{"gene":"HOXB5","run_date":"2026-04-28T18:06:53","timeline":{"discoveries":[{"year":1993,"finding":"The human HoxB5 protein binds DNA in a sequence-specific manner; cooperative DNA binding to tandem sites is stabilized by at least 100-fold relative to a single site and requires a small domain adjacent to the homeodomain on the amino-terminal side. Cooperative binding is under redox regulation: a cysteine residue in the turn between homeodomain helices 2 and 3 is necessary for cooperativity, and oxidation of HoxB5 enhances (rather than inhibits) cooperative DNA binding, opposite to the redox regulation of Fos, Jun, and other transcription factors.","method":"In vitro DNA binding assays, mutational analysis of cysteine residues, domain deletion experiments","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution with mutagenesis identifying specific residue and domain requirements","pmids":["8101633"],"is_preprint":false},{"year":1992,"finding":"HoxB5 (Hox-2.5) transactivates the mouse N-CAM gene promoter through a specific homeodomain binding site (site II) in cotransfection assays; the adjacent HoxB4 (Hox-2.4) protein antagonizes this activation, demonstrating that two adjacent Hox gene products can differentially regulate a downstream cell adhesion molecule gene.","method":"Cotransfection/reporter gene assay (CAT) in NIH 3T3 cells, mutational analysis of homeodomain binding sites","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 — functional promoter reporter assay with mutational validation of binding site; identifies N-CAM as downstream target","pmids":["1347944"],"is_preprint":false},{"year":2003,"finding":"HoxB5 acts as an upstream transcriptional activator of flk1 (VEGFR2/KDR) in endothelial precursor differentiation. A cis-acting element in the first intron of flk1 (HoxB5-binding element, HBE) is required for endothelium-dependent expression; HoxB5 binds this element (identified by yeast one-hybrid), transactivates the flk1 promoter in an HBE-dependent fashion, and overexpression of HoxB5 expands flk1+ angioblasts and increases PECAM+ primitive blood vessels in embryoid bodies.","method":"Yeast one-hybrid screen, transient transfection reporter assay, overexpression in embryoid bodies, transgenic reporter assay","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods: yeast one-hybrid, reporter assay, and in vivo embryoid body overexpression with specific phenotypic readout","pmids":["12897140"],"is_preprint":false},{"year":2009,"finding":"HoxB5 promotes endothelial cell sprouting in vitro and modifies intussusceptive angiogenesis in vivo; HoxB5 overexpression upregulates angiopoietin-2 (Ang2) transcriptionally, and the HoxB5-induced sprouting effect is abolished by soluble Tie-2 (angiopoietin antagonist), placing Ang2 as a functional downstream mediator.","method":"HUVEC spheroid sprouting assay, chick chorioallantoic membrane assay, luciferase reporter assay for Ang2 promoter, soluble Tie-2 functional blockade","journal":"Cardiovascular research","confidence":"High","confidence_rationale":"Tier 1-2 — reporter assay + in vitro and in vivo functional assays with pathway blockade","pmids":["19403561"],"is_preprint":false},{"year":2008,"finding":"Hoxb5 acts as a transcriptional activator upstream of Ret in vagal neural crest cells; a dominant-negative Hoxb5 (enb5, fused to Engrailed repressor domain) in vagal NCCs reduces Ret expression, impairs NCC migration to distal intestine, and causes hypoganglionosis. Hoxb5 directly induces Ret transcription in neuroblastoma cells.","method":"Transgenic dominant-negative expression in mice, in vitro Ret reporter assay in neuroblastoma cells, histological analysis of ganglia","journal":"Gastroenterology","confidence":"High","confidence_rationale":"Tier 2 — dominant-negative epistasis in vivo combined with in vitro transcriptional assay; replicated by subsequent studies","pmids":["18395091"],"is_preprint":false},{"year":2011,"finding":"HOXB5 directly binds the promoter region upstream of the NKX2-1 binding site in the RET gene and transactivates RET expression. HOXB5 and NKX2-1 form a protein complex and synergistically activate RET transcription; HSCR-associated SNPs at the NKX2-1 binding site abolish this synergism. HOXB5 cooperates additively (not synergistically) with SOX10, PAX3, and PHOX2B in RET transactivation.","method":"Chromatin immunoprecipitation, luciferase reporter assay, co-immunoprecipitation (protein complex), promoter deletion analysis","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1-2 — ChIP, Co-IP, and reporter assays with multiple binding partners; mechanistic detail on synergistic vs. additive cooperativity","pmids":["21677782"],"is_preprint":false},{"year":2014,"finding":"HOXB5 binds to a multi-species conserved sequence (MCS+9.7) in the first intron of the RET gene and enhances RET transcription in an MCS+9.7-dependent manner. HOXB5 binding to MCS+9.7 alters chromatin conformation and induces histone H3K4 trimethylation at RET locus chromatin, facilitating transcription complex formation and RET expression.","method":"ChIP, RET mini-gene reporter system, deletion of HOXB5 binding site, histone modification analysis, TBP co-precipitation assay, in ovo chick embryo reporter","journal":"The international journal of biochemistry & cell biology","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods including ChIP, reporter assay, chromatin modification analysis, and in vivo validation","pmids":["24794774"],"is_preprint":false},{"year":2013,"finding":"Perturbation of Hoxb5 signaling in trunk and vagal neural crest cells causes Sox9 downregulation, NCC apoptosis, and multiple neurocristopathies. Hoxb5 directly binds and transactivates the Sox9 promoter in vitro and in vivo; Sox9 expression in ovo alleviates apoptosis induced by perturbed Hoxb5 signaling; ectopic Hoxb5 induces ectopic Sox9 in chick neural tube.","method":"Transgenic dominant-negative expression, Sox9 promoter ChIP and reporter assay in neuroblastoma cells, in ovo gain/loss-of-function, genetic epistasis with NCC-specific Sox9 deletion mice","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 2 — epistasis in vivo combined with ChIP and reporter assays; multiple orthogonal methods","pmids":["24141719"],"is_preprint":false},{"year":2014,"finding":"Hoxb5 directly binds and transactivates the Foxd3 promoter in neural crest-derived neuroblastoma cells. In vivo, Wnt1-Cre-mediated perturbation of Hoxb5 signaling causes Foxd3 downregulation in mouse embryos. In ovo, Hoxb5 induces ectopic Foxd3 in chick neural tube, and Foxd3 alleviates apoptosis induced by perturbed Hoxb5 signaling.","method":"Luciferase reporter assay, ChIP in brain/neural tube, in ovo gain/loss-of-function, mouse conditional perturbation","journal":"The international journal of biochemistry & cell biology","confidence":"High","confidence_rationale":"Tier 2 — ChIP in vivo, reporter assay, in ovo epistasis, and conditional mouse model","pmids":["25220476"],"is_preprint":false},{"year":2015,"finding":"HOXB5 directly binds the CTNNB1 (β-catenin) promoter and transcriptionally activates β-catenin expression in human gastric cancer cells, leading to upregulation of downstream targets cyclin D1 and c-Myc, and promoting invasion and migration. HOXB5 knockdown reduces β-catenin levels and invasive capacity.","method":"ChIP, luciferase reporter assay, siRNA knockdown, correlation analysis in patient tissues","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1-2 — ChIP and reporter assay with functional validation; identifies direct transcriptional target","pmids":["26467157"],"is_preprint":false},{"year":2018,"finding":"Hoxb5 reprograms pro-pre-B cells into functional T lymphocytes in vivo by repressing B cell master genes, activating T cell regulators, and modulating chromatin modifiers. Reprogramming begins in bone marrow and completes in thymus, generating T cells with normal transcriptomes, tissue distribution, and immunological function.","method":"Retroviral overexpression in pro-pre-B cells, transplantation into mice, transcriptome analysis, functional immunological assays","journal":"Nature immunology","confidence":"High","confidence_rationale":"Tier 2 — defined cellular reprogramming with transcriptome, functional, and lineage characterization; strong mechanistic evidence","pmids":["29434353"],"is_preprint":false},{"year":2018,"finding":"HOXB5 directly binds the EGFR promoter and transcriptionally activates EGFR expression in ER-positive breast cancer cells; HOXB5 promotes phosphorylation of EGFR and its downstream effectors; EGFR knockdown reverses HOXB5-induced invasion.","method":"ChIP, luciferase reporter assay, EGFR knockdown rescue experiment, western blot for phosphorylation","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1-2 — ChIP and reporter assay with functional epistasis via EGFR knockdown rescue","pmids":["30115380"],"is_preprint":false},{"year":2019,"finding":"HOXB5 directly binds the EGFR promoter and activates EGFR transcription in head and neck squamous cell carcinoma cells, consequently regulating the Akt/Wnt/β-catenin signaling axis; HOXB5 knockdown reduces proliferation, tumor growth, and EMT-associated protein expression in vitro and in vivo.","method":"ChIP, luciferase reporter assay, HOXB5 knockdown in cell lines and xenograft, western blot for pathway components","journal":"European journal of surgical oncology","confidence":"High","confidence_rationale":"Tier 1-2 — ChIP and reporter assay with in vivo xenograft validation","pmids":["31864826"],"is_preprint":false},{"year":2021,"finding":"HOXB5 transcriptionally activates CXCR4 and ITGB3 to promote colorectal cancer metastasis. CXCL12 upregulates HOXB5 through the ERK/ETS1 pathway, creating a positive feedback loop (CXCL12-HOXB5-CXCR4). AMD3100 (CXCR4 inhibitor) suppresses HOXB5-mediated metastasis.","method":"ChIP, luciferase reporter assay, siRNA knockdown, in vivo lung/liver metastasis models, pharmacological inhibition","journal":"Theranostics","confidence":"High","confidence_rationale":"Tier 1-2 — ChIP and reporter assay with multiple in vivo metastasis models and pharmacological validation","pmids":["33456563"],"is_preprint":false},{"year":2021,"finding":"HOXB5 transcriptionally regulates IL6 expression in glioma stem cells, promoting GSC proliferation via JAK2/STAT3 signaling. HOXB5 also transcriptionally activates SRSF1, which promotes circATP5B biogenesis; circATP5B sponges miR-185-5p to upregulate HOXB5, forming a positive feedback loop.","method":"ChIP, luciferase reporter assay, RNA-binding protein immunoprecipitation, RNA pulldown, neurosphere/limiting dilution assay","journal":"Journal of experimental & clinical cancer research","confidence":"High","confidence_rationale":"Tier 1-2 — ChIP and reporter assays plus RNA interaction assays with functional GSC proliferation readout","pmids":["33858489"],"is_preprint":false},{"year":2019,"finding":"In Tmem67 knockout mouse cerebella, HOXB5 protein levels are elevated and HOXB5 occupancy at the β-catenin promoter is significantly increased upon activation of canonical Wnt signaling; increased canonical Wnt signaling following loss of TMEM67 is dependent on HOXB5, linking HOXB5 to ciliary Wnt/β-catenin pathway regulation in cerebellar development.","method":"ChIP, western blot, Tmem67 knockout mouse model, transcriptome profiling","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP with defined mouse knockout model, but single lab study","pmids":["30931988"],"is_preprint":false},{"year":2013,"finding":"HoxB5 overexpression in endothelial cells increases expression of MCP-1 and IL-6 in vitro and in vivo; HoxB5-induced monocyte migration is antagonized by MCP-1 blocking antibody, indicating that HoxB5-driven vascular remodeling is mediated partly through MCP-1 and IL-6 upregulation and leucocyte infiltration.","method":"Adenoviral overexpression in mice (femoral artery ligation), proteome profiler array, MCP-1 blocking antibody experiment, immunohistochemistry","journal":"Cardiovascular research","confidence":"Medium","confidence_rationale":"Tier 2-3 — in vivo overexpression with proteome profiling and functional antibody blockade; single lab","pmids":["24189625"],"is_preprint":false},{"year":2016,"finding":"Hoxb5 expression marks long-term hematopoietic stem cells (LT-HSCs) specifically in mouse bone marrow; only Hoxb5+ HSCs exhibit long-term multi-lineage reconstitution in primary and secondary transplant recipients; in situ imaging shows >94% of Hoxb5+ (LT-HSCs) are directly attached to VE-cadherin+ (perivascular) cells, establishing a near-homogeneous perivascular niche.","method":"Endogenous reporter knock-in (tri-mCherry), prospective isolation, serial transplantation, in situ bone marrow imaging","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — endogenous reporter with functional reconstitution assay and in situ imaging; strong mechanistic evidence","pmids":["26863982"],"is_preprint":false},{"year":1997,"finding":"A HoxB5 epitope-specific antibody was used to immunopurify chromatin from mouse CNS; a 910 bp genomic fragment containing a consensus Antennapedia-like binding site was recovered, identified as the promoter of the SPI3 gene (serine protease inhibitor); SPI3 and HoxB5 show overlapping expression in CNS of E15 mouse embryos, suggesting SPI3 is a candidate direct target of HoxB5.","method":"Immunoaffinity chromatin purification, gel mobility shift assay, in situ hybridization","journal":"Brain research. Developmental brain research","confidence":"Low","confidence_rationale":"Tier 3 — single method (immunoaffinity pulldown) without ChIP-grade specificity; no functional validation of transcriptional activation","pmids":["9174240"],"is_preprint":false},{"year":2000,"finding":"Hoxb5 protein levels in developing mouse lung are regulated by retinoic acid (upregulation) and antisense oligonucleotide knockdown; RA increases branching with elongated primary branches, while Hoxb5 antisense decreases both primary and secondary branching, demonstrating that regional and quantitative Hoxb5 expression controls early airway morphogenesis.","method":"Antisense oligonucleotide knockdown, RA treatment of embryonic lung cultures, immunohistochemistry, western blot, morphometric branching analysis","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 — direct protein manipulation in ex vivo organ culture with quantitative morphological readout","pmids":["10913834"],"is_preprint":false},{"year":2013,"finding":"Hoxa5 and Hoxb5 display partial functional redundancy during mouse lung morphogenesis; Hoxa5;Hoxb5 compound mutants carrying four mutated alleles exhibit aggravated lung phenotype (death at birth) compared to single mutants, with Hoxb5 contributing to branching morphogenesis, goblet cell specification, and postnatal air space structure.","method":"Compound knockout mouse genetics, morphological and histological phenotyping, genetic complementation analysis","journal":"American journal of physiology. Lung cellular and molecular physiology","confidence":"High","confidence_rationale":"Tier 2 — classical genetic epistasis through compound knockout with specific morphological and cellular phenotype readouts","pmids":["23585229"],"is_preprint":false},{"year":1995,"finding":"Targeted disruption of hoxb-5 in mice causes a rostral shift of the shoulder girdle (analogous to human Sprengel anomaly), establishing a role for hoxb-5 in specifying limb position along the anteroposterior axis. hoxb-5/hoxb-6 transheterozygotes exhibit anteriorizing homeotic transformation of cervicothoracic vertebrae (C6–T1), demonstrating nonallelic noncomplementation and that hoxb-5 and hoxb-6 function together to specify this region.","method":"Gene targeting (knockout) in mice, skeletal phenotype analysis, genetic complementation test (transheterozygotes)","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 — clean knockout with specific skeletal phenotype; genetic epistasis via transheterozygote analysis","pmids":["7828847"],"is_preprint":false},{"year":2022,"finding":"HOXB5 directly transcriptionally activates ANGPT2 (angiopoietin-2) in esophageal cancer cells; HOXB5-activated ANGPT2 promotes proliferation, migration, invasion, and angiogenesis via the ERK/AKT signaling pathway; HOXB5 overexpression reverses the effects of ANGPT2 silencing.","method":"ChIP, luciferase reporter assay, siRNA knockdown, HOXB5 overexpression rescue, tube formation assay, western blot for ERK/AKT pathway","journal":"Experimental and therapeutic medicine","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP and reporter assay with functional rescue; single lab","pmids":["35949323"],"is_preprint":false},{"year":2024,"finding":"SUMOylation of CARD9 (mediated by PIAS3) promotes CARD9 binding to HOXB5 and inhibits HOXB5 O-GlcNAc glycosylation, which is required for HOXB5 nuclear translocation. Dissociation of CARD9 from HOXB5 (via PIAS3 knockdown) allows O-GlcNAc glycosylation of HOXB5 and subsequent nuclear translocation, where HOXB5 transcriptionally activates Parkin to promote mitophagy and attenuate myocardial I/R injury.","method":"Co-immunoprecipitation, PIAS3 knockdown, CARD9 SUMOylation assay, O-GlcNAc modification assay, nuclear fractionation, luciferase reporter for Parkin","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP and modification assays with functional outcome; single lab, novel post-translational mechanism","pmids":["39496070"],"is_preprint":false}],"current_model":"HOXB5 is a homeodomain transcription factor that binds DNA cooperatively (regulated by redox state via a specific homeodomain cysteine), directly transactivates multiple target genes including FLK1/VEGFR2, RET, SOX9, FOXD3, β-catenin (CTNNB1), EGFR, ANGPT2, ANGIOPOIETIN-2, IL6, and N-CAM in a context-dependent manner, cooperates with cofactors such as NKX2-1 synergistically; regulates neural crest cell survival, migration, and fate specification (via RET, SOX9, FOXD3), controls vascular endothelial differentiation and angiogenesis, directs lung branching morphogenesis, marks long-term hematopoietic stem cells in the bone marrow perivascular niche, and can reprogram B cells into functional T lymphocytes, while its nuclear translocation is regulated post-translationally by CARD9 SUMOylation-dependent inhibition of O-GlcNAc glycosylation."},"narrative":{"teleology":[{"year":1992,"claim":"Identifying HOXB5 as a transcriptional activator of specific downstream genes established that individual HOX proteins regulate distinct adhesion-molecule targets, not just axial identity.","evidence":"Cotransfection reporter assay showing HOXB5 transactivates N-CAM promoter through a specific binding site, antagonized by HOXB4, in NIH 3T3 cells","pmids":["1347944"],"confidence":"High","gaps":["Endogenous chromatin context not tested","N-CAM regulation not validated in vivo","Mechanism of HOXB4 antagonism undefined"]},{"year":1993,"claim":"Demonstrating cooperative DNA binding regulated by a redox-sensitive cysteine revealed a distinctive biochemical property that distinguishes HOXB5 from most other homeodomain proteins and from Fos/Jun-type transcription factors.","evidence":"In vitro DNA binding with mutagenesis showing cooperative binding at tandem sites requires N-terminal domain and is enhanced by oxidation of Cys in helix 2-3 turn","pmids":["8101633"],"confidence":"High","gaps":["In vivo relevance of redox regulation untested","Structural basis of oxidation-enhanced cooperativity unknown","Identity of physiological redox signals unclear"]},{"year":1995,"claim":"Knockout mice established that HOXB5 specifies axial position of the shoulder girdle and cooperates with HOXB6 in cervicothoracic vertebral identity, resolving its developmental patterning role.","evidence":"Gene targeting in mice producing rostral shoulder girdle shift; HOXB5/HOXB6 transheterozygotes show homeotic vertebral transformation","pmids":["7828847"],"confidence":"High","gaps":["Downstream transcriptional targets mediating skeletal phenotype unknown","Single versus redundant function with paralogous group 5 Hox genes not fully resolved"]},{"year":2000,"claim":"Ex vivo lung culture experiments showed that HOXB5 protein levels, regulated by retinoic acid, quantitatively control airway branching morphogenesis, extending its role beyond skeletal patterning.","evidence":"Antisense knockdown and RA treatment in embryonic mouse lung explants with morphometric analysis","pmids":["10913834"],"confidence":"Medium","gaps":["Antisense approach lacks genetic specificity","Direct transcriptional targets in lung not identified","Interaction with RA signaling pathway not molecularly defined"]},{"year":2003,"claim":"Identification of FLK1/VEGFR2 as a direct HOXB5 target linked HOXB5 to vascular endothelial specification, explaining how a HOX transcription factor can instruct angioblast fate.","evidence":"Yeast one-hybrid identification of intronic HOXB5-binding element, reporter assays, and embryoid body overexpression expanding flk1+ angioblasts","pmids":["12897140"],"confidence":"High","gaps":["Loss-of-function in endothelial lineage not performed","Sufficiency versus necessity not distinguished in vivo"]},{"year":2008,"claim":"Demonstrating that HOXB5 directly activates RET in vagal neural crest cells, with dominant-negative HOXB5 causing hypoganglionosis, established a transcriptional hierarchy controlling enteric nervous system colonization.","evidence":"Dominant-negative transgenic mice with reduced Ret, impaired NCC migration, and gut hypoganglionosis; Ret reporter activation in neuroblastoma cells","pmids":["18395091"],"confidence":"High","gaps":["Full knockout of HOXB5 in NCC lineage not reported at this time","Relationship to Hirschsprung disease causation in humans not established"]},{"year":2009,"claim":"Showing HOXB5 transcriptionally activates angiopoietin-2 and that Tie-2 blockade abolishes HOXB5-driven sprouting angiogenesis defined the downstream effector pathway for HOXB5 in vascular remodeling.","evidence":"HUVEC spheroid sprouting, CAM assay, Ang2 promoter reporter, and soluble Tie-2 functional blockade","pmids":["19403561"],"confidence":"High","gaps":["Endogenous HOXB5 loss-of-function in endothelium not tested","Relative contribution of Ang2 versus FLK1 to HOXB5 angiogenic function unclear"]},{"year":2011,"claim":"ChIP and co-immunoprecipitation revealed that HOXB5 and NKX2-1 form a protein complex that synergistically activates RET, and that Hirschsprung-associated SNPs at the NKX2-1 site abolish this synergism, providing a molecular mechanism for disease-associated regulatory variation.","evidence":"ChIP, co-IP, and luciferase reporter with SNP analysis in RET promoter","pmids":["21677782"],"confidence":"High","gaps":["Crystal structure of HOXB5–NKX2-1 complex unavailable","Functional consequence of SNP on enteric NCC development not shown in vivo"]},{"year":2013,"claim":"Identification of SOX9 and FOXD3 as direct HOXB5 transcriptional targets in neural crest cells, with genetic epistasis showing rescue of apoptosis, built a HOXB5→SOX9/FOXD3 survival circuit governing NCC fate.","evidence":"ChIP, reporter assays, in ovo gain/loss-of-function, and compound mutant mouse analysis for SOX9 (2013) and FOXD3 (2014)","pmids":["24141719","25220476"],"confidence":"High","gaps":["Whether SOX9 and FOXD3 are independent or epistatic downstream of HOXB5 is unclear","NCC-specific HOXB5 conditional knockout not reported"]},{"year":2013,"claim":"Compound Hoxa5;Hoxb5 knockout mice revealed functional redundancy in lung morphogenesis, with lethality demonstrating that HOXB5 contributes non-redundantly to branching, goblet cell specification, and postnatal lung structure.","evidence":"Compound knockout mouse genetics with histological and morphological phenotyping","pmids":["23585229"],"confidence":"High","gaps":["Direct transcriptional targets mediating lung phenotype not identified","Cell-type-specific contributions of HOXB5 in lung epithelium versus mesenchyme unknown"]},{"year":2016,"claim":"An endogenous knock-in reporter demonstrated that Hoxb5 expression exclusively marks long-term HSCs in bone marrow, with >94% residing in a perivascular niche, redefining the HSC identity marker landscape.","evidence":"Tri-mCherry knock-in reporter at Hoxb5 locus, prospective isolation, serial transplantation, in situ imaging","pmids":["26863982"],"confidence":"High","gaps":["Whether HOXB5 is functionally required for HSC self-renewal is unknown","Mechanism by which HOXB5 expression is restricted to LT-HSCs not defined"]},{"year":2018,"claim":"HOXB5 overexpression was shown to reprogram pro-pre-B cells into functional T lymphocytes by repressing B-cell genes and activating T-cell regulators, revealing an unexpected lineage-reprogramming capacity.","evidence":"Retroviral HOXB5 overexpression, transplantation, transcriptome analysis, and functional immunological assays in mice","pmids":["29434353"],"confidence":"High","gaps":["Direct chromatin targets mediating B-to-T reprogramming not comprehensively mapped","Whether endogenous HOXB5 levels influence normal lymphoid lineage decisions is untested"]},{"year":2015,"claim":"Identifying CTNNB1 and EGFR as direct HOXB5 targets in cancer cells linked HOXB5 transcriptional activity to oncogenic signaling through Wnt/β-catenin and EGFR pathways, extending its role beyond development.","evidence":"ChIP and reporter assays in gastric cancer (CTNNB1) and breast/HNSCC (EGFR) cells with knockdown rescue","pmids":["26467157","30115380","31864826"],"confidence":"High","gaps":["Whether HOXB5 activates these targets in normal adult tissues is unknown","Genome-wide target landscape in cancer not defined by unbiased approaches"]},{"year":2021,"claim":"Discovery of HOXB5-driven positive feedback loops (CXCL12→HOXB5→CXCR4 in colorectal cancer; circATP5B→miR-185-5p→HOXB5 in glioma) revealed that HOXB5 expression is itself amplified through feed-forward circuits in malignancy.","evidence":"ChIP, reporter assays, RNA pulldown, RIP, and in vivo metastasis models with pharmacological inhibition (AMD3100)","pmids":["33456563","33858489"],"confidence":"High","gaps":["Relevance of these feedback loops in non-cancer contexts unknown","Therapeutic targeting of HOXB5 itself not explored"]},{"year":2024,"claim":"A novel post-translational regulatory mechanism was uncovered in which CARD9 SUMOylation inhibits HOXB5 O-GlcNAc glycosylation and nuclear translocation, linking innate immune adaptor signaling to HOXB5 transcriptional activity.","evidence":"Co-IP, SUMOylation and O-GlcNAc assays, nuclear fractionation, Parkin reporter, in cardiomyocyte ischemia-reperfusion model","pmids":["39496070"],"confidence":"Medium","gaps":["Single-lab finding not independently replicated","Sites of O-GlcNAc modification on HOXB5 not mapped","Generality beyond cardiomyocyte I/R context unknown"]},{"year":null,"claim":"Key open questions include whether HOXB5 is functionally required for LT-HSC self-renewal, the genome-wide direct target landscape by unbiased ChIP-seq, the structural basis of redox-regulated cooperative DNA binding, and the physiological significance of CARD9-mediated post-translational regulation of HOXB5 nuclear entry.","evidence":"","pmids":[],"confidence":"High","gaps":["No conditional knockout in HSCs reported","No genome-wide binding profile (ChIP-seq) published","No structural model of HOXB5 homeodomain cooperativity","CARD9–HOXB5 axis awaits independent confirmation"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,1,2,5,6,7,8,9,11,13,14]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[1,2,4,5,7,8,9,11,13,14]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,5,6,23]}],"pathway":[{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[4,7,8,19,20,21]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[1,2,5,6,9,11,14]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3,9,12,13,15,22]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[10,17]}],"complexes":[],"partners":["NKX2-1","CARD9","HOXB6","HOXA5"],"other_free_text":[]},"mechanistic_narrative":"HOXB5 is a homeodomain transcription factor that directs cell fate specification and tissue morphogenesis across multiple developmental and adult contexts, including axial patterning, neural crest survival and migration, vascular endothelial differentiation, lung branching morphogenesis, and hematopoietic stem cell identity. It binds DNA cooperatively at tandem sites through a homeodomain-adjacent N-terminal domain, with cooperativity regulated by a redox-sensitive cysteine between homeodomain helices 2 and 3 [PMID:8101633]; direct transcriptional targets include FLK1/VEGFR2 [PMID:12897140], RET (synergistically with NKX2-1) [PMID:21677782, PMID:24794774], SOX9 [PMID:24141719], FOXD3 [PMID:25220476], CTNNB1 [PMID:26467157], EGFR [PMID:30115380], ANGPT2 [PMID:19403561], IL6 [PMID:33858489], and CXCR4 [PMID:33456563]. In vivo, Hoxb5 knockout causes rostral homeotic shifts of the shoulder girdle and, in compound mutants with Hoxa5, lethal lung branching defects [PMID:7828847, PMID:23585229]; Hoxb5 marks long-term hematopoietic stem cells in a perivascular bone marrow niche and can reprogram B-lineage cells into functional T lymphocytes [PMID:26863982, PMID:29434353]. Nuclear translocation of HOXB5 is regulated post-translationally by CARD9 SUMOylation-dependent inhibition of O-GlcNAc glycosylation [PMID:39496070]."},"prefetch_data":{"uniprot":{"accession":"P09067","full_name":"Homeobox protein Hox-B5","aliases":["Homeobox protein HHO.C10","Homeobox protein Hox-2A","Homeobox protein Hu-1"],"length_aa":269,"mass_kda":29.4,"function":"Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/P09067/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/HOXB5","classification":"Not 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practice","url":"https://pubmed.ncbi.nlm.nih.gov/34118725","citation_count":15,"is_preprint":false},{"pmid":"34497766","id":"PMC_34497766","title":"LncRNA DCST1-AS1 Promotes Endometrial Cancer Progression by Modulating the MiR-665/HOXB5 and MiR-873-5p/CADM1 Pathways.","date":"2021","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34497766","citation_count":15,"is_preprint":false},{"pmid":"33418191","id":"PMC_33418191","title":"Hoxb5 defines the heterogeneity of self-renewal capacity in the hematopoietic stem cell compartment.","date":"2021","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/33418191","citation_count":14,"is_preprint":false},{"pmid":"8097725","id":"PMC_8097725","title":"Induction of HOX-2 genes in P19 embryocarcinoma cells is dependent on retinoic acid receptor alpha.","date":"1993","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/8097725","citation_count":13,"is_preprint":false},{"pmid":"35170372","id":"PMC_35170372","title":"Circ_0020123 enhances the cisplatin resistance in non-small cell lung cancer cells partly by sponging miR-140-3p to regulate homeobox B5 (HOXB5).","date":"2022","source":"Bioengineered","url":"https://pubmed.ncbi.nlm.nih.gov/35170372","citation_count":12,"is_preprint":false},{"pmid":"32796404","id":"PMC_32796404","title":"HOXB5 promotes proliferation, migration, and invasion of pancreatic cancer cell through the activation of the GSK3β/β-catenin pathway.","date":"2020","source":"Anti-cancer drugs","url":"https://pubmed.ncbi.nlm.nih.gov/32796404","citation_count":11,"is_preprint":false},{"pmid":"1349742","id":"PMC_1349742","title":"The murine Hox-2.4 promoter contains a functional octamer motif.","date":"1992","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/1349742","citation_count":11,"is_preprint":false},{"pmid":"16051213","id":"PMC_16051213","title":"Ets identified as a trans-regulatory factor of amphioxus Hox2 by transgenic analysis using ascidian embryos.","date":"2005","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/16051213","citation_count":10,"is_preprint":false},{"pmid":"2907403","id":"PMC_2907403","title":"Restriction fragment length polymorphism and chromosome mapping of a mouse homeo box gene, Hox-2.1.","date":"1988","source":"Biochemical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/2907403","citation_count":10,"is_preprint":false},{"pmid":"31115501","id":"PMC_31115501","title":"MicroRNA-625 inhibits the progression of non‑small cell lung cancer by directly targeting HOXB5 and deactivating the Wnt/β-catenin pathway.","date":"2019","source":"International journal of molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/31115501","citation_count":10,"is_preprint":false},{"pmid":"35847904","id":"PMC_35847904","title":"miR-200a-3p- and miR-181-5p-Mediated HOXB5 Upregulation Promotes HCC Progression by Transcriptional Activation of EGFR.","date":"2022","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/35847904","citation_count":9,"is_preprint":false},{"pmid":"31876226","id":"PMC_31876226","title":"HOXB5 promotes malignant progression in pancreatic cancer via the miR-6732 pathway.","date":"2019","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/31876226","citation_count":9,"is_preprint":false},{"pmid":"24078914","id":"PMC_24078914","title":"Regulatory interactions between androgens, Hoxb5, and TGF β signaling in murine lung development.","date":"2013","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/24078914","citation_count":9,"is_preprint":false},{"pmid":"16870358","id":"PMC_16870358","title":"Developmental methylation of the regulatory region of HoxB5 gene in mouse correlates with its tissue-specific expression.","date":"2006","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/16870358","citation_count":9,"is_preprint":false},{"pmid":"9174240","id":"PMC_9174240","title":"A target of the HoxB5 gene from the mouse nervous system.","date":"1997","source":"Brain research. Developmental brain research","url":"https://pubmed.ncbi.nlm.nih.gov/9174240","citation_count":8,"is_preprint":false},{"pmid":"25220476","id":"PMC_25220476","title":"Homeobox b5 (Hoxb5) regulates the expression of Forkhead box D3 gene (Foxd3) in neural crest.","date":"2014","source":"The international journal of biochemistry & cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/25220476","citation_count":7,"is_preprint":false},{"pmid":"39496070","id":"PMC_39496070","title":"CARD9 protein SUMOylation regulates HOXB5 nuclear translocation and Parkin-mediated mitophagy in myocardial I/R injury.","date":"2024","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/39496070","citation_count":7,"is_preprint":false},{"pmid":"21228548","id":"PMC_21228548","title":"Overexpression of HOXB5, cyclin D1 and PCNA in congenital cystic adenomatoid malformation.","date":"2011","source":"Fetal diagnosis and therapy","url":"https://pubmed.ncbi.nlm.nih.gov/21228548","citation_count":7,"is_preprint":false},{"pmid":"32319550","id":"PMC_32319550","title":"Long non‑coding RNA PRNCR1 exerts oncogenic effects in tongue squamous cell carcinoma in vitro and in vivo by sponging microRNA‑944 and thereby increasing HOXB5 expression.","date":"2020","source":"International journal of molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/32319550","citation_count":7,"is_preprint":false},{"pmid":"35949323","id":"PMC_35949323","title":"HOXB5-activated ANGPT2 promotes the proliferation, migration, invasion and angiogenic effect of esophageal cancer cells via activating ERK/AKT signaling pathway.","date":"2022","source":"Experimental and therapeutic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35949323","citation_count":6,"is_preprint":false},{"pmid":"7890121","id":"PMC_7890121","title":"The 5'-sequence of the murine Hox-b3 (Hox-2.7) gene and its intron contain multiple transcription-regulatory elements.","date":"1994","source":"The International journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/7890121","citation_count":6,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":47957,"output_tokens":6212,"usd":0.118526},"stage2":{"model":"claude-opus-4-6","input_tokens":9803,"output_tokens":3860,"usd":0.218273},"total_usd":0.336799,"stage1_batch_id":"msgbatch_01DzrsgVgYngY1hvM3DU1yF2","stage2_batch_id":"msgbatch_01KA9b7iRzKFdhoBUT7vCvSe","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1993,\n      \"finding\": \"The human HoxB5 protein binds DNA in a sequence-specific manner; cooperative DNA binding to tandem sites is stabilized by at least 100-fold relative to a single site and requires a small domain adjacent to the homeodomain on the amino-terminal side. Cooperative binding is under redox regulation: a cysteine residue in the turn between homeodomain helices 2 and 3 is necessary for cooperativity, and oxidation of HoxB5 enhances (rather than inhibits) cooperative DNA binding, opposite to the redox regulation of Fos, Jun, and other transcription factors.\",\n      \"method\": \"In vitro DNA binding assays, mutational analysis of cysteine residues, domain deletion experiments\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with mutagenesis identifying specific residue and domain requirements\",\n      \"pmids\": [\"8101633\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"HoxB5 (Hox-2.5) transactivates the mouse N-CAM gene promoter through a specific homeodomain binding site (site II) in cotransfection assays; the adjacent HoxB4 (Hox-2.4) protein antagonizes this activation, demonstrating that two adjacent Hox gene products can differentially regulate a downstream cell adhesion molecule gene.\",\n      \"method\": \"Cotransfection/reporter gene assay (CAT) in NIH 3T3 cells, mutational analysis of homeodomain binding sites\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — functional promoter reporter assay with mutational validation of binding site; identifies N-CAM as downstream target\",\n      \"pmids\": [\"1347944\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"HoxB5 acts as an upstream transcriptional activator of flk1 (VEGFR2/KDR) in endothelial precursor differentiation. A cis-acting element in the first intron of flk1 (HoxB5-binding element, HBE) is required for endothelium-dependent expression; HoxB5 binds this element (identified by yeast one-hybrid), transactivates the flk1 promoter in an HBE-dependent fashion, and overexpression of HoxB5 expands flk1+ angioblasts and increases PECAM+ primitive blood vessels in embryoid bodies.\",\n      \"method\": \"Yeast one-hybrid screen, transient transfection reporter assay, overexpression in embryoid bodies, transgenic reporter assay\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods: yeast one-hybrid, reporter assay, and in vivo embryoid body overexpression with specific phenotypic readout\",\n      \"pmids\": [\"12897140\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"HoxB5 promotes endothelial cell sprouting in vitro and modifies intussusceptive angiogenesis in vivo; HoxB5 overexpression upregulates angiopoietin-2 (Ang2) transcriptionally, and the HoxB5-induced sprouting effect is abolished by soluble Tie-2 (angiopoietin antagonist), placing Ang2 as a functional downstream mediator.\",\n      \"method\": \"HUVEC spheroid sprouting assay, chick chorioallantoic membrane assay, luciferase reporter assay for Ang2 promoter, soluble Tie-2 functional blockade\",\n      \"journal\": \"Cardiovascular research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — reporter assay + in vitro and in vivo functional assays with pathway blockade\",\n      \"pmids\": [\"19403561\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Hoxb5 acts as a transcriptional activator upstream of Ret in vagal neural crest cells; a dominant-negative Hoxb5 (enb5, fused to Engrailed repressor domain) in vagal NCCs reduces Ret expression, impairs NCC migration to distal intestine, and causes hypoganglionosis. Hoxb5 directly induces Ret transcription in neuroblastoma cells.\",\n      \"method\": \"Transgenic dominant-negative expression in mice, in vitro Ret reporter assay in neuroblastoma cells, histological analysis of ganglia\",\n      \"journal\": \"Gastroenterology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — dominant-negative epistasis in vivo combined with in vitro transcriptional assay; replicated by subsequent studies\",\n      \"pmids\": [\"18395091\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"HOXB5 directly binds the promoter region upstream of the NKX2-1 binding site in the RET gene and transactivates RET expression. HOXB5 and NKX2-1 form a protein complex and synergistically activate RET transcription; HSCR-associated SNPs at the NKX2-1 binding site abolish this synergism. HOXB5 cooperates additively (not synergistically) with SOX10, PAX3, and PHOX2B in RET transactivation.\",\n      \"method\": \"Chromatin immunoprecipitation, luciferase reporter assay, co-immunoprecipitation (protein complex), promoter deletion analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — ChIP, Co-IP, and reporter assays with multiple binding partners; mechanistic detail on synergistic vs. additive cooperativity\",\n      \"pmids\": [\"21677782\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"HOXB5 binds to a multi-species conserved sequence (MCS+9.7) in the first intron of the RET gene and enhances RET transcription in an MCS+9.7-dependent manner. HOXB5 binding to MCS+9.7 alters chromatin conformation and induces histone H3K4 trimethylation at RET locus chromatin, facilitating transcription complex formation and RET expression.\",\n      \"method\": \"ChIP, RET mini-gene reporter system, deletion of HOXB5 binding site, histone modification analysis, TBP co-precipitation assay, in ovo chick embryo reporter\",\n      \"journal\": \"The international journal of biochemistry & cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods including ChIP, reporter assay, chromatin modification analysis, and in vivo validation\",\n      \"pmids\": [\"24794774\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Perturbation of Hoxb5 signaling in trunk and vagal neural crest cells causes Sox9 downregulation, NCC apoptosis, and multiple neurocristopathies. Hoxb5 directly binds and transactivates the Sox9 promoter in vitro and in vivo; Sox9 expression in ovo alleviates apoptosis induced by perturbed Hoxb5 signaling; ectopic Hoxb5 induces ectopic Sox9 in chick neural tube.\",\n      \"method\": \"Transgenic dominant-negative expression, Sox9 promoter ChIP and reporter assay in neuroblastoma cells, in ovo gain/loss-of-function, genetic epistasis with NCC-specific Sox9 deletion mice\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — epistasis in vivo combined with ChIP and reporter assays; multiple orthogonal methods\",\n      \"pmids\": [\"24141719\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Hoxb5 directly binds and transactivates the Foxd3 promoter in neural crest-derived neuroblastoma cells. In vivo, Wnt1-Cre-mediated perturbation of Hoxb5 signaling causes Foxd3 downregulation in mouse embryos. In ovo, Hoxb5 induces ectopic Foxd3 in chick neural tube, and Foxd3 alleviates apoptosis induced by perturbed Hoxb5 signaling.\",\n      \"method\": \"Luciferase reporter assay, ChIP in brain/neural tube, in ovo gain/loss-of-function, mouse conditional perturbation\",\n      \"journal\": \"The international journal of biochemistry & cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ChIP in vivo, reporter assay, in ovo epistasis, and conditional mouse model\",\n      \"pmids\": [\"25220476\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"HOXB5 directly binds the CTNNB1 (β-catenin) promoter and transcriptionally activates β-catenin expression in human gastric cancer cells, leading to upregulation of downstream targets cyclin D1 and c-Myc, and promoting invasion and migration. HOXB5 knockdown reduces β-catenin levels and invasive capacity.\",\n      \"method\": \"ChIP, luciferase reporter assay, siRNA knockdown, correlation analysis in patient tissues\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — ChIP and reporter assay with functional validation; identifies direct transcriptional target\",\n      \"pmids\": [\"26467157\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Hoxb5 reprograms pro-pre-B cells into functional T lymphocytes in vivo by repressing B cell master genes, activating T cell regulators, and modulating chromatin modifiers. Reprogramming begins in bone marrow and completes in thymus, generating T cells with normal transcriptomes, tissue distribution, and immunological function.\",\n      \"method\": \"Retroviral overexpression in pro-pre-B cells, transplantation into mice, transcriptome analysis, functional immunological assays\",\n      \"journal\": \"Nature immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — defined cellular reprogramming with transcriptome, functional, and lineage characterization; strong mechanistic evidence\",\n      \"pmids\": [\"29434353\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"HOXB5 directly binds the EGFR promoter and transcriptionally activates EGFR expression in ER-positive breast cancer cells; HOXB5 promotes phosphorylation of EGFR and its downstream effectors; EGFR knockdown reverses HOXB5-induced invasion.\",\n      \"method\": \"ChIP, luciferase reporter assay, EGFR knockdown rescue experiment, western blot for phosphorylation\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — ChIP and reporter assay with functional epistasis via EGFR knockdown rescue\",\n      \"pmids\": [\"30115380\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"HOXB5 directly binds the EGFR promoter and activates EGFR transcription in head and neck squamous cell carcinoma cells, consequently regulating the Akt/Wnt/β-catenin signaling axis; HOXB5 knockdown reduces proliferation, tumor growth, and EMT-associated protein expression in vitro and in vivo.\",\n      \"method\": \"ChIP, luciferase reporter assay, HOXB5 knockdown in cell lines and xenograft, western blot for pathway components\",\n      \"journal\": \"European journal of surgical oncology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — ChIP and reporter assay with in vivo xenograft validation\",\n      \"pmids\": [\"31864826\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"HOXB5 transcriptionally activates CXCR4 and ITGB3 to promote colorectal cancer metastasis. CXCL12 upregulates HOXB5 through the ERK/ETS1 pathway, creating a positive feedback loop (CXCL12-HOXB5-CXCR4). AMD3100 (CXCR4 inhibitor) suppresses HOXB5-mediated metastasis.\",\n      \"method\": \"ChIP, luciferase reporter assay, siRNA knockdown, in vivo lung/liver metastasis models, pharmacological inhibition\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — ChIP and reporter assay with multiple in vivo metastasis models and pharmacological validation\",\n      \"pmids\": [\"33456563\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"HOXB5 transcriptionally regulates IL6 expression in glioma stem cells, promoting GSC proliferation via JAK2/STAT3 signaling. HOXB5 also transcriptionally activates SRSF1, which promotes circATP5B biogenesis; circATP5B sponges miR-185-5p to upregulate HOXB5, forming a positive feedback loop.\",\n      \"method\": \"ChIP, luciferase reporter assay, RNA-binding protein immunoprecipitation, RNA pulldown, neurosphere/limiting dilution assay\",\n      \"journal\": \"Journal of experimental & clinical cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — ChIP and reporter assays plus RNA interaction assays with functional GSC proliferation readout\",\n      \"pmids\": [\"33858489\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In Tmem67 knockout mouse cerebella, HOXB5 protein levels are elevated and HOXB5 occupancy at the β-catenin promoter is significantly increased upon activation of canonical Wnt signaling; increased canonical Wnt signaling following loss of TMEM67 is dependent on HOXB5, linking HOXB5 to ciliary Wnt/β-catenin pathway regulation in cerebellar development.\",\n      \"method\": \"ChIP, western blot, Tmem67 knockout mouse model, transcriptome profiling\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP with defined mouse knockout model, but single lab study\",\n      \"pmids\": [\"30931988\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"HoxB5 overexpression in endothelial cells increases expression of MCP-1 and IL-6 in vitro and in vivo; HoxB5-induced monocyte migration is antagonized by MCP-1 blocking antibody, indicating that HoxB5-driven vascular remodeling is mediated partly through MCP-1 and IL-6 upregulation and leucocyte infiltration.\",\n      \"method\": \"Adenoviral overexpression in mice (femoral artery ligation), proteome profiler array, MCP-1 blocking antibody experiment, immunohistochemistry\",\n      \"journal\": \"Cardiovascular research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — in vivo overexpression with proteome profiling and functional antibody blockade; single lab\",\n      \"pmids\": [\"24189625\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Hoxb5 expression marks long-term hematopoietic stem cells (LT-HSCs) specifically in mouse bone marrow; only Hoxb5+ HSCs exhibit long-term multi-lineage reconstitution in primary and secondary transplant recipients; in situ imaging shows >94% of Hoxb5+ (LT-HSCs) are directly attached to VE-cadherin+ (perivascular) cells, establishing a near-homogeneous perivascular niche.\",\n      \"method\": \"Endogenous reporter knock-in (tri-mCherry), prospective isolation, serial transplantation, in situ bone marrow imaging\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — endogenous reporter with functional reconstitution assay and in situ imaging; strong mechanistic evidence\",\n      \"pmids\": [\"26863982\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"A HoxB5 epitope-specific antibody was used to immunopurify chromatin from mouse CNS; a 910 bp genomic fragment containing a consensus Antennapedia-like binding site was recovered, identified as the promoter of the SPI3 gene (serine protease inhibitor); SPI3 and HoxB5 show overlapping expression in CNS of E15 mouse embryos, suggesting SPI3 is a candidate direct target of HoxB5.\",\n      \"method\": \"Immunoaffinity chromatin purification, gel mobility shift assay, in situ hybridization\",\n      \"journal\": \"Brain research. Developmental brain research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single method (immunoaffinity pulldown) without ChIP-grade specificity; no functional validation of transcriptional activation\",\n      \"pmids\": [\"9174240\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Hoxb5 protein levels in developing mouse lung are regulated by retinoic acid (upregulation) and antisense oligonucleotide knockdown; RA increases branching with elongated primary branches, while Hoxb5 antisense decreases both primary and secondary branching, demonstrating that regional and quantitative Hoxb5 expression controls early airway morphogenesis.\",\n      \"method\": \"Antisense oligonucleotide knockdown, RA treatment of embryonic lung cultures, immunohistochemistry, western blot, morphometric branching analysis\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct protein manipulation in ex vivo organ culture with quantitative morphological readout\",\n      \"pmids\": [\"10913834\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Hoxa5 and Hoxb5 display partial functional redundancy during mouse lung morphogenesis; Hoxa5;Hoxb5 compound mutants carrying four mutated alleles exhibit aggravated lung phenotype (death at birth) compared to single mutants, with Hoxb5 contributing to branching morphogenesis, goblet cell specification, and postnatal air space structure.\",\n      \"method\": \"Compound knockout mouse genetics, morphological and histological phenotyping, genetic complementation analysis\",\n      \"journal\": \"American journal of physiology. Lung cellular and molecular physiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — classical genetic epistasis through compound knockout with specific morphological and cellular phenotype readouts\",\n      \"pmids\": [\"23585229\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"Targeted disruption of hoxb-5 in mice causes a rostral shift of the shoulder girdle (analogous to human Sprengel anomaly), establishing a role for hoxb-5 in specifying limb position along the anteroposterior axis. hoxb-5/hoxb-6 transheterozygotes exhibit anteriorizing homeotic transformation of cervicothoracic vertebrae (C6–T1), demonstrating nonallelic noncomplementation and that hoxb-5 and hoxb-6 function together to specify this region.\",\n      \"method\": \"Gene targeting (knockout) in mice, skeletal phenotype analysis, genetic complementation test (transheterozygotes)\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean knockout with specific skeletal phenotype; genetic epistasis via transheterozygote analysis\",\n      \"pmids\": [\"7828847\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"HOXB5 directly transcriptionally activates ANGPT2 (angiopoietin-2) in esophageal cancer cells; HOXB5-activated ANGPT2 promotes proliferation, migration, invasion, and angiogenesis via the ERK/AKT signaling pathway; HOXB5 overexpression reverses the effects of ANGPT2 silencing.\",\n      \"method\": \"ChIP, luciferase reporter assay, siRNA knockdown, HOXB5 overexpression rescue, tube formation assay, western blot for ERK/AKT pathway\",\n      \"journal\": \"Experimental and therapeutic medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP and reporter assay with functional rescue; single lab\",\n      \"pmids\": [\"35949323\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SUMOylation of CARD9 (mediated by PIAS3) promotes CARD9 binding to HOXB5 and inhibits HOXB5 O-GlcNAc glycosylation, which is required for HOXB5 nuclear translocation. Dissociation of CARD9 from HOXB5 (via PIAS3 knockdown) allows O-GlcNAc glycosylation of HOXB5 and subsequent nuclear translocation, where HOXB5 transcriptionally activates Parkin to promote mitophagy and attenuate myocardial I/R injury.\",\n      \"method\": \"Co-immunoprecipitation, PIAS3 knockdown, CARD9 SUMOylation assay, O-GlcNAc modification assay, nuclear fractionation, luciferase reporter for Parkin\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP and modification assays with functional outcome; single lab, novel post-translational mechanism\",\n      \"pmids\": [\"39496070\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"HOXB5 is a homeodomain transcription factor that binds DNA cooperatively (regulated by redox state via a specific homeodomain cysteine), directly transactivates multiple target genes including FLK1/VEGFR2, RET, SOX9, FOXD3, β-catenin (CTNNB1), EGFR, ANGPT2, ANGIOPOIETIN-2, IL6, and N-CAM in a context-dependent manner, cooperates with cofactors such as NKX2-1 synergistically; regulates neural crest cell survival, migration, and fate specification (via RET, SOX9, FOXD3), controls vascular endothelial differentiation and angiogenesis, directs lung branching morphogenesis, marks long-term hematopoietic stem cells in the bone marrow perivascular niche, and can reprogram B cells into functional T lymphocytes, while its nuclear translocation is regulated post-translationally by CARD9 SUMOylation-dependent inhibition of O-GlcNAc glycosylation.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"HOXB5 is a homeodomain transcription factor that directs cell fate specification and tissue morphogenesis across multiple developmental and adult contexts, including axial patterning, neural crest survival and migration, vascular endothelial differentiation, lung branching morphogenesis, and hematopoietic stem cell identity. It binds DNA cooperatively at tandem sites through a homeodomain-adjacent N-terminal domain, with cooperativity regulated by a redox-sensitive cysteine between homeodomain helices 2 and 3 [PMID:8101633]; direct transcriptional targets include FLK1/VEGFR2 [PMID:12897140], RET (synergistically with NKX2-1) [PMID:21677782, PMID:24794774], SOX9 [PMID:24141719], FOXD3 [PMID:25220476], CTNNB1 [PMID:26467157], EGFR [PMID:30115380], ANGPT2 [PMID:19403561], IL6 [PMID:33858489], and CXCR4 [PMID:33456563]. In vivo, Hoxb5 knockout causes rostral homeotic shifts of the shoulder girdle and, in compound mutants with Hoxa5, lethal lung branching defects [PMID:7828847, PMID:23585229]; Hoxb5 marks long-term hematopoietic stem cells in a perivascular bone marrow niche and can reprogram B-lineage cells into functional T lymphocytes [PMID:26863982, PMID:29434353]. Nuclear translocation of HOXB5 is regulated post-translationally by CARD9 SUMOylation-dependent inhibition of O-GlcNAc glycosylation [PMID:39496070].\",\n  \"teleology\": [\n    {\n      \"year\": 1992,\n      \"claim\": \"Identifying HOXB5 as a transcriptional activator of specific downstream genes established that individual HOX proteins regulate distinct adhesion-molecule targets, not just axial identity.\",\n      \"evidence\": \"Cotransfection reporter assay showing HOXB5 transactivates N-CAM promoter through a specific binding site, antagonized by HOXB4, in NIH 3T3 cells\",\n      \"pmids\": [\"1347944\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Endogenous chromatin context not tested\", \"N-CAM regulation not validated in vivo\", \"Mechanism of HOXB4 antagonism undefined\"]\n    },\n    {\n      \"year\": 1993,\n      \"claim\": \"Demonstrating cooperative DNA binding regulated by a redox-sensitive cysteine revealed a distinctive biochemical property that distinguishes HOXB5 from most other homeodomain proteins and from Fos/Jun-type transcription factors.\",\n      \"evidence\": \"In vitro DNA binding with mutagenesis showing cooperative binding at tandem sites requires N-terminal domain and is enhanced by oxidation of Cys in helix 2-3 turn\",\n      \"pmids\": [\"8101633\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo relevance of redox regulation untested\", \"Structural basis of oxidation-enhanced cooperativity unknown\", \"Identity of physiological redox signals unclear\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Knockout mice established that HOXB5 specifies axial position of the shoulder girdle and cooperates with HOXB6 in cervicothoracic vertebral identity, resolving its developmental patterning role.\",\n      \"evidence\": \"Gene targeting in mice producing rostral shoulder girdle shift; HOXB5/HOXB6 transheterozygotes show homeotic vertebral transformation\",\n      \"pmids\": [\"7828847\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream transcriptional targets mediating skeletal phenotype unknown\", \"Single versus redundant function with paralogous group 5 Hox genes not fully resolved\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Ex vivo lung culture experiments showed that HOXB5 protein levels, regulated by retinoic acid, quantitatively control airway branching morphogenesis, extending its role beyond skeletal patterning.\",\n      \"evidence\": \"Antisense knockdown and RA treatment in embryonic mouse lung explants with morphometric analysis\",\n      \"pmids\": [\"10913834\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Antisense approach lacks genetic specificity\", \"Direct transcriptional targets in lung not identified\", \"Interaction with RA signaling pathway not molecularly defined\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Identification of FLK1/VEGFR2 as a direct HOXB5 target linked HOXB5 to vascular endothelial specification, explaining how a HOX transcription factor can instruct angioblast fate.\",\n      \"evidence\": \"Yeast one-hybrid identification of intronic HOXB5-binding element, reporter assays, and embryoid body overexpression expanding flk1+ angioblasts\",\n      \"pmids\": [\"12897140\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Loss-of-function in endothelial lineage not performed\", \"Sufficiency versus necessity not distinguished in vivo\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Demonstrating that HOXB5 directly activates RET in vagal neural crest cells, with dominant-negative HOXB5 causing hypoganglionosis, established a transcriptional hierarchy controlling enteric nervous system colonization.\",\n      \"evidence\": \"Dominant-negative transgenic mice with reduced Ret, impaired NCC migration, and gut hypoganglionosis; Ret reporter activation in neuroblastoma cells\",\n      \"pmids\": [\"18395091\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full knockout of HOXB5 in NCC lineage not reported at this time\", \"Relationship to Hirschsprung disease causation in humans not established\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Showing HOXB5 transcriptionally activates angiopoietin-2 and that Tie-2 blockade abolishes HOXB5-driven sprouting angiogenesis defined the downstream effector pathway for HOXB5 in vascular remodeling.\",\n      \"evidence\": \"HUVEC spheroid sprouting, CAM assay, Ang2 promoter reporter, and soluble Tie-2 functional blockade\",\n      \"pmids\": [\"19403561\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Endogenous HOXB5 loss-of-function in endothelium not tested\", \"Relative contribution of Ang2 versus FLK1 to HOXB5 angiogenic function unclear\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"ChIP and co-immunoprecipitation revealed that HOXB5 and NKX2-1 form a protein complex that synergistically activates RET, and that Hirschsprung-associated SNPs at the NKX2-1 site abolish this synergism, providing a molecular mechanism for disease-associated regulatory variation.\",\n      \"evidence\": \"ChIP, co-IP, and luciferase reporter with SNP analysis in RET promoter\",\n      \"pmids\": [\"21677782\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Crystal structure of HOXB5–NKX2-1 complex unavailable\", \"Functional consequence of SNP on enteric NCC development not shown in vivo\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identification of SOX9 and FOXD3 as direct HOXB5 transcriptional targets in neural crest cells, with genetic epistasis showing rescue of apoptosis, built a HOXB5→SOX9/FOXD3 survival circuit governing NCC fate.\",\n      \"evidence\": \"ChIP, reporter assays, in ovo gain/loss-of-function, and compound mutant mouse analysis for SOX9 (2013) and FOXD3 (2014)\",\n      \"pmids\": [\"24141719\", \"25220476\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether SOX9 and FOXD3 are independent or epistatic downstream of HOXB5 is unclear\", \"NCC-specific HOXB5 conditional knockout not reported\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Compound Hoxa5;Hoxb5 knockout mice revealed functional redundancy in lung morphogenesis, with lethality demonstrating that HOXB5 contributes non-redundantly to branching, goblet cell specification, and postnatal lung structure.\",\n      \"evidence\": \"Compound knockout mouse genetics with histological and morphological phenotyping\",\n      \"pmids\": [\"23585229\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct transcriptional targets mediating lung phenotype not identified\", \"Cell-type-specific contributions of HOXB5 in lung epithelium versus mesenchyme unknown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"An endogenous knock-in reporter demonstrated that Hoxb5 expression exclusively marks long-term HSCs in bone marrow, with >94% residing in a perivascular niche, redefining the HSC identity marker landscape.\",\n      \"evidence\": \"Tri-mCherry knock-in reporter at Hoxb5 locus, prospective isolation, serial transplantation, in situ imaging\",\n      \"pmids\": [\"26863982\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether HOXB5 is functionally required for HSC self-renewal is unknown\", \"Mechanism by which HOXB5 expression is restricted to LT-HSCs not defined\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"HOXB5 overexpression was shown to reprogram pro-pre-B cells into functional T lymphocytes by repressing B-cell genes and activating T-cell regulators, revealing an unexpected lineage-reprogramming capacity.\",\n      \"evidence\": \"Retroviral HOXB5 overexpression, transplantation, transcriptome analysis, and functional immunological assays in mice\",\n      \"pmids\": [\"29434353\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct chromatin targets mediating B-to-T reprogramming not comprehensively mapped\", \"Whether endogenous HOXB5 levels influence normal lymphoid lineage decisions is untested\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identifying CTNNB1 and EGFR as direct HOXB5 targets in cancer cells linked HOXB5 transcriptional activity to oncogenic signaling through Wnt/β-catenin and EGFR pathways, extending its role beyond development.\",\n      \"evidence\": \"ChIP and reporter assays in gastric cancer (CTNNB1) and breast/HNSCC (EGFR) cells with knockdown rescue\",\n      \"pmids\": [\"26467157\", \"30115380\", \"31864826\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether HOXB5 activates these targets in normal adult tissues is unknown\", \"Genome-wide target landscape in cancer not defined by unbiased approaches\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Discovery of HOXB5-driven positive feedback loops (CXCL12→HOXB5→CXCR4 in colorectal cancer; circATP5B→miR-185-5p→HOXB5 in glioma) revealed that HOXB5 expression is itself amplified through feed-forward circuits in malignancy.\",\n      \"evidence\": \"ChIP, reporter assays, RNA pulldown, RIP, and in vivo metastasis models with pharmacological inhibition (AMD3100)\",\n      \"pmids\": [\"33456563\", \"33858489\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relevance of these feedback loops in non-cancer contexts unknown\", \"Therapeutic targeting of HOXB5 itself not explored\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"A novel post-translational regulatory mechanism was uncovered in which CARD9 SUMOylation inhibits HOXB5 O-GlcNAc glycosylation and nuclear translocation, linking innate immune adaptor signaling to HOXB5 transcriptional activity.\",\n      \"evidence\": \"Co-IP, SUMOylation and O-GlcNAc assays, nuclear fractionation, Parkin reporter, in cardiomyocyte ischemia-reperfusion model\",\n      \"pmids\": [\"39496070\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab finding not independently replicated\", \"Sites of O-GlcNAc modification on HOXB5 not mapped\", \"Generality beyond cardiomyocyte I/R context unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include whether HOXB5 is functionally required for LT-HSC self-renewal, the genome-wide direct target landscape by unbiased ChIP-seq, the structural basis of redox-regulated cooperative DNA binding, and the physiological significance of CARD9-mediated post-translational regulation of HOXB5 nuclear entry.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No conditional knockout in HSCs reported\", \"No genome-wide binding profile (ChIP-seq) published\", \"No structural model of HOXB5 homeodomain cooperativity\", \"CARD9–HOXB5 axis awaits independent confirmation\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 1, 2, 5, 6, 7, 8, 9, 11, 13, 14]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [1, 2, 4, 5, 7, 8, 9, 11, 13, 14]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 5, 6, 23]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [4, 7, 8, 19, 20, 21]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [1, 2, 5, 6, 9, 11, 14]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3, 9, 12, 13, 15, 22]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [10, 17]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"NKX2-1\",\n      \"CARD9\",\n      \"HOXB6\",\n      \"HOXA5\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}