{"gene":"HADHB","run_date":"2026-06-10T01:55:21","timeline":{"discoveries":[{"year":1997,"finding":"The HADHB gene encodes the β-subunit of the mitochondrial trifunctional protein (MTP), an α4β4 hetero-octameric complex; HADHB contains the 3-ketoacyl-CoA thiolase domain while the α-subunit (HADHA) contains enoyl-CoA hydratase and 3-hydroxyacyl-CoA dehydrogenase domains. The two genes (HADHA and HADHB) co-map to chromosome band 2p23 and are adjacently located, similar to bacterial fatty acid β-oxidation multienzyme complex subunit gene organization.","method":"Genomic mutational analysis, FISH mapping, biochemical enzyme activity assays in patient fibroblasts","journal":"Human molecular genetics / Cytogenetics and cell genetics","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — enzyme activity assays combined with genomic analysis, replicated across two independent papers (PMID:9259266, PMID:9605857)","pmids":["9259266","9605857"],"is_preprint":false},{"year":2003,"finding":"HADHB protein binds specifically to a 34-nucleotide AU-rich 'renin stability regulatory element' in the 3'-UTR of REN mRNA and acts as a destabilizer of renin mRNA: RNAi-mediated knockdown of HADHB increased renin mRNA stability and renin protein levels, while a specific thiolase inhibitor (4-bromocrotonic acid) decreased HADHB binding to the 3'-UTR and elevated renin protein. HADHB was confirmed to associate with REN mRNA in vivo by immunoprecipitation/RT-PCR and localizes to mitochondria by intracellular imaging.","method":"Yeast three-hybrid screening, recombinant protein RNA-binding assay, RNAi knockdown, immunoprecipitation/RT-PCR, intracellular imaging, reporter construct transfection","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (yeast three-hybrid, RNAi, co-IP/RT-PCR, inhibitor experiments) from a single lab","pmids":["12933794"],"is_preprint":false},{"year":2006,"finding":"Mutations in HADHB alone (compound heterozygous R62H and F431S) can cause isolated long-chain ketoacyl-CoA thiolase (LCTH) deficiency with near-absent LCTH activity (4% of normal) and normal LCHAD activity, establishing that HADHB encodes specifically the LCTH catalytic function within MTP.","method":"Enzyme activity assays (LCTH and LCHAD measured separately), molecular mutation analysis of patient fibroblasts","journal":"Clinical chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct enzymatic activity measurement with mutation confirmation, first case of isolated LCTH deficiency from HADHB mutation","pmids":["16423905"],"is_preprint":false},{"year":2012,"finding":"Estrogen receptor alpha (ERα) directly binds to HADHB in mitochondria: interaction was verified by affinity purification/proteomics, co-immunoprecipitation with whole-cell and purified mitochondrial extracts, in vitro binding assay, and co-localization by confocal microscopy. ERα expression modulates HADHB thiolase (β-oxidation) enzyme activity, and combined 17β-estradiol plus tamoxifen treatment affects the ERα–HADHB association and HADHB activity in ERα-positive but not ERα-negative breast cancer cells.","method":"Affinity purification/2D-gel/mass spectrometry, co-immunoprecipitation (whole cell and purified mitochondria), in vitro binding assay, confocal microscopy, enzyme activity assay, RNAi/pharmacological manipulation","journal":"Molecular & cellular proteomics","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (in vitro binding, reciprocal co-IP from purified mitochondria, enzyme activity, confocal), single lab but rigorous experimental design","pmids":["22375075"],"is_preprint":false},{"year":2012,"finding":"Estrogen receptor beta (ERβ) also associates and co-localizes with HADHB within mitochondria, shown by co-immunoprecipitation and confocal microscopy in MCF7 cells. In contrast to ERα (which stimulates HADHB activity), ERβ silencing enhanced HADHB enzyme activity, indicating an inhibitory role of ERβ on HADHB β-oxidation activity.","method":"Co-immunoprecipitation, confocal microscopy, siRNA silencing, enzyme activity assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — co-IP plus enzyme activity assay and confocal microscopy, single lab, extends prior ERα findings with ERβ","pmids":["23000159"],"is_preprint":false},{"year":2014,"finding":"Structural analysis of the HADHB β-subunit showed that disease-associated missense mutations (A392V and the previously reported N389D) are located near the active site of MTP and affect conformation of the β-subunit, providing a structural basis for MTP deficiency with hypoparathyroidism and peripheral polyneuropathy.","method":"Structural modeling/analysis of mutation positions relative to active site, biochemical analysis confirming MTP deficiency, HADHB sequencing","journal":"American journal of medical genetics. Part A","confidence":"Low","confidence_rationale":"Tier 4 / Weak — structural analysis appears computational/modeling rather than experimental structure determination; single case report","pmids":["24664533"],"is_preprint":false},{"year":2018,"finding":"HADHB protein binds to precursor microRNAs (pre-miR-329, pre-miR-495) as identified by RNA pull-down SILAC mass spectrometry. HADHB knockout (CRISPR/Cas9) in 3T3 cells reduced expression of mature miR-329 and miR-495 but not their precursors, suggesting HADHB plays a role in posttranscriptional processing of 14q32 microRNAs after precursor formation.","method":"RNA pull-down SILAC mass spectrometry, CRISPR/Cas9 knockout, RBP immunoprecipitation, immunohistochemistry","journal":"Molecular therapy. Nucleic acids","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RP-SMS identification plus CRISPR functional validation, multiple orthogonal methods, single lab","pmids":["30665182"],"is_preprint":false},{"year":2019,"finding":"Neuron-specific knockdown of Drosophila HADHB (dHADHB/CG4581) reduced locomotor ability, shortened lifespan, impaired learning, caused abnormal neuromuscular junction (NMJ) synapse morphology, and reduced both ATP and ROS levels in the CNS, establishing a critical role for HADHB in glutamatergic neuron morphogenesis and function.","method":"Neuron-specific RNAi knockdown in Drosophila, behavioral assays (lifespan, locomotion, learning), NMJ morphology analysis, ATP and ROS measurement","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean tissue-specific KD with multiple defined phenotypic readouts in a validated ortholog model, single lab","pmids":["30953623"],"is_preprint":false},{"year":2019,"finding":"HADHB mutations M136T and A141T (compound heterozygous) compromise MTP complex stability but do not alter subcellular localization of HADHB; mutant protein levels are lower at 37°C but partially restored at 30°C (temperature-sensitive), establishing a loss-of-function/instability mechanism for the mild neuromyopathic phenotype.","method":"In vitro cell functional studies, immunoblotting, subcellular localization analysis, temperature-shift experiments in patient-derived cells","journal":"Mitochondrion","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional cell studies with temperature-sensitivity experiments and localization analysis, single lab","pmids":["31521624"],"is_preprint":false},{"year":2024,"finding":"Chronic cadmium exposure leads to hypermethylation of the HADHB promoter region via inhibition of the DNA demethylase TET2, resulting in decreased HADHB expression, activation of the FAK signaling pathway, and enhanced CRC cell migration and invasion.","method":"RNA-seq, qRT-PCR, tissue microarray, chromatin/promoter methylation analysis, in vitro migration/invasion assays, in vivo lung metastasis model","journal":"Ecotoxicology and environmental safety","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — TET2-HADHB promoter methylation mechanism supported by multiple assays in vitro and in vivo, single lab","pmids":["38865940"],"is_preprint":false},{"year":2025,"finding":"HADHB interacts with DUOX2 (identified by co-immunoprecipitation); knockdown of HADHB in CRC cells improved 5-FU sensitivity and reduced ROS production, while DUOX2 overexpression reversed the ROS reduction caused by HADHB knockdown, establishing a functional HADHB–DUOX2–ROS axis that modulates 5-FU chemosensitivity.","method":"Co-immunoprecipitation, CCK-8, flow cytometry (apoptosis, cell cycle), siRNA knockdown, overexpression, ROS measurement, metabolomics/transcriptomics","journal":"Discover oncology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — co-IP plus functional rescue experiments with multiple readouts, single lab","pmids":["40875107"],"is_preprint":false},{"year":2025,"finding":"ZNF460 transcription factor activates HADHB transcription: ChIP-qPCR and dual-luciferase reporter assays demonstrated ZNF460 binding to the HADHB promoter and transcriptional upregulation, with downstream effects on fatty acid metabolism and CTCL tumor progression and pulmonary invasion.","method":"ChIP-qPCR, dual-luciferase reporter assay, siRNA knockdown, overexpression, in vivo tumor model","journal":"Archives of biochemistry and biophysics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct ChIP and reporter assay evidence for transcriptional regulation, supported by functional in vivo data, single lab","pmids":["40404004"],"is_preprint":false},{"year":2026,"finding":"HADHB loss induces ER stress (increased ATF6(N), phospho-eIF2α, and upregulated CHOP), and CHOP knockdown partially restores oncogenic potential in Hadhb-deficient mice and rescues growth defects of HADHB-depleted cells, establishing CHOP as a key downstream mediator of a HADHB–ER stress–CHOP axis in lung tumor suppression.","method":"Hadhb knockout mouse model with K-Ras G12D-driven lung tumors, immunoblotting for ER stress markers, Chop knockdown rescue experiments, cell proliferation and apoptosis assays","journal":"Journal of Cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo KO mouse model combined with rescue experiments (Chop KD) establishing pathway epistasis, single lab","pmids":["42179784"],"is_preprint":false},{"year":2026,"finding":"MALAT1 lncRNA interacts with HADHB protein and enhances its thiolase activity during the late phase of macrophage inflammation; this interaction is facilitated by HuR-MTCH2-mediated mitochondrial targeting of MALAT1. MALAT1 knockdown causes metabolic reprogramming (enhanced glycolysis, increased fatty acid synthesis, reduced FAO) and augments pro-inflammatory macrophage activation, placing HADHB as a mediator of MALAT1's metabolic and anti-inflammatory effects.","method":"RNA immunoprecipitation, thiolase activity assay, MALAT1 knockdown, metabolic flux measurements (glycolysis, FAO, fatty acid synthesis), macrophage activation assays","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct interaction identified by RIP with functional enzyme activity measurement and metabolic phenotyping, single lab","pmids":["41816300"],"is_preprint":false},{"year":2026,"finding":"Ginsenoside compound K (GCK) activates glucocorticoid receptor (GR/NR3C1) to upregulate HADHB expression (confirmed by dual-luciferase reporter assay), promoting fatty acid oxidation in macrophages and restoring M1/M2 macrophage polarization balance in ulcerative colitis models, placing HADHB downstream of GR signaling in macrophage metabolic reprogramming.","method":"Dual-luciferase reporter assay, western blot, RT-qPCR, flow cytometry, DSS-induced UC mouse model, LPS-stimulated RAW264.7 cells, metabolite detection","journal":"British journal of pharmacology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — promoter reporter assay and GR activation mechanistically linked to HADHB upregulation with in vivo validation, single lab","pmids":["41918496"],"is_preprint":false}],"current_model":"HADHB encodes the β-subunit of the mitochondrial trifunctional protein (MTP) α4β4 hetero-octamer, providing the long-chain 3-ketoacyl-CoA thiolase (LCTH) catalytic activity for the final step in mitochondrial fatty acid β-oxidation of long-chain fatty acids; beyond this canonical metabolic role, HADHB also functions as an RNA-binding protein that destabilizes REN mRNA via a 3'-UTR AU-rich element, interacts directly with estrogen receptors ERα (activating) and ERβ (inhibitory) in mitochondria to modulate β-oxidation activity, participates in posttranscriptional processing of 14q32 microRNAs, interacts with DUOX2 to regulate ROS levels affecting chemosensitivity, and is transcriptionally regulated by ZNF460 and the GR-GCK axis, while MALAT1 lncRNA directly enhances HADHB thiolase activity in macrophages and its loss triggers ER stress via an ATF6/eIF2α/CHOP axis."},"narrative":{"mechanistic_narrative":"HADHB encodes the β-subunit of the mitochondrial trifunctional protein (MTP), an α4β4 hetero-octamer that carries out the long-chain 3-ketoacyl-CoA thiolase (LCTH) step in the final stage of mitochondrial fatty acid β-oxidation, with the HADHA α-subunit providing the upstream enoyl-CoA hydratase and 3-hydroxyacyl-CoA dehydrogenase activities [PMID:9259266, PMID:9605857]. Compound heterozygous HADHB mutations can produce isolated LCTH deficiency with near-absent thiolase activity but preserved LCHAD activity, establishing that the β-subunit specifically supplies the thiolase catalytic function within MTP [PMID:16423905]; other disease-associated missense substitutions compromise MTP complex stability and lower mutant protein levels in a temperature-sensitive manner, defining a loss-of-function/instability basis for the resulting neuromyopathic and MTP-deficiency phenotypes [PMID:31521624]. Beyond catalysis, HADHB is a mitochondrial RNA-binding protein: it binds an AU-rich element in the REN mRNA 3'-UTR and destabilizes renin transcripts in a manner sensitive to a thiolase inhibitor [PMID:12933794], and it binds precursor 14q32 microRNAs to support maturation of miR-329 and miR-495 after precursor formation [PMID:30665182]. Its β-oxidation activity is modulated by direct mitochondrial interactions with estrogen receptors, with ERα activating and ERβ inhibiting HADHB thiolase activity [PMID:22375075, PMID:23000159], and by MALAT1 lncRNA, which enhances thiolase activity to sustain fatty acid oxidation and restrain pro-inflammatory macrophage activation [PMID:41816300]. HADHB expression is set transcriptionally by ZNF460 and by glucocorticoid-receptor signaling, and epigenetically by promoter methylation, linking its level to fatty acid metabolism in tumor and immune contexts [PMID:38865940, PMID:40404004, PMID:41918496]; its loss triggers an ATF6/eIF2α/CHOP ER-stress axis that mediates lung tumor suppression [PMID:42179784].","teleology":[{"year":1997,"claim":"Established the molecular identity and architecture of HADHB, answering which catalytic step of long-chain β-oxidation it provides and how it relates to its partner subunit.","evidence":"Genomic mutational analysis, FISH mapping, and enzyme activity assays in patient fibroblasts defining HADHB as the thiolase-bearing β-subunit of the α4β4 MTP","pmids":["9259266","9605857"],"confidence":"High","gaps":["No experimental structure of the assembled MTP at this stage","Regulation of complex assembly not addressed"]},{"year":2003,"claim":"Revealed an unexpected moonlighting role: HADHB binds REN mRNA and destabilizes it, separating a metabolic enzyme's catalytic surface from a post-transcriptional regulatory function.","evidence":"Yeast three-hybrid screen, recombinant RNA-binding assay, RNAi knockdown, co-IP/RT-PCR, and thiolase-inhibitor experiments","pmids":["12933794"],"confidence":"Medium","gaps":["Single lab; physiological relevance to renin regulation in vivo unproven","Structural basis for AU-rich element recognition unknown"]},{"year":2006,"claim":"Demonstrated that HADHB mutation alone causes isolated LCTH deficiency, formally assigning the thiolase activity of MTP to the β-subunit.","evidence":"Separate LCTH and LCHAD enzyme assays plus mutation analysis in patient fibroblasts","pmids":["16423905"],"confidence":"High","gaps":["Genotype–phenotype correlation across mutation spectrum not resolved"]},{"year":2012,"claim":"Showed that estrogen receptors directly bind HADHB in mitochondria and bidirectionally tune its β-oxidation activity, defining hormone-responsive control of the thiolase.","evidence":"Affinity purification/MS, reciprocal co-IP from purified mitochondria, in vitro binding, confocal microscopy, and enzyme activity assays for ERα; co-IP, confocal, siRNA, and activity assays for ERβ","pmids":["22375075","23000159"],"confidence":"High","gaps":["Mechanism by which ER binding alters thiolase activity unresolved","Significance outside breast cancer cell lines not established"]},{"year":2018,"claim":"Extended HADHB's RNA-binding repertoire to precursor miRNAs, implicating it in post-transcriptional maturation of 14q32 microRNAs.","evidence":"RNA pull-down SILAC mass spectrometry and CRISPR/Cas9 knockout measuring mature versus precursor miR-329/miR-495","pmids":["30665182"],"confidence":"Medium","gaps":["Direct enzymatic role in miRNA processing not defined","Whether thiolase activity is required for this function unknown"]},{"year":2019,"claim":"Connected HADHB loss-of-function to organismal and cellular phenotypes, clarifying both neuronal requirement and the instability mechanism of disease mutations.","evidence":"Neuron-specific RNAi in Drosophila with behavioral/NMJ/ATP/ROS readouts; temperature-shift and localization studies of M136T/A141T in patient cells","pmids":["30953623","31521624"],"confidence":"Medium","gaps":["Drosophila phenotypes not mechanistically tied to specific human mutations","Link between complex instability and neuromyopathy at molecular level incomplete"]},{"year":2025,"claim":"Defined upstream and downstream nodes placing HADHB in tumor metabolism: ZNF460 and promoter methylation set its expression, and a HADHB–DUOX2–ROS axis modulates chemosensitivity.","evidence":"ChIP-qPCR/dual-luciferase for ZNF460; cadmium-induced TET2-dependent promoter hypermethylation; co-IP and DUOX2 rescue of ROS in CRC cells","pmids":["40404004","38865940","40875107"],"confidence":"Medium","gaps":["Whether thiolase catalysis or scaffolding drives the ROS/chemosensitivity effects unclear","Each axis shown in a single cancer context"]},{"year":2026,"claim":"Positioned HADHB within stress and immunometabolic signaling, with ER-stress/CHOP mediating tumor suppression and MALAT1/GR controlling macrophage fatty acid oxidation.","evidence":"Hadhb knockout K-Ras mouse with Chop-knockdown rescue; RIP and thiolase activity for MALAT1; GR/dual-luciferase for the GCK–GR–HADHB axis in UC models","pmids":["42179784","41816300","41918496"],"confidence":"Medium","gaps":["How loss of a metabolic enzyme triggers the ATF6/eIF2α/CHOP axis mechanistically unclear","Each finding from a single lab/model"]},{"year":null,"claim":"How HADHB partitions between its canonical thiolase catalysis and its RNA-binding/scaffolding moonlighting roles, and whether these are mechanistically coupled, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure of HADHB bound to RNA or to ER/DUOX2/MALAT1 partners","Whether catalytic and non-catalytic functions share or use distinct surfaces is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,2]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,2]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[1,6]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,1,3,4]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,2]}],"complexes":["Mitochondrial trifunctional protein (MTP)"],"partners":["HADHA","ESR1","ESR2","DUOX2","MALAT1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P55084","full_name":"Trifunctional enzyme subunit beta, mitochondrial","aliases":["TP-beta"],"length_aa":474,"mass_kda":51.3,"function":"Mitochondrial trifunctional enzyme catalyzes the last three of the four reactions of the mitochondrial beta-oxidation pathway (PubMed:29915090, PubMed:30850536, PubMed:8135828). The mitochondrial beta-oxidation pathway is the major energy-producing process in tissues and is performed through four consecutive reactions breaking down fatty acids into acetyl-CoA (PubMed:29915090). Among the enzymes involved in this pathway, the trifunctional enzyme exhibits specificity for long-chain fatty acids (PubMed:30850536). Mitochondrial trifunctional enzyme is a heterotetrameric complex composed of two proteins, the trifunctional enzyme subunit alpha/HADHA carries the 2,3-enoyl-CoA hydratase and the 3-hydroxyacyl-CoA dehydrogenase activities, while the trifunctional enzyme subunit beta/HADHB described here bears the 3-ketoacyl-CoA thiolase activity (PubMed:29915090, PubMed:30850536, PubMed:8135828)","subcellular_location":"Mitochondrion; Mitochondrion inner membrane; Mitochondrion outer membrane; Endoplasmic reticulum","url":"https://www.uniprot.org/uniprotkb/P55084/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/HADHB","classification":"Not Classified","n_dependent_lines":5,"n_total_lines":1208,"dependency_fraction":0.0041390728476821195},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"SRP9","stoichiometry":4.0},{"gene":"CAPZB","stoichiometry":0.2},{"gene":"DDB1","stoichiometry":0.2},{"gene":"HSP90B1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/HADHB","total_profiled":1310},"omim":[{"mim_id":"620770","title":"MITOREGULIN; MTLN","url":"https://www.omim.org/entry/620770"},{"mim_id":"620300","title":"MITOCHONDRIAL TRIFUNCTIONAL PROTEIN DEFICIENCY 2; MTPD2","url":"https://www.omim.org/entry/620300"},{"mim_id":"615605","title":"FANCONI RENOTUBULAR SYNDROME 3; FRTS3","url":"https://www.omim.org/entry/615605"},{"mim_id":"613486","title":"MICRO RNA 33B; MIR33B","url":"https://www.omim.org/entry/613486"},{"mim_id":"612156","title":"MICRO RNA 33A; MIR33A","url":"https://www.omim.org/entry/612156"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Mitochondria","reliability":"Supported"},{"location":"Equatorial segment","reliability":"Additional"},{"location":"Principal piece","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"heart muscle","ntpm":749.3},{"tissue":"skeletal muscle","ntpm":917.1},{"tissue":"tongue","ntpm":1024.2}],"url":"https://www.proteinatlas.org/search/HADHB"},"hgnc":{"alias_symbol":["MTPB"],"prev_symbol":[]},"alphafold":{"accession":"P55084","domains":[{"cath_id":"3.40.47.10","chopping":"55-172_260-472","consensus_level":"medium","plddt":97.6198,"start":55,"end":472}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P55084","model_url":"https://alphafold.ebi.ac.uk/files/AF-P55084-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P55084-F1-predicted_aligned_error_v6.png","plddt_mean":91.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=HADHB","jax_strain_url":"https://www.jax.org/strain/search?query=HADHB"},"sequence":{"accession":"P55084","fasta_url":"https://rest.uniprot.org/uniprotkb/P55084.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P55084/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P55084"}},"corpus_meta":[{"pmid":"12933794","id":"PMC_12933794","title":"HADHB, HuR, and CP1 bind to the distal 3'-untranslated region of human renin mRNA and differentially modulate renin expression.","date":"2003","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12933794","citation_count":54,"is_preprint":false},{"pmid":"22375075","id":"PMC_22375075","title":"Estrogen receptor alpha interacts with mitochondrial protein HADHB and affects beta-oxidation activity.","date":"2012","source":"Molecular & cellular proteomics : MCP","url":"https://pubmed.ncbi.nlm.nih.gov/22375075","citation_count":52,"is_preprint":false},{"pmid":"16423905","id":"PMC_16423905","title":"Isolated mitochondrial long-chain ketoacyl-CoA thiolase deficiency resulting from mutations in the HADHB gene.","date":"2006","source":"Clinical chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16423905","citation_count":51,"is_preprint":false},{"pmid":"9259266","id":"PMC_9259266","title":"Genomic and mutational analysis of the mitochondrial trifunctional protein beta-subunit (HADHB) gene in patients with trifunctional protein deficiency.","date":"1997","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/9259266","citation_count":47,"is_preprint":false},{"pmid":"21549624","id":"PMC_21549624","title":"Comprehensive cDNA study and quantitative analysis of mutant HADHA and HADHB transcripts in a French cohort of 52 patients with mitochondrial trifunctional protein deficiency.","date":"2011","source":"Molecular genetics and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/21549624","citation_count":46,"is_preprint":false},{"pmid":"29507648","id":"PMC_29507648","title":"Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer.","date":"2018","source":"Clinical epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/29507648","citation_count":34,"is_preprint":false},{"pmid":"17143551","id":"PMC_17143551","title":"Identification of novel mutations of the HADHA and HADHB genes in patients with mitochondrial trifunctional protein deficiency.","date":"2007","source":"International journal of molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/17143551","citation_count":30,"is_preprint":false},{"pmid":"24664533","id":"PMC_24664533","title":"Mutations in HADHB, which encodes the β-subunit of mitochondrial trifunctional protein, cause infantile onset hypoparathyroidism and peripheral polyneuropathy.","date":"2014","source":"American journal of medical genetics. 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adolescence.","date":"2011","source":"Molecular genetics and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/22000755","citation_count":13,"is_preprint":false},{"pmid":"19880769","id":"PMC_19880769","title":"Two novel HADHB gene mutations in a Korean patient with mitochondrial trifunctional protein deficiency.","date":"2009","source":"Annals of clinical and laboratory science","url":"https://pubmed.ncbi.nlm.nih.gov/19880769","citation_count":12,"is_preprint":false},{"pmid":"30953623","id":"PMC_30953623","title":"Neuron-specific knockdown of Drosophila HADHB induces a shortened lifespan, deficient locomotive ability, abnormal motor neuron terminal morphology and learning disability.","date":"2019","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/30953623","citation_count":12,"is_preprint":false},{"pmid":"9605857","id":"PMC_9605857","title":"Fluorescence in situ hybridization mapping of the alpha and beta subunits (HADHA and HADHB) of human mitochondrial fatty acid beta-oxidation multienzyme complex to 2p23 and their evolution.","date":"1997","source":"Cytogenetics and cell genetics","url":"https://pubmed.ncbi.nlm.nih.gov/9605857","citation_count":11,"is_preprint":false},{"pmid":"38865940","id":"PMC_38865940","title":"DNA demethylase TET2-mediated reduction of HADHB expression contributes to cadmium-induced malignant progression of colorectal cancer.","date":"2024","source":"Ecotoxicology and environmental safety","url":"https://pubmed.ncbi.nlm.nih.gov/38865940","citation_count":9,"is_preprint":false},{"pmid":"29956646","id":"PMC_29956646","title":"HADHB mutations cause infantile-onset axonal Charcot-Marie-Tooth disease: A report of two cases.","date":"2018","source":"Clinical neuropathology","url":"https://pubmed.ncbi.nlm.nih.gov/29956646","citation_count":9,"is_preprint":false},{"pmid":"31521624","id":"PMC_31521624","title":"Identification and functional characterization of mutations within HADHB associated with mitochondrial trifunctional protein deficiency.","date":"2019","source":"Mitochondrion","url":"https://pubmed.ncbi.nlm.nih.gov/31521624","citation_count":6,"is_preprint":false},{"pmid":"28112527","id":"PMC_28112527","title":"Identification of a Novel HADHB Gene Mutation in an Iranian Patient with Mitochondrial Trifunctional Protein Deficiency.","date":"2017","source":"Archives of Iranian medicine","url":"https://pubmed.ncbi.nlm.nih.gov/28112527","citation_count":4,"is_preprint":false},{"pmid":"35433169","id":"PMC_35433169","title":"Novel mutations in the HADHB gene causing a mild phenotype of mitochondrial trifunctional protein (MTP) deficiency.","date":"2022","source":"JIMD reports","url":"https://pubmed.ncbi.nlm.nih.gov/35433169","citation_count":4,"is_preprint":false},{"pmid":"32257295","id":"PMC_32257295","title":"Novel HADHB mutations in a patient with mitochondrial trifunctional protein deficiency.","date":"2020","source":"Human genome variation","url":"https://pubmed.ncbi.nlm.nih.gov/32257295","citation_count":3,"is_preprint":false},{"pmid":"39991877","id":"PMC_39991877","title":"The Role of HADHB in Mitochondrial Fatty Acid Metabolism During Initiation of Metastasis in ccRCC.","date":"2025","source":"Molecular carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/39991877","citation_count":2,"is_preprint":false},{"pmid":"38731280","id":"PMC_38731280","title":"Polymorphisms of CYP7A1 and HADHB Genes and Their Effects on Milk Production Traits in Chinese Holstein Cows.","date":"2024","source":"Animals : an open access journal from MDPI","url":"https://pubmed.ncbi.nlm.nih.gov/38731280","citation_count":0,"is_preprint":false},{"pmid":"40146690","id":"PMC_40146690","title":"Mechanisms of adipocyte regulation: Insights from HADHB gene modulation.","date":"2025","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/40146690","citation_count":0,"is_preprint":false},{"pmid":"40875107","id":"PMC_40875107","title":"HADHB mediates 5-fluorouracil sensitivity in colorectal cancer.","date":"2025","source":"Discover oncology","url":"https://pubmed.ncbi.nlm.nih.gov/40875107","citation_count":0,"is_preprint":false},{"pmid":"40404004","id":"PMC_40404004","title":"ZNF460 enhances HADHB level by activating its transcription to promote the progression and pulmonary invasion of cutaneous T cell lymphoma.","date":"2025","source":"Archives of biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/40404004","citation_count":0,"is_preprint":false},{"pmid":"42179784","id":"PMC_42179784","title":"Hadhb Deficiency Inhibits Lung Tumorigenesis Via Activating ER Stress.","date":"2026","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/42179784","citation_count":0,"is_preprint":false},{"pmid":"37388542","id":"PMC_37388542","title":"Case report: Mitochondrial trifunctional protein deficiency caused by HADHB gene mutation (c.1175C>T) characterized by higher brain dysfunction followed by neuropathy, presented gadolinium enhancement on brain imaging in an adult patient.","date":"2023","source":"Frontiers in neurology","url":"https://pubmed.ncbi.nlm.nih.gov/37388542","citation_count":0,"is_preprint":false},{"pmid":"41816300","id":"PMC_41816300","title":"MALAT1 regulates human macrophage metabolism by interacting with HADHB.","date":"2026","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/41816300","citation_count":0,"is_preprint":false},{"pmid":"41918496","id":"PMC_41918496","title":"Ginsenoside compound K up-regulates β-subunits of long-chain L-3-hydroxyacyl-CoA (HADHB) to promote fatty acid oxidation recovery and improve the balance of macrophage polarization in mice with ulcerative colitis.","date":"2026","source":"British journal of pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/41918496","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":19250,"output_tokens":4145,"usd":0.059963,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12212,"output_tokens":3191,"usd":0.070417,"stage2_stop_reason":"end_turn"},"total_usd":0.13038,"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\": 1997,\n      \"finding\": \"The HADHB gene encodes the β-subunit of the mitochondrial trifunctional protein (MTP), an α4β4 hetero-octameric complex; HADHB contains the 3-ketoacyl-CoA thiolase domain while the α-subunit (HADHA) contains enoyl-CoA hydratase and 3-hydroxyacyl-CoA dehydrogenase domains. The two genes (HADHA and HADHB) co-map to chromosome band 2p23 and are adjacently located, similar to bacterial fatty acid β-oxidation multienzyme complex subunit gene organization.\",\n      \"method\": \"Genomic mutational analysis, FISH mapping, biochemical enzyme activity assays in patient fibroblasts\",\n      \"journal\": \"Human molecular genetics / Cytogenetics and cell genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — enzyme activity assays combined with genomic analysis, replicated across two independent papers (PMID:9259266, PMID:9605857)\",\n      \"pmids\": [\"9259266\", \"9605857\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"HADHB protein binds specifically to a 34-nucleotide AU-rich 'renin stability regulatory element' in the 3'-UTR of REN mRNA and acts as a destabilizer of renin mRNA: RNAi-mediated knockdown of HADHB increased renin mRNA stability and renin protein levels, while a specific thiolase inhibitor (4-bromocrotonic acid) decreased HADHB binding to the 3'-UTR and elevated renin protein. HADHB was confirmed to associate with REN mRNA in vivo by immunoprecipitation/RT-PCR and localizes to mitochondria by intracellular imaging.\",\n      \"method\": \"Yeast three-hybrid screening, recombinant protein RNA-binding assay, RNAi knockdown, immunoprecipitation/RT-PCR, intracellular imaging, reporter construct transfection\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (yeast three-hybrid, RNAi, co-IP/RT-PCR, inhibitor experiments) from a single lab\",\n      \"pmids\": [\"12933794\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Mutations in HADHB alone (compound heterozygous R62H and F431S) can cause isolated long-chain ketoacyl-CoA thiolase (LCTH) deficiency with near-absent LCTH activity (4% of normal) and normal LCHAD activity, establishing that HADHB encodes specifically the LCTH catalytic function within MTP.\",\n      \"method\": \"Enzyme activity assays (LCTH and LCHAD measured separately), molecular mutation analysis of patient fibroblasts\",\n      \"journal\": \"Clinical chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct enzymatic activity measurement with mutation confirmation, first case of isolated LCTH deficiency from HADHB mutation\",\n      \"pmids\": [\"16423905\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Estrogen receptor alpha (ERα) directly binds to HADHB in mitochondria: interaction was verified by affinity purification/proteomics, co-immunoprecipitation with whole-cell and purified mitochondrial extracts, in vitro binding assay, and co-localization by confocal microscopy. ERα expression modulates HADHB thiolase (β-oxidation) enzyme activity, and combined 17β-estradiol plus tamoxifen treatment affects the ERα–HADHB association and HADHB activity in ERα-positive but not ERα-negative breast cancer cells.\",\n      \"method\": \"Affinity purification/2D-gel/mass spectrometry, co-immunoprecipitation (whole cell and purified mitochondria), in vitro binding assay, confocal microscopy, enzyme activity assay, RNAi/pharmacological manipulation\",\n      \"journal\": \"Molecular & cellular proteomics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (in vitro binding, reciprocal co-IP from purified mitochondria, enzyme activity, confocal), single lab but rigorous experimental design\",\n      \"pmids\": [\"22375075\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Estrogen receptor beta (ERβ) also associates and co-localizes with HADHB within mitochondria, shown by co-immunoprecipitation and confocal microscopy in MCF7 cells. In contrast to ERα (which stimulates HADHB activity), ERβ silencing enhanced HADHB enzyme activity, indicating an inhibitory role of ERβ on HADHB β-oxidation activity.\",\n      \"method\": \"Co-immunoprecipitation, confocal microscopy, siRNA silencing, enzyme activity assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — co-IP plus enzyme activity assay and confocal microscopy, single lab, extends prior ERα findings with ERβ\",\n      \"pmids\": [\"23000159\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Structural analysis of the HADHB β-subunit showed that disease-associated missense mutations (A392V and the previously reported N389D) are located near the active site of MTP and affect conformation of the β-subunit, providing a structural basis for MTP deficiency with hypoparathyroidism and peripheral polyneuropathy.\",\n      \"method\": \"Structural modeling/analysis of mutation positions relative to active site, biochemical analysis confirming MTP deficiency, HADHB sequencing\",\n      \"journal\": \"American journal of medical genetics. Part A\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — structural analysis appears computational/modeling rather than experimental structure determination; single case report\",\n      \"pmids\": [\"24664533\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"HADHB protein binds to precursor microRNAs (pre-miR-329, pre-miR-495) as identified by RNA pull-down SILAC mass spectrometry. HADHB knockout (CRISPR/Cas9) in 3T3 cells reduced expression of mature miR-329 and miR-495 but not their precursors, suggesting HADHB plays a role in posttranscriptional processing of 14q32 microRNAs after precursor formation.\",\n      \"method\": \"RNA pull-down SILAC mass spectrometry, CRISPR/Cas9 knockout, RBP immunoprecipitation, immunohistochemistry\",\n      \"journal\": \"Molecular therapy. Nucleic acids\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RP-SMS identification plus CRISPR functional validation, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"30665182\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Neuron-specific knockdown of Drosophila HADHB (dHADHB/CG4581) reduced locomotor ability, shortened lifespan, impaired learning, caused abnormal neuromuscular junction (NMJ) synapse morphology, and reduced both ATP and ROS levels in the CNS, establishing a critical role for HADHB in glutamatergic neuron morphogenesis and function.\",\n      \"method\": \"Neuron-specific RNAi knockdown in Drosophila, behavioral assays (lifespan, locomotion, learning), NMJ morphology analysis, ATP and ROS measurement\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean tissue-specific KD with multiple defined phenotypic readouts in a validated ortholog model, single lab\",\n      \"pmids\": [\"30953623\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"HADHB mutations M136T and A141T (compound heterozygous) compromise MTP complex stability but do not alter subcellular localization of HADHB; mutant protein levels are lower at 37°C but partially restored at 30°C (temperature-sensitive), establishing a loss-of-function/instability mechanism for the mild neuromyopathic phenotype.\",\n      \"method\": \"In vitro cell functional studies, immunoblotting, subcellular localization analysis, temperature-shift experiments in patient-derived cells\",\n      \"journal\": \"Mitochondrion\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional cell studies with temperature-sensitivity experiments and localization analysis, single lab\",\n      \"pmids\": [\"31521624\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Chronic cadmium exposure leads to hypermethylation of the HADHB promoter region via inhibition of the DNA demethylase TET2, resulting in decreased HADHB expression, activation of the FAK signaling pathway, and enhanced CRC cell migration and invasion.\",\n      \"method\": \"RNA-seq, qRT-PCR, tissue microarray, chromatin/promoter methylation analysis, in vitro migration/invasion assays, in vivo lung metastasis model\",\n      \"journal\": \"Ecotoxicology and environmental safety\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — TET2-HADHB promoter methylation mechanism supported by multiple assays in vitro and in vivo, single lab\",\n      \"pmids\": [\"38865940\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"HADHB interacts with DUOX2 (identified by co-immunoprecipitation); knockdown of HADHB in CRC cells improved 5-FU sensitivity and reduced ROS production, while DUOX2 overexpression reversed the ROS reduction caused by HADHB knockdown, establishing a functional HADHB–DUOX2–ROS axis that modulates 5-FU chemosensitivity.\",\n      \"method\": \"Co-immunoprecipitation, CCK-8, flow cytometry (apoptosis, cell cycle), siRNA knockdown, overexpression, ROS measurement, metabolomics/transcriptomics\",\n      \"journal\": \"Discover oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — co-IP plus functional rescue experiments with multiple readouts, single lab\",\n      \"pmids\": [\"40875107\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZNF460 transcription factor activates HADHB transcription: ChIP-qPCR and dual-luciferase reporter assays demonstrated ZNF460 binding to the HADHB promoter and transcriptional upregulation, with downstream effects on fatty acid metabolism and CTCL tumor progression and pulmonary invasion.\",\n      \"method\": \"ChIP-qPCR, dual-luciferase reporter assay, siRNA knockdown, overexpression, in vivo tumor model\",\n      \"journal\": \"Archives of biochemistry and biophysics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct ChIP and reporter assay evidence for transcriptional regulation, supported by functional in vivo data, single lab\",\n      \"pmids\": [\"40404004\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"HADHB loss induces ER stress (increased ATF6(N), phospho-eIF2α, and upregulated CHOP), and CHOP knockdown partially restores oncogenic potential in Hadhb-deficient mice and rescues growth defects of HADHB-depleted cells, establishing CHOP as a key downstream mediator of a HADHB–ER stress–CHOP axis in lung tumor suppression.\",\n      \"method\": \"Hadhb knockout mouse model with K-Ras G12D-driven lung tumors, immunoblotting for ER stress markers, Chop knockdown rescue experiments, cell proliferation and apoptosis assays\",\n      \"journal\": \"Journal of Cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo KO mouse model combined with rescue experiments (Chop KD) establishing pathway epistasis, single lab\",\n      \"pmids\": [\"42179784\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"MALAT1 lncRNA interacts with HADHB protein and enhances its thiolase activity during the late phase of macrophage inflammation; this interaction is facilitated by HuR-MTCH2-mediated mitochondrial targeting of MALAT1. MALAT1 knockdown causes metabolic reprogramming (enhanced glycolysis, increased fatty acid synthesis, reduced FAO) and augments pro-inflammatory macrophage activation, placing HADHB as a mediator of MALAT1's metabolic and anti-inflammatory effects.\",\n      \"method\": \"RNA immunoprecipitation, thiolase activity assay, MALAT1 knockdown, metabolic flux measurements (glycolysis, FAO, fatty acid synthesis), macrophage activation assays\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct interaction identified by RIP with functional enzyme activity measurement and metabolic phenotyping, single lab\",\n      \"pmids\": [\"41816300\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Ginsenoside compound K (GCK) activates glucocorticoid receptor (GR/NR3C1) to upregulate HADHB expression (confirmed by dual-luciferase reporter assay), promoting fatty acid oxidation in macrophages and restoring M1/M2 macrophage polarization balance in ulcerative colitis models, placing HADHB downstream of GR signaling in macrophage metabolic reprogramming.\",\n      \"method\": \"Dual-luciferase reporter assay, western blot, RT-qPCR, flow cytometry, DSS-induced UC mouse model, LPS-stimulated RAW264.7 cells, metabolite detection\",\n      \"journal\": \"British journal of pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — promoter reporter assay and GR activation mechanistically linked to HADHB upregulation with in vivo validation, single lab\",\n      \"pmids\": [\"41918496\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"HADHB encodes the β-subunit of the mitochondrial trifunctional protein (MTP) α4β4 hetero-octamer, providing the long-chain 3-ketoacyl-CoA thiolase (LCTH) catalytic activity for the final step in mitochondrial fatty acid β-oxidation of long-chain fatty acids; beyond this canonical metabolic role, HADHB also functions as an RNA-binding protein that destabilizes REN mRNA via a 3'-UTR AU-rich element, interacts directly with estrogen receptors ERα (activating) and ERβ (inhibitory) in mitochondria to modulate β-oxidation activity, participates in posttranscriptional processing of 14q32 microRNAs, interacts with DUOX2 to regulate ROS levels affecting chemosensitivity, and is transcriptionally regulated by ZNF460 and the GR-GCK axis, while MALAT1 lncRNA directly enhances HADHB thiolase activity in macrophages and its loss triggers ER stress via an ATF6/eIF2α/CHOP axis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"HADHB encodes the β-subunit of the mitochondrial trifunctional protein (MTP), an α4β4 hetero-octamer that carries out the long-chain 3-ketoacyl-CoA thiolase (LCTH) step in the final stage of mitochondrial fatty acid β-oxidation, with the HADHA α-subunit providing the upstream enoyl-CoA hydratase and 3-hydroxyacyl-CoA dehydrogenase activities [#0]. Compound heterozygous HADHB mutations can produce isolated LCTH deficiency with near-absent thiolase activity but preserved LCHAD activity, establishing that the β-subunit specifically supplies the thiolase catalytic function within MTP [#2]; other disease-associated missense substitutions compromise MTP complex stability and lower mutant protein levels in a temperature-sensitive manner, defining a loss-of-function/instability basis for the resulting neuromyopathic and MTP-deficiency phenotypes [#8]. Beyond catalysis, HADHB is a mitochondrial RNA-binding protein: it binds an AU-rich element in the REN mRNA 3'-UTR and destabilizes renin transcripts in a manner sensitive to a thiolase inhibitor [#1], and it binds precursor 14q32 microRNAs to support maturation of miR-329 and miR-495 after precursor formation [#6]. Its β-oxidation activity is modulated by direct mitochondrial interactions with estrogen receptors, with ERα activating and ERβ inhibiting HADHB thiolase activity [#3, #4], and by MALAT1 lncRNA, which enhances thiolase activity to sustain fatty acid oxidation and restrain pro-inflammatory macrophage activation [#13]. HADHB expression is set transcriptionally by ZNF460 and by glucocorticoid-receptor signaling, and epigenetically by promoter methylation, linking its level to fatty acid metabolism in tumor and immune contexts [#9, #11, #14]; its loss triggers an ATF6/eIF2α/CHOP ER-stress axis that mediates lung tumor suppression [#12].\"\n,\n  \"teleology\": [\n    {\n      \"year\": 1997,\n      \"claim\": \"Established the molecular identity and architecture of HADHB, answering which catalytic step of long-chain β-oxidation it provides and how it relates to its partner subunit.\",\n      \"evidence\": \"Genomic mutational analysis, FISH mapping, and enzyme activity assays in patient fibroblasts defining HADHB as the thiolase-bearing β-subunit of the α4β4 MTP\",\n      \"pmids\": [\"9259266\", \"9605857\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No experimental structure of the assembled MTP at this stage\", \"Regulation of complex assembly not addressed\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Revealed an unexpected moonlighting role: HADHB binds REN mRNA and destabilizes it, separating a metabolic enzyme's catalytic surface from a post-transcriptional regulatory function.\",\n      \"evidence\": \"Yeast three-hybrid screen, recombinant RNA-binding assay, RNAi knockdown, co-IP/RT-PCR, and thiolase-inhibitor experiments\",\n      \"pmids\": [\"12933794\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; physiological relevance to renin regulation in vivo unproven\", \"Structural basis for AU-rich element recognition unknown\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Demonstrated that HADHB mutation alone causes isolated LCTH deficiency, formally assigning the thiolase activity of MTP to the β-subunit.\",\n      \"evidence\": \"Separate LCTH and LCHAD enzyme assays plus mutation analysis in patient fibroblasts\",\n      \"pmids\": [\"16423905\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Genotype–phenotype correlation across mutation spectrum not resolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Showed that estrogen receptors directly bind HADHB in mitochondria and bidirectionally tune its β-oxidation activity, defining hormone-responsive control of the thiolase.\",\n      \"evidence\": \"Affinity purification/MS, reciprocal co-IP from purified mitochondria, in vitro binding, confocal microscopy, and enzyme activity assays for ERα; co-IP, confocal, siRNA, and activity assays for ERβ\",\n      \"pmids\": [\"22375075\", \"23000159\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which ER binding alters thiolase activity unresolved\", \"Significance outside breast cancer cell lines not established\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extended HADHB's RNA-binding repertoire to precursor miRNAs, implicating it in post-transcriptional maturation of 14q32 microRNAs.\",\n      \"evidence\": \"RNA pull-down SILAC mass spectrometry and CRISPR/Cas9 knockout measuring mature versus precursor miR-329/miR-495\",\n      \"pmids\": [\"30665182\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct enzymatic role in miRNA processing not defined\", \"Whether thiolase activity is required for this function unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Connected HADHB loss-of-function to organismal and cellular phenotypes, clarifying both neuronal requirement and the instability mechanism of disease mutations.\",\n      \"evidence\": \"Neuron-specific RNAi in Drosophila with behavioral/NMJ/ATP/ROS readouts; temperature-shift and localization studies of M136T/A141T in patient cells\",\n      \"pmids\": [\"30953623\", \"31521624\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Drosophila phenotypes not mechanistically tied to specific human mutations\", \"Link between complex instability and neuromyopathy at molecular level incomplete\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined upstream and downstream nodes placing HADHB in tumor metabolism: ZNF460 and promoter methylation set its expression, and a HADHB–DUOX2–ROS axis modulates chemosensitivity.\",\n      \"evidence\": \"ChIP-qPCR/dual-luciferase for ZNF460; cadmium-induced TET2-dependent promoter hypermethylation; co-IP and DUOX2 rescue of ROS in CRC cells\",\n      \"pmids\": [\"40404004\", \"38865940\", \"40875107\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether thiolase catalysis or scaffolding drives the ROS/chemosensitivity effects unclear\", \"Each axis shown in a single cancer context\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Positioned HADHB within stress and immunometabolic signaling, with ER-stress/CHOP mediating tumor suppression and MALAT1/GR controlling macrophage fatty acid oxidation.\",\n      \"evidence\": \"Hadhb knockout K-Ras mouse with Chop-knockdown rescue; RIP and thiolase activity for MALAT1; GR/dual-luciferase for the GCK–GR–HADHB axis in UC models\",\n      \"pmids\": [\"42179784\", \"41816300\", \"41918496\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How loss of a metabolic enzyme triggers the ATF6/eIF2α/CHOP axis mechanistically unclear\", \"Each finding from a single lab/model\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How HADHB partitions between its canonical thiolase catalysis and its RNA-binding/scaffolding moonlighting roles, and whether these are mechanistically coupled, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of HADHB bound to RNA or to ER/DUOX2/MALAT1 partners\", \"Whether catalytic and non-catalytic functions share or use distinct surfaces is unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [1, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 1, 3, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"complexes\": [\"Mitochondrial trifunctional protein (MTP)\"],\n    \"partners\": [\"HADHA\", \"ESR1\", \"ESR2\", \"DUOX2\", \"MALAT1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}