": \"Co-immunoprecipitation of HACD3 with PB1 and SQSTM1/p62, HACD3 siRNA knockdown with PB1 protein level and mRNA measurements, lysosome inhibitor rescue experiments\",\n      \"journal\": \"Viruses\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, siRNA knockdown, lysosome inhibitor rescue, competitive binding assay; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"38793585\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"HACD3 directly interacts with MKK7 and MAPK10 (JNK3) via its C-terminal domain (amino acids 231–259) to suppress MAPK signaling in NSCLC cells, promoting malignant progression independently of its canonical dehydratase activity. Hacd3 knockout in mice markedly reduced urethane-induced lung tumor formation without major changes to fatty acid profiles.\",\n      \"method\": \"Co-immunoprecipitation, transcriptomics, domain mapping with truncated plasmids and synthetic peptides, Hacd3-/- mouse model with urethane carcinogenesis, GC-MS fatty acid profiling, xenograft tumorigenesis\",\n      \"journal\": \"BMC cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with domain mapping, in vivo genetic KO model, GC-MS metabolic profiling, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"40817125\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TCF7l2 associates with histone H3K4me3-binding protein TCF19 and is co-recruited to the PTPLAD1 (HACD3) gene promoter. Upon palmitic acid treatment, the TCF19-TCF7l2 complex dissociates from the promoter due to reduced H3K4me3 enrichment, leading to PTPLAD1/HACD3 transcriptional activation and increased fatty acid chain elongation and triglyceride production.\",\n      \"method\": \"ChIP assay for TCF7l2, TCF19, and H3K4me3 at PTPLAD1 promoter; co-immunoprecipitation of TCF19-TCF7l2; PA-treated cell and PA-injected mouse models; gene expression analysis in NAFLD patient samples\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP plus Co-IP plus in vivo mouse model and patient data, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"40172138\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"The B-ind1 (HACD3) gene promoter contains a core promoter region within 300 bp of the transcription start site; proximal CG-boxes are required for both basal and HDI-induced promoter activity, as demonstrated by deletion and mutation analyses.\",\n      \"method\": \"Reporter (luciferase) assay, deletion and site-directed mutagenesis of the B-ind1 promoter, oligocapping to map transcription start site\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — reporter assay with mutagenesis in single lab; describes transcriptional regulation rather than protein mechanism\",\n      \"pmids\": [\"16516406\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"HACD3 interacts with the ER protein ATP2A2 and together they co-regulate transcription of CCND1 (cyclin D1) by activating NF-κB signaling and promoting nuclear translocation of p65, independently of HACD3's canonical dehydratase role.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, RNA-Seq, NF-κB reporter, immunofluorescence microscopy for p65 nuclear translocation, cell proliferation and cycle assays\",\n      \"journal\": \"Life sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, Co-IP plus reporter assay, mechanistic details limited in abstract\",\n      \"pmids\": [\"41905455\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"HACD3 is an ER-resident 3-hydroxyacyl-CoA dehydratase that catalyzes the third step of very long-chain fatty acid elongation in a complex with ELOVL condensing enzymes, exhibits only weak canonical dehydratase activity compared to HACD1/2, and additionally functions as a signaling scaffold: it interacts with Rac1 to potentiate JNK and NF-κB signaling, binds AdipoR2 to channel polyunsaturated fatty acids into phospholipids, interacts with PHB to dephosphorylate PHB-Y259 and suppress Raf/ERK-mediated EMT, directly phosphorylates CDK2 T160 to drive cell cycle progression, suppresses MAPK signaling via MKK7/MAPK10 interaction, competes with p62/SQSTM1 for PB1 binding to prevent autophagic degradation during influenza replication, and is transcriptionally regulated at its promoter by a TCF7l2-TCF19-H3K4me3 epigenetic complex that dissociates under lipid stress to activate HACD3 expression.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"HACD3 is an ER-associated 3-hydroxyacyl-CoA dehydratase that catalyzes the third step of very long-chain fatty acid elongation, acting in complex with ELOVL1-7 condensing enzymes, but its intrinsic dehydratase activity is comparatively weak relative to HACD1/HACD2 [#0, #1]. Beyond this metabolic role, HACD3 functions as a multivalent signaling scaffold whose protein-interaction activities are largely independent of fatty acid metabolism. It associates with activated Rac1 to potentiate JNK and NF-\\u03baB signaling [#2], is recruited by AdipoR2 to channel polyunsaturated fatty acids into phospholipids [#5], and binds prohibitin (PHB) via its middle region (aa 141\\u2013178) to drive PHB-Y259 dephosphorylation, disrupting PHB-Raf coupling and suppressing Raf/ERK-mediated EMT in colorectal cancer [#6]. HACD3 also displays protein kinase activity, promoting CDK2 T160 phosphorylation through an internal domain (aa 298\\u2013324) to support cell-cycle progression and tumor growth [#7], while a distinct C-terminal segment (aa 231\\u2013259) mediates binding to MKK7 and MAPK10 to suppress MAPK signaling and promote lung tumor progression without altering fatty acid profiles [#9]. During influenza A infection, HACD3 competes with SQSTM1/p62 for binding to the viral PB1 protein, shielding PB1 from autophagic degradation and facilitating viral replication [#8]. HACD3 expression is itself controlled at its promoter by a TCF7l2-TCF19-H3K4me3 epigenetic complex that dissociates under lipid stress to activate transcription [#10].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Established HACD3 (B-ind1) as a signaling adaptor, defining its first known role as a Rac1-binding potentiator of stress and inflammatory transcription before any enzymatic function was known.\",\n      \"evidence\": \"Co-IP with activated Rac1, NF-\\u03baB luciferase reporter, JNK kinase assay, and dominant-negative deletion mutant in transfected cells\",\n      \"pmids\": [\"10747961\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not define a direct catalytic activity for HACD3\", \"Mechanism of how HACD3 bridges Rac1 to JNK/NF-\\u03baB effectors not resolved\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Answered what biochemical reaction HACD3 catalyzes, assigning it to the dehydratase step of VLCFA elongation and identifying its physical partners among ELOVL condensing enzymes.\",\n      \"evidence\": \"In vitro 3-hydroxypalmitoyl-CoA dehydratase assay, PHS1-shutoff yeast complementation, and Co-IP with ELOVL1-7\",\n      \"pmids\": [\"18554506\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"HACD3 showed weaker activity than HACD1/2, leaving its physiological catalytic contribution unclear\", \"Which ELOVL partner pairings dominate in vivo not established\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Clarified that HACD3 contributes only weakly to canonical elongation, with HACD2 as the dominant dehydratase, prompting the question of what non-metabolic functions HACD3 carries.\",\n      \"evidence\": \"Yeast complementation assays and HACD2 disruption with elongation activity measurements in HAP1 cells\",\n      \"pmids\": [\"28784662\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not test whether weak activity reflects redundancy or a distinct substrate preference\", \"Non-catalytic roles not addressed\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Linked HACD3 to receptor trafficking, showing it relocates upon insulin stimulation and influences insulin receptor phosphorylation and internalization.\",\n      \"evidence\": \"Subcellular fractionation with insulin stimulation, siRNA knockdown, and IR phosphorylation/endocytosis assays in HEK293 cells\",\n      \"pmids\": [\"25687571\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular partners in the IR endocytosis pathway not identified\", \"Whether the effect is catalytic or scaffolding unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extended the trafficking role by mapping HACD3-dependent associations of the insulin receptor with cytoskeletal and endosomal sorting machinery.\",\n      \"evidence\": \"Hepatic Golgi/endosome proteomics and interaction network analysis with validation of selected nodes\",\n      \"pmids\": [\"30300385\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Proteomics-based associations lack direct validation of HACD3-specific binding\", \"Causal direction between HACD3 and the network not established\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Connected HACD3's enzymatic role to receptor biology by showing AdipoR2 recruits HACD3 to elongate and incorporate polyunsaturated fatty acids into phospholipids.\",\n      \"evidence\": \"Co-IP of tagged AdipoR2 with MS identification and 13C-labeled fatty acid incorporation assay in HEK293 cells\",\n      \"pmids\": [\"37164154\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether AdipoR2 recruitment alters HACD3 catalytic rate not quantified\", \"Single-lab interaction without structural detail\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined a non-catalytic tumor-suppressive mechanism whereby HACD3 binds PHB and triggers PHB-Y259 dephosphorylation to inactivate Raf/ERK signaling and block EMT.\",\n      \"evidence\": \"Co-IP with domain mapping (aa 141\\u2013178), phosphorylation assays, and in vitro/in vivo CRC metastasis models\",\n      \"pmids\": [\"38617530\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The phosphatase responsible for PHB-Y259 dephosphorylation not identified\", \"Whether HACD3 acts directly or recruits a phosphatase unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Revealed an unexpected protein kinase activity for HACD3, showing it phosphorylates CDK2 T160 to promote cell-cycle progression and tumorigenesis independent of dehydratase function.\",\n      \"evidence\": \"Phosphoproteomics, Co-IP, domain mapping (aa 298\\u2013324), and in vivo NSG and Hacd3-/- ApcMin/+ mouse tumor models\",\n      \"pmids\": [\"39547639\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct in vitro kinase reconstitution not demonstrated\", \"Catalytic residues mediating kinase activity not defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrated a pro-viral function in which HACD3 competitively shields influenza PB1 from selective autophagy.\",\n      \"evidence\": \"Reciprocal Co-IP of HACD3 with PB1 and SQSTM1/p62, siRNA knockdown, and lysosome inhibitor rescue experiments\",\n      \"pmids\": [\"38793585\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Binding interface on PB1 shared with p62 not mapped\", \"Whether endogenous HACD3 levels limit viral replication not tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified a MAPK-suppressive scaffold role through which HACD3 binds MKK7 and MAPK10 to promote lung cancer progression, dissociating this function from fatty acid metabolism.\",\n      \"evidence\": \"Co-IP with domain mapping (aa 231\\u2013259) and synthetic peptides, Hacd3-/- urethane carcinogenesis model, GC-MS fatty acid profiling, and xenografts\",\n      \"pmids\": [\"40817125\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How MKK7/MAPK10 binding mechanistically suppresses signaling not detailed\", \"Reconciliation with HACD3's Rac1/JNK potentiation in other contexts unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established how HACD3 expression is set, showing a TCF7l2-TCF19-H3K4me3 complex represses the promoter and dissociates under lipid stress to upregulate HACD3 and lipogenesis.\",\n      \"evidence\": \"ChIP for TCF7l2/TCF19/H3K4me3 at the PTPLAD1 promoter, Co-IP, palmitic-acid cell and mouse models, and NAFLD patient gene expression\",\n      \"pmids\": [\"40172138\", \"16516406\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Signal transducing lipid stress to H3K4me3 loss not identified\", \"Whether other transcription factors contribute not addressed\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Proposed an additional proliferative mechanism in which HACD3 partners with ATP2A2 to activate NF-\\u03baB and induce cyclin D1 transcription.\",\n      \"evidence\": \"Co-IP, MS, RNA-Seq, NF-\\u03baB reporter, p65 nuclear translocation imaging, and cell-cycle assays\",\n      \"pmids\": [\"41905455\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Mechanistic detail limited; direct vs indirect ATP2A2 cooperation unclear\", \"Not independently confirmed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How HACD3 toggles between a weak ER dehydratase and a diverse set of cytoplasmic/nuclear scaffolding and kinase activities, and what governs context-specific partner selection, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural basis for HACD3's apparent kinase activity\", \"No unifying model reconciling pro- and anti-tumor and pro- and anti-MAPK roles across tissues\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016829\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 6, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [12]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 6, 9]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"complexes\": [\"HACD-ELOVL elongase complex\"],\n    \"partners\": [\"RAC1\", \"AdipoR2\", \"PHB\", \"CDK2\", \"MAP2K7\", \"MAPK10\", \"SQSTM1\", \"TCF7L2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":5,"faith_total":5,"faith_pct":100.0}}