{"gene":"TIFAB","run_date":"2026-06-10T10:51:55","timeline":{"discoveries":[{"year":2004,"finding":"TIFAB was identified as a TIFA-related protein that inhibits TIFA-mediated activation of NF-κB. TIFAB does not associate with members of the TRAF family directly but binds TIFA. Immunoprecipitation experiments showed that TIFAB significantly increased the amount of TRAF6 co-precipitated with TIFA (via TIFA IP), suggesting TIFAB inhibits TIFA-mediated TRAF6 activation possibly by inducing a conformational change in TIFA.","method":"Co-immunoprecipitation, NF-κB reporter assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — reciprocal co-IP with functional NF-κB reporter readout, single lab","pmids":["15047173"],"is_preprint":false},{"year":2009,"finding":"TIFAB is mainly expressed in B cells, dendritic cells, and macrophages in the spleen, and its expression is downregulated when these cells are stimulated by TRAF6-mediated signals (CD40, sIgM, TLRs). Microinjection of TIFAB into NIH3T3 cells inhibited S-phase entry, establishing TIFAB as a negative regulator of TRAF6-induced cellular functions including B cell proliferation and DC/macrophage maturation.","method":"Immunofluorescence/cell-type expression analysis, microinjection, cell cycle analysis","journal":"Journal of biochemistry","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization tied to functional readout (cell cycle inhibition) via microinjection, single lab, two methods","pmids":["19470519"],"is_preprint":false},{"year":2015,"finding":"TIFAB forms a complex with TRAF6 and reduces TRAF6 protein stability by a lysosome-dependent mechanism. Loss of TIFAB increases TRAF6 protein levels and amplifies the dynamic range of TLR4 signaling, resulting in hypersensitivity to TLR4 stimulation and impaired hematopoiesis. Combined deletion of TIFAB and miR-146a cooperatively increases TRAF6 expression and hematopoietic dysfunction.","method":"Co-immunoprecipitation, protein stability assay with lysosome inhibitors, Tifab knockout mouse transplantation, gene expression analysis, TLR4 stimulation assays","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Co-IP, lysosomal inhibitor assay, KO mouse transplant, epistasis with miR-146a), replicated across conditions","pmids":["26458771"],"is_preprint":false},{"year":2020,"finding":"TIFAB regulates USP15 ubiquitin hydrolase activity in hematopoietic stem/progenitor cells (HSPCs). TIFAB expression permits USP15 signaling to substrates MDM2 and KEAP1, thereby mitigating p53 expression. TIFAB-deficient HSPCs show compromised USP15 signaling and are sensitized to hematopoietic stress via derepression of p53. In MLL-AF9 leukemia, TIFAB deletion increases p53 signaling and decreases leukemic cell function; restoring USP15 partially rescues TIFAB-deficient MLL-AF9 cell function.","method":"Proteomic (mass spectrometry) interaction screen, genetic epistasis (TIFAB KO + USP15 rescue), ubiquitin hydrolase activity assay, p53/MDM2/KEAP1 protein level analysis","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — proteomic identification combined with genetic epistasis and enzymatic activity assay, multiple orthogonal methods in a single study","pmids":["32101751"],"is_preprint":false},{"year":2021,"finding":"TIFAB accelerates MLL-AF9-induced AML by upregulating HOXA9. RelB (a non-canonical NF-κB component) directly suppresses TIFAB expression, and forced TIFAB expression reverses NIK-induced impaired AML development through downregulation of RelB and upregulation of HOXA9, increasing leukemia stem cell signatures.","method":"Forced expression/overexpression in MLL-AF9 AML model, gene set enrichment analysis, genetic deletion of RelB, in vivo AML transplantation","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo genetic model with forced expression and deletion, single lab, multiple methods","pmids":["34877491"],"is_preprint":false},{"year":2024,"finding":"TIFAB forms a stable heterodimer specifically with monomeric TIFA (not the TIFA dimer). Crystal/structural analysis of the TIFA/TIFAB complex showed that the resulting pseudo-TIFA dimer lacks the phosphorylation site and TRAF6-binding motif present in TIFAB, thereby inhibiting TIFA dimer formation and suppressing ALPK1-TIFA-TRAF6-mediated NF-κB activation.","method":"Structural analysis (crystallography), biochemical binding assays, cell-based NF-κB activation assays, mutagenesis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with biochemical and cell-based functional validation, mutagenesis, rigorous single study with multiple orthogonal methods","pmids":["38442163"],"is_preprint":false},{"year":2025,"finding":"TIFAB deletion in KMT2A::MLLT3-induced AML impairs leukemia stem/progenitor cell (LSPC) engraftment, glucose uptake, and mitochondrial function. TIFAB promotes expression of HNF4A by inhibiting NF-κB component RelB (which suppresses HNF4A). HNF4A rescues metabolic defects caused by TIFAB deletion; conversely, HNF4A knockdown attenuates TIFAB-mediated enhancement of LSPC function, establishing a TIFAB–RelB–HNF4A metabolic axis in AML.","method":"Tifab conditional KO in AML mouse model, gene set enrichment analysis, glucose uptake and mitochondrial function assays, HNF4A rescue/knockdown experiments, in vivo engraftment","journal":"Blood advances","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO combined with rescue experiments and metabolic assays, single lab, multiple methods","pmids":["39626355"],"is_preprint":false}],"current_model":"TIFAB is an FHA-domain protein that functions as a negative regulator of innate immune and NF-κB signaling: it forms a stable heterodimer with monomeric TIFA to block TIFA oligomerization and TIFA-TRAF6-mediated NF-κB activation (structural/biochemical basis established), directly complexes with TRAF6 and promotes its lysosomal degradation to dampen TLR4 signaling in hematopoietic stem/progenitor cells, and acts as an effector of USP15 ubiquitin hydrolase activity toward MDM2 and KEAP1 to repress p53 signaling; in myeloid malignancy contexts, TIFAB also activates a RelB–HNF4A metabolic axis and upregulates HOXA9 to promote leukemic stem cell function."},"narrative":{"mechanistic_narrative":"TIFAB is a TIFA-related FHA-domain protein that functions as a negative regulator of innate immune and NF-κB signaling in hematopoietic and immune cells [PMID:15047173, PMID:26458771]. It binds monomeric TIFA and forms a stable heterodimer, generating a pseudo-TIFA dimer that lacks the phosphorylation site and TRAF6-binding motif, thereby blocking TIFA oligomerization and suppressing ALPK1–TIFA–TRAF6-mediated NF-κB activation [PMID:38442163, PMID:15047173]. In parallel, TIFAB complexes with TRAF6 and reduces its protein stability through a lysosome-dependent mechanism, so that loss of TIFAB raises TRAF6 levels and renders hematopoietic stem/progenitor cells hypersensitive to TLR4 stimulation, impairing hematopoiesis [PMID:26458771]. TIFAB additionally acts as an effector of USP15 deubiquitinase activity toward MDM2 and KEAP1, restraining p53 signaling and protecting HSPCs from hematopoietic stress [PMID:32101751]. In myeloid malignancy, TIFAB promotes leukemic stem/progenitor cell function by suppressing the non-canonical NF-κB component RelB to derepress HOXA9 and HNF4A, the latter driving a metabolic program supporting glucose uptake and mitochondrial function [PMID:34877491, PMID:39626355].","teleology":[{"year":2004,"claim":"Established TIFAB's founding identity as a TIFA-binding inhibitor of NF-κB, answering whether this TIFA paralog acts in the same signaling axis but with opposite sign.","evidence":"Co-immunoprecipitation and NF-κB reporter assays in cell lines","pmids":["15047173"],"confidence":"Medium","gaps":["Mechanism of inhibition inferred as conformational change without structural proof","No direct TRAF-family binding demonstrated","Cellular and physiological context untested"]},{"year":2009,"claim":"Tied TIFAB expression to immune cell types and demonstrated functional consequence, showing it is a negative regulator of TRAF6-induced proliferation and maturation rather than a passive binding partner.","evidence":"Cell-type expression analysis plus microinjection and cell cycle analysis in NIH3T3 cells","pmids":["19470519"],"confidence":"Medium","gaps":["Molecular target of cell cycle inhibition not defined","Microinjection readout not linked to endogenous TIFAB levels","No in vivo loss-of-function"]},{"year":2015,"claim":"Defined a direct biochemical mechanism for TIFAB on TRAF6 and an in vivo hematopoietic role, answering how TIFAB constrains innate immune signal amplitude.","evidence":"Co-IP, lysosome-inhibitor stability assays, Tifab knockout mouse transplantation, and miR-146a epistasis","pmids":["26458771"],"confidence":"High","gaps":["Molecular route directing TRAF6 to lysosomes unresolved","Relationship between TRAF6 degradation and the TIFA-blocking activity not integrated"]},{"year":2020,"claim":"Revealed an NF-κB-independent arm by which TIFAB licenses USP15 deubiquitinase activity to restrain p53, expanding its role to stress protection of HSPCs and leukemic cells.","evidence":"Mass-spectrometry interaction screen, genetic epistasis with USP15 rescue, deubiquitinase activity assays, and p53/MDM2/KEAP1 protein analysis in MLL-AF9 leukemia","pmids":["32101751"],"confidence":"High","gaps":["How TIFAB binding modulates USP15 catalytic activity at the molecular level unknown","Direct TIFAB–USP15 interface not structurally defined"]},{"year":2021,"claim":"Connected TIFAB to leukemic transformation through a RelB–HOXA9 transcriptional circuit, showing it accelerates AML and enforces stem cell signatures.","evidence":"Forced expression in MLL-AF9 AML, RelB deletion, GSEA, and in vivo transplantation","pmids":["34877491"],"confidence":"Medium","gaps":["Direct versus indirect control of HOXA9 not separated","Mechanism by which RelB suppresses TIFAB not defined"]},{"year":2024,"claim":"Provided the structural basis for TIFA inhibition, showing TIFAB heterodimerizes with monomeric TIFA to form a pseudo-dimer lacking the phosphorylation site and TRAF6 motif.","evidence":"Crystallography, biochemical binding assays, mutagenesis, and cell-based NF-κB assays of the ALPK1–TIFA–TRAF6 axis","pmids":["38442163"],"confidence":"High","gaps":["Does not address how the structural TIFA-blocking model relates to TIFAB's separate TRAF6-degradation and USP15 functions","In vivo relevance of the heterodimer in immune cells not tested"]},{"year":2025,"claim":"Extended the RelB axis to leukemic metabolism, showing TIFAB drives an HNF4A-dependent program supporting glucose uptake and mitochondrial function in AML stem/progenitor cells.","evidence":"Tifab conditional KO in KMT2A::MLLT3 AML, GSEA, metabolic assays, and HNF4A rescue/knockdown with in vivo engraftment","pmids":["39626355"],"confidence":"Medium","gaps":["Mechanistic link between TIFAB and RelB suppression of HNF4A not resolved","Whether the metabolic axis operates outside leukemia unknown"]},{"year":null,"claim":"How TIFAB's distinct activities—TIFA heterodimerization, lysosomal TRAF6 degradation, USP15/p53 regulation, and the RelB–HNF4A/HOXA9 transcriptional axis—are coordinated within a single cell, and which dominates in physiological versus malignant contexts, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model integrating the four reported activities","Domain requirements for each function not systematically mapped"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,2,3,5]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,5]}],"localization":[],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,2,5]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,5]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[3,4,6]}],"complexes":[],"partners":["TIFA","TRAF6","USP15"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q6ZNK6","full_name":"TRAF-interacting protein with FHA domain-containing protein B","aliases":["TIFA-like protein"],"length_aa":161,"mass_kda":17.9,"function":"Inhibits TIFA-mediated TRAF6 activation possibly by inducing a conformational change in TIFA","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q6ZNK6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TIFAB","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TIFAB","total_profiled":1310},"omim":[{"mim_id":"620469","title":"CRANIAL DYSINNERVATION DISORDER, CONGENITAL, WITH ABSENT CORNEAL REFLEX AND DEVELOPMENTAL DELAY; CCDDRD","url":"https://www.omim.org/entry/620469"},{"mim_id":"612663","title":"TRAF-INTERACTING PROTEIN WITH FORKHEAD-ASSOCIATED DOMAIN, FAMILY MEMBER B; TIFAB","url":"https://www.omim.org/entry/612663"},{"mim_id":"153550","title":"CHROMOSOME 5q DELETION SYNDROME","url":"https://www.omim.org/entry/153550"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"lymphoid tissue","ntpm":5.3}],"url":"https://www.proteinatlas.org/search/TIFAB"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q6ZNK6","domains":[{"cath_id":"2.60.200.20","chopping":"6-132","consensus_level":"high","plddt":95.998,"start":6,"end":132}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6ZNK6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6ZNK6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6ZNK6-F1-predicted_aligned_error_v6.png","plddt_mean":89.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TIFAB","jax_strain_url":"https://www.jax.org/strain/search?query=TIFAB"},"sequence":{"accession":"Q6ZNK6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6ZNK6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6ZNK6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6ZNK6"}},"corpus_meta":[{"pmid":"26458771","id":"PMC_26458771","title":"Loss of Tifab, a del(5q) MDS gene, alters hematopoiesis through derepression of Toll-like receptor-TRAF6 signaling.","date":"2015","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/26458771","citation_count":96,"is_preprint":false},{"pmid":"29860346","id":"PMC_29860346","title":"DNA methylation as a marker for prenatal smoke exposure in adults.","date":"2018","source":"International journal of epidemiology","url":"https://pubmed.ncbi.nlm.nih.gov/29860346","citation_count":91,"is_preprint":false},{"pmid":"32101751","id":"PMC_32101751","title":"TIFAB Regulates USP15-Mediated p53 Signaling during Stressed and Malignant Hematopoiesis.","date":"2020","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/32101751","citation_count":34,"is_preprint":false},{"pmid":"32910997","id":"PMC_32910997","title":"TIFA and TIFAB: FHA-domain proteins involved in inflammation, hematopoiesis, and disease.","date":"2020","source":"Experimental hematology","url":"https://pubmed.ncbi.nlm.nih.gov/32910997","citation_count":24,"is_preprint":false},{"pmid":"15047173","id":"PMC_15047173","title":"TIFAB inhibits TIFA, TRAF-interacting protein with a forkhead-associated domain.","date":"2004","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/15047173","citation_count":20,"is_preprint":false},{"pmid":"19470519","id":"PMC_19470519","title":"TRAF-interacting protein with a forkhead-associated domain B (TIFAB) is a negative regulator of the TRAF6-induced cellular functions.","date":"2009","source":"Journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19470519","citation_count":18,"is_preprint":false},{"pmid":"30267110","id":"PMC_30267110","title":"Identification of the TIFAB Gene as a Susceptibility Locus for Coronary Artery Aneurysm in Patients with Kawasaki Disease.","date":"2018","source":"Pediatric cardiology","url":"https://pubmed.ncbi.nlm.nih.gov/30267110","citation_count":16,"is_preprint":false},{"pmid":"27733012","id":"PMC_27733012","title":"Constitutive Activation of NIK Impairs the Self-Renewal of Hematopoietic Stem/Progenitor Cells and Induces Bone Marrow Failure.","date":"2016","source":"Stem cells (Dayton, Ohio)","url":"https://pubmed.ncbi.nlm.nih.gov/27733012","citation_count":15,"is_preprint":false},{"pmid":"23419067","id":"PMC_23419067","title":"A boy with homozygous microdeletion of NEUROG1 presents with a congenital cranial dysinnervation disorder [Moebius syndrome variant].","date":"2013","source":"Behavioral and brain functions : BBF","url":"https://pubmed.ncbi.nlm.nih.gov/23419067","citation_count":13,"is_preprint":false},{"pmid":"38442163","id":"PMC_38442163","title":"TIFAB regulates the TIFA-TRAF6 signaling pathway involved in innate immunity by forming a heterodimer complex with TIFA.","date":"2024","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/38442163","citation_count":6,"is_preprint":false},{"pmid":"34877491","id":"PMC_34877491","title":"TIFAB accelerates MLL-AF9-Induced acute myeloid leukemia through upregulation of HOXA9.","date":"2021","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/34877491","citation_count":3,"is_preprint":false},{"pmid":"39626355","id":"PMC_39626355","title":"TIFAB modulates metabolic pathways in KMT2A::MLLT3-induced AML through HNF4A.","date":"2025","source":"Blood advances","url":"https://pubmed.ncbi.nlm.nih.gov/39626355","citation_count":1,"is_preprint":false},{"pmid":"35549438","id":"PMC_35549438","title":"miR-626 Inhibition Enhanced the Radiosensitivity to Oral Squamous Cell Carcinoma via the Downregulation of Nuclear Factor Kappa-B Signaling.","date":"2022","source":"Cancer biotherapy & radiopharmaceuticals","url":"https://pubmed.ncbi.nlm.nih.gov/35549438","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8858,"output_tokens":2136,"usd":0.029307,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9129,"output_tokens":2704,"usd":0.056622,"stage2_stop_reason":"end_turn"},"total_usd":0.085929,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2004,\n      \"finding\": \"TIFAB was identified as a TIFA-related protein that inhibits TIFA-mediated activation of NF-κB. TIFAB does not associate with members of the TRAF family directly but binds TIFA. Immunoprecipitation experiments showed that TIFAB significantly increased the amount of TRAF6 co-precipitated with TIFA (via TIFA IP), suggesting TIFAB inhibits TIFA-mediated TRAF6 activation possibly by inducing a conformational change in TIFA.\",\n      \"method\": \"Co-immunoprecipitation, NF-κB reporter assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — reciprocal co-IP with functional NF-κB reporter readout, single lab\",\n      \"pmids\": [\"15047173\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"TIFAB is mainly expressed in B cells, dendritic cells, and macrophages in the spleen, and its expression is downregulated when these cells are stimulated by TRAF6-mediated signals (CD40, sIgM, TLRs). Microinjection of TIFAB into NIH3T3 cells inhibited S-phase entry, establishing TIFAB as a negative regulator of TRAF6-induced cellular functions including B cell proliferation and DC/macrophage maturation.\",\n      \"method\": \"Immunofluorescence/cell-type expression analysis, microinjection, cell cycle analysis\",\n      \"journal\": \"Journal of biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization tied to functional readout (cell cycle inhibition) via microinjection, single lab, two methods\",\n      \"pmids\": [\"19470519\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"TIFAB forms a complex with TRAF6 and reduces TRAF6 protein stability by a lysosome-dependent mechanism. Loss of TIFAB increases TRAF6 protein levels and amplifies the dynamic range of TLR4 signaling, resulting in hypersensitivity to TLR4 stimulation and impaired hematopoiesis. Combined deletion of TIFAB and miR-146a cooperatively increases TRAF6 expression and hematopoietic dysfunction.\",\n      \"method\": \"Co-immunoprecipitation, protein stability assay with lysosome inhibitors, Tifab knockout mouse transplantation, gene expression analysis, TLR4 stimulation assays\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Co-IP, lysosomal inhibitor assay, KO mouse transplant, epistasis with miR-146a), replicated across conditions\",\n      \"pmids\": [\"26458771\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TIFAB regulates USP15 ubiquitin hydrolase activity in hematopoietic stem/progenitor cells (HSPCs). TIFAB expression permits USP15 signaling to substrates MDM2 and KEAP1, thereby mitigating p53 expression. TIFAB-deficient HSPCs show compromised USP15 signaling and are sensitized to hematopoietic stress via derepression of p53. In MLL-AF9 leukemia, TIFAB deletion increases p53 signaling and decreases leukemic cell function; restoring USP15 partially rescues TIFAB-deficient MLL-AF9 cell function.\",\n      \"method\": \"Proteomic (mass spectrometry) interaction screen, genetic epistasis (TIFAB KO + USP15 rescue), ubiquitin hydrolase activity assay, p53/MDM2/KEAP1 protein level analysis\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — proteomic identification combined with genetic epistasis and enzymatic activity assay, multiple orthogonal methods in a single study\",\n      \"pmids\": [\"32101751\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TIFAB accelerates MLL-AF9-induced AML by upregulating HOXA9. RelB (a non-canonical NF-κB component) directly suppresses TIFAB expression, and forced TIFAB expression reverses NIK-induced impaired AML development through downregulation of RelB and upregulation of HOXA9, increasing leukemia stem cell signatures.\",\n      \"method\": \"Forced expression/overexpression in MLL-AF9 AML model, gene set enrichment analysis, genetic deletion of RelB, in vivo AML transplantation\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo genetic model with forced expression and deletion, single lab, multiple methods\",\n      \"pmids\": [\"34877491\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TIFAB forms a stable heterodimer specifically with monomeric TIFA (not the TIFA dimer). Crystal/structural analysis of the TIFA/TIFAB complex showed that the resulting pseudo-TIFA dimer lacks the phosphorylation site and TRAF6-binding motif present in TIFAB, thereby inhibiting TIFA dimer formation and suppressing ALPK1-TIFA-TRAF6-mediated NF-κB activation.\",\n      \"method\": \"Structural analysis (crystallography), biochemical binding assays, cell-based NF-κB activation assays, mutagenesis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with biochemical and cell-based functional validation, mutagenesis, rigorous single study with multiple orthogonal methods\",\n      \"pmids\": [\"38442163\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TIFAB deletion in KMT2A::MLLT3-induced AML impairs leukemia stem/progenitor cell (LSPC) engraftment, glucose uptake, and mitochondrial function. TIFAB promotes expression of HNF4A by inhibiting NF-κB component RelB (which suppresses HNF4A). HNF4A rescues metabolic defects caused by TIFAB deletion; conversely, HNF4A knockdown attenuates TIFAB-mediated enhancement of LSPC function, establishing a TIFAB–RelB–HNF4A metabolic axis in AML.\",\n      \"method\": \"Tifab conditional KO in AML mouse model, gene set enrichment analysis, glucose uptake and mitochondrial function assays, HNF4A rescue/knockdown experiments, in vivo engraftment\",\n      \"journal\": \"Blood advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO combined with rescue experiments and metabolic assays, single lab, multiple methods\",\n      \"pmids\": [\"39626355\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TIFAB is an FHA-domain protein that functions as a negative regulator of innate immune and NF-κB signaling: it forms a stable heterodimer with monomeric TIFA to block TIFA oligomerization and TIFA-TRAF6-mediated NF-κB activation (structural/biochemical basis established), directly complexes with TRAF6 and promotes its lysosomal degradation to dampen TLR4 signaling in hematopoietic stem/progenitor cells, and acts as an effector of USP15 ubiquitin hydrolase activity toward MDM2 and KEAP1 to repress p53 signaling; in myeloid malignancy contexts, TIFAB also activates a RelB–HNF4A metabolic axis and upregulates HOXA9 to promote leukemic stem cell function.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TIFAB is a TIFA-related FHA-domain protein that functions as a negative regulator of innate immune and NF-\\u03baB signaling in hematopoietic and immune cells [#0, #2]. It binds monomeric TIFA and forms a stable heterodimer, generating a pseudo-TIFA dimer that lacks the phosphorylation site and TRAF6-binding motif, thereby blocking TIFA oligomerization and suppressing ALPK1\\u2013TIFA\\u2013TRAF6-mediated NF-\\u03baB activation [#5, #0]. In parallel, TIFAB complexes with TRAF6 and reduces its protein stability through a lysosome-dependent mechanism, so that loss of TIFAB raises TRAF6 levels and renders hematopoietic stem/progenitor cells hypersensitive to TLR4 stimulation, impairing hematopoiesis [#2]. TIFAB additionally acts as an effector of USP15 deubiquitinase activity toward MDM2 and KEAP1, restraining p53 signaling and protecting HSPCs from hematopoietic stress [#3]. In myeloid malignancy, TIFAB promotes leukemic stem/progenitor cell function by suppressing the non-canonical NF-\\u03baB component RelB to derepress HOXA9 and HNF4A, the latter driving a metabolic program supporting glucose uptake and mitochondrial function [#4, #6].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Established TIFAB's founding identity as a TIFA-binding inhibitor of NF-\\u03baB, answering whether this TIFA paralog acts in the same signaling axis but with opposite sign.\",\n      \"evidence\": \"Co-immunoprecipitation and NF-\\u03baB reporter assays in cell lines\",\n      \"pmids\": [\"15047173\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of inhibition inferred as conformational change without structural proof\", \"No direct TRAF-family binding demonstrated\", \"Cellular and physiological context untested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Tied TIFAB expression to immune cell types and demonstrated functional consequence, showing it is a negative regulator of TRAF6-induced proliferation and maturation rather than a passive binding partner.\",\n      \"evidence\": \"Cell-type expression analysis plus microinjection and cell cycle analysis in NIH3T3 cells\",\n      \"pmids\": [\"19470519\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular target of cell cycle inhibition not defined\", \"Microinjection readout not linked to endogenous TIFAB levels\", \"No in vivo loss-of-function\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined a direct biochemical mechanism for TIFAB on TRAF6 and an in vivo hematopoietic role, answering how TIFAB constrains innate immune signal amplitude.\",\n      \"evidence\": \"Co-IP, lysosome-inhibitor stability assays, Tifab knockout mouse transplantation, and miR-146a epistasis\",\n      \"pmids\": [\"26458771\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular route directing TRAF6 to lysosomes unresolved\", \"Relationship between TRAF6 degradation and the TIFA-blocking activity not integrated\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Revealed an NF-\\u03baB-independent arm by which TIFAB licenses USP15 deubiquitinase activity to restrain p53, expanding its role to stress protection of HSPCs and leukemic cells.\",\n      \"evidence\": \"Mass-spectrometry interaction screen, genetic epistasis with USP15 rescue, deubiquitinase activity assays, and p53/MDM2/KEAP1 protein analysis in MLL-AF9 leukemia\",\n      \"pmids\": [\"32101751\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How TIFAB binding modulates USP15 catalytic activity at the molecular level unknown\", \"Direct TIFAB\\u2013USP15 interface not structurally defined\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Connected TIFAB to leukemic transformation through a RelB\\u2013HOXA9 transcriptional circuit, showing it accelerates AML and enforces stem cell signatures.\",\n      \"evidence\": \"Forced expression in MLL-AF9 AML, RelB deletion, GSEA, and in vivo transplantation\",\n      \"pmids\": [\"34877491\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct versus indirect control of HOXA9 not separated\", \"Mechanism by which RelB suppresses TIFAB not defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Provided the structural basis for TIFA inhibition, showing TIFAB heterodimerizes with monomeric TIFA to form a pseudo-dimer lacking the phosphorylation site and TRAF6 motif.\",\n      \"evidence\": \"Crystallography, biochemical binding assays, mutagenesis, and cell-based NF-\\u03baB assays of the ALPK1\\u2013TIFA\\u2013TRAF6 axis\",\n      \"pmids\": [\"38442163\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not address how the structural TIFA-blocking model relates to TIFAB's separate TRAF6-degradation and USP15 functions\", \"In vivo relevance of the heterodimer in immune cells not tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended the RelB axis to leukemic metabolism, showing TIFAB drives an HNF4A-dependent program supporting glucose uptake and mitochondrial function in AML stem/progenitor cells.\",\n      \"evidence\": \"Tifab conditional KO in KMT2A::MLLT3 AML, GSEA, metabolic assays, and HNF4A rescue/knockdown with in vivo engraftment\",\n      \"pmids\": [\"39626355\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic link between TIFAB and RelB suppression of HNF4A not resolved\", \"Whether the metabolic axis operates outside leukemia unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TIFAB's distinct activities\\u2014TIFA heterodimerization, lysosomal TRAF6 degradation, USP15/p53 regulation, and the RelB\\u2013HNF4A/HOXA9 transcriptional axis\\u2014are coordinated within a single cell, and which dominates in physiological versus malignant contexts, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model integrating the four reported activities\", \"Domain requirements for each function not systematically mapped\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 2, 3, 5]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 5]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 2, 5]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [3, 4, 6]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"TIFA\", \"TRAF6\", \"USP15\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}