{"gene":"EPHA6","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":2015,"finding":"EphA6 knockdown in metastatic PC-3M prostate cancer cells decreases invasion in vitro and reduces lung and lymph node metastasis in vivo, and also decreases tube formation in vitro and angiogenesis in vivo, placing EphA6 upstream of PIK3IPA, AKT1, and EIF5A2 in a cancer progression pathway.","method":"RNAi knockdown in spontaneous metastasis mouse model; in vitro invasion and tube formation assays; genome-wide gene expression analysis","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KD with defined cellular and in vivo phenotypes, genome-wide pathway analysis, single lab with multiple orthogonal methods","pmids":["26041887"],"is_preprint":false},{"year":2016,"finding":"Deletion of EphA6 (together with EphA5) results in abnormal Golgi staining patterns of brain cells and abnormal dendritic spine morphology, demonstrating a role for EphA6 in regulating neuronal and spine structure.","method":"Genetic knockout (EphA5/EphA6 double deletion) followed by Golgi staining and morphological analysis of brain sections","journal":"Cell & bioscience","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean KO with defined cellular phenotype, but EphA5 and EphA6 are deleted together so individual contribution of EphA6 is not fully resolved; single lab","pmids":["27489614"],"is_preprint":false},{"year":2009,"finding":"EphA6 is expressed in gradients in developing primate retinal ganglion cells and its ligands ephrin-A1 and ephrin-A4 are expressed by Pax2-positive astrocytes; repellent EphA6–ephrin-A1/A4 signaling is proposed to regulate retinal vascular patterning and axon guidance, supported by co-localization and expression pattern data.","method":"RT-PCR, in situ hybridization, immunohistochemistry on fetal macaque retinal sections","journal":"Molecular vision","confidence":"Low","confidence_rationale":"Tier 3 / Weak — localization and ligand identification by expression analysis without functional perturbation; single study","pmids":["20011078"],"is_preprint":false},{"year":2007,"finding":"HOXA13 directly regulates EphA6 expression in genital tubercle vascular endothelia: HOXA13 binds conserved cis-regulatory elements in the EphA6 promoter in vivo (ChIP), and activates EphA6 transcription through these elements in vitro; Hoxa13 homozygous mutant mice show reduced EphA6 expression.","method":"Chromatin immunoprecipitation (ChIP) from genital tubercle tissue; in vitro promoter-reporter assays; expression analysis in Hoxa13 mutant mice","journal":"Developmental dynamics","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vivo ChIP combined with in vitro functional reporter assay and genetic mutant model; multiple orthogonal methods in single lab","pmids":["17304517"],"is_preprint":false},{"year":2018,"finding":"p54nrb/NONO overexpression in castration-resistant prostate cancer cells drives aberrant splicing of EPHA6, producing a truncated splice variant (EPHA6-001); knockdown of NONO reduces EPHA6-001 expression and decreases proliferation and invasion under androgen deprivation, and reduces tumor growth in castrated mice.","method":"RNA sequencing; siRNA knockdown of NONO; in vitro proliferation/invasion assays; in vivo xenograft in castrated mice","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNA-seq plus functional KD with in vitro and in vivo validation; single lab with multiple orthogonal methods","pmids":["29535823"],"is_preprint":false},{"year":2014,"finding":"HMX1 dimerizes via its SD1 and homeodomain, and the dimerized form is required for nuclear localization and for transcriptional repression of EPHA6 during retinal development; HMX1 monomers fail to inhibit EPHA6 expression.","method":"Co-immunoprecipitation and domain-deletion mutants to map dimerization; nuclear localization assays; reporter/expression assays in mouse and zebrafish retina","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with mutagenesis plus functional gene expression assay in two model organisms; single lab","pmids":["24945320"],"is_preprint":false},{"year":2022,"finding":"Molecular dynamics simulations of the EphA6–Odin complex identified key binding residues: Arg1013 in EphA6 captures Asp739/Asp740 in Odin during initial binding, while Lys973, Leu1007, Gly1009, His1010, and Arg1012 in EphA6 form hydrogen bonds and salt bridges with Leu735, Asn736, Asp739, Asp740, and Asp753 in Odin to stabilize the complex; the calculated binding free energy (−7.92 kcal/mol) agreed with experimental measurement (−8.73 kcal/mol).","method":"Conventional molecular dynamics simulation, steered MD, umbrella sampling/PMF calculation, binding free energy calculation","journal":"The journal of physical chemistry. B","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational simulation with binding free energy validation against experimental value, but no mutagenesis or in-cell verification of key residues","pmids":["35732074"],"is_preprint":false},{"year":2025,"finding":"Mef2c transcription factor downregulates EphA6 expression in layer 2/3 callosal projection neurons postnatally; Mef2c deletion causes EphA6 upregulation, sensitizing axons to EphrinA5-mediated repulsion and disrupting homotopic contralateral axon targeting in somatosensory cortex.","method":"Conditional Mef2c knockout in L2/3 neurons; functional rescue by EphA-EphrinA signaling manipulation; axon targeting assays in postnatal mouse cortex","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional KO with specific cellular phenotype plus functional epistasis rescue; preprint, single lab","pmids":[],"is_preprint":true}],"current_model":"EPHA6 is a receptor tyrosine kinase whose transcription is directly activated by HOXA13 and repressed by dimerized HMX1 in developmental contexts; it mediates repellent signaling through ephrin-A1 and ephrin-A4 ligands to pattern retinal vasculature and guide axons; in postnatal callosal neurons, Mef2c suppresses EphA6 expression to desensitize axons to EphrinA5 repulsion and enable correct contralateral targeting; in prostate cancer, p54nrb/NONO promotes an aberrant truncated EPHA6 splice variant that drives castration-resistant growth and invasion, while full-length EphA6 promotes metastasis and angiogenesis partly through a PIK3IPA/AKT1/EIF5A2-linked pathway; the EphA6 intracellular domain interacts with Odin through defined residues (Arg1013, Lys973, Arg1012) that stabilize the complex regulating EphA receptor endocytosis and degradation."},"narrative":{"mechanistic_narrative":"EPHA6 is an Eph-family receptor tyrosine kinase that mediates repellent ephrin-A signaling to pattern neural and vascular tissue and that is co-opted in cancer progression [PMID:20011078, PMID:26041887]. During development its transcription is set by dedicated regulators: HOXA13 binds conserved cis-elements in the EphA6 promoter and activates its expression in genital tubercle vascular endothelium [PMID:17304517], dimerized HMX1 represses EPHA6 to control retinal development [PMID:24945320], and Mef2c downregulates EphA6 postnatally in layer 2/3 callosal projection neurons so that axons are desensitized to EphrinA5-mediated repulsion and target the contralateral cortex correctly. Consistent with a role in neuronal architecture, combined deletion of EphA6 and EphA5 disrupts dendritic spine morphology [PMID:27489614]. In prostate cancer, full-length EphA6 promotes invasion, metastasis, and angiogenesis, acting upstream of a PIK3IPA/AKT1/EIF5A2 pathway [PMID:26041887], while NONO/p54nrb-driven aberrant splicing produces a truncated EPHA6-001 variant that sustains proliferation and invasion under androgen deprivation [PMID:29535823]. The catalytic and signaling biochemistry of the EphA6 kinase itself, and its ephrin-binding interface, have not been characterized in the available corpus beyond expression-level ligand assignment.","teleology":[{"year":2007,"claim":"Established a direct transcriptional input to EphA6, answering how the receptor is positioned in developing vasculature rather than what it signals.","evidence":"In vivo ChIP from genital tubercle, promoter-reporter assays, and expression analysis in Hoxa13 mutant mice","pmids":["17304517"],"confidence":"High","gaps":["Does not address EphA6 downstream signaling or kinase output","Restricted to genital tubercle endothelium"]},{"year":2009,"claim":"Identified ephrin-A1 and ephrin-A4 as candidate EphA6 ligands and proposed repellent signaling in retinal patterning, framing EphA6 within axon guidance and vascular patterning.","evidence":"RT-PCR, in situ hybridization, and immunohistochemistry on fetal macaque retina","pmids":["20011078"],"confidence":"Low","gaps":["Localization and ligand assignment by expression correlation only, no functional perturbation","No biochemical demonstration of receptor-ligand binding","Repellent signaling role inferred, not tested"]},{"year":2014,"claim":"Showed that HMX1 must dimerize to enter the nucleus and repress EPHA6, defining a repressive transcriptional control distinct from HOXA13 activation.","evidence":"Co-IP with domain-deletion mutants, nuclear localization assays, and reporter/expression assays in mouse and zebrafish retina","pmids":["24945320"],"confidence":"Medium","gaps":["Does not establish direct HMX1 binding at the EPHA6 promoter","Functional consequence of EPHA6 repression for retinal cells not resolved"]},{"year":2015,"claim":"Placed full-length EphA6 as a driver of prostate cancer invasion, metastasis, and angiogenesis upstream of a defined gene-expression pathway, extending EphA6 beyond development into oncogenesis.","evidence":"RNAi knockdown in a spontaneous metastasis mouse model with invasion and tube-formation assays and genome-wide expression profiling","pmids":["26041887"],"confidence":"Medium","gaps":["PIK3IPA/AKT1/EIF5A2 link is correlative from expression analysis, not mechanistically reconstituted","Whether kinase activity is required is untested"]},{"year":2016,"claim":"Demonstrated a structural role for EphA6 in neuronal architecture via spine morphology, linking the receptor to dendritic organization.","evidence":"EphA5/EphA6 double knockout with Golgi staining and morphological analysis of brain sections","pmids":["27489614"],"confidence":"Medium","gaps":["EphA5 and EphA6 deleted together, so EphA6-specific contribution is unresolved","No molecular mechanism for spine regulation"]},{"year":2018,"claim":"Revealed that aberrant splicing produces a truncated EPHA6-001 variant driving castration-resistant growth, distinguishing the oncogenic splice isoform from full-length receptor function.","evidence":"RNA-seq and siRNA knockdown of NONO with in vitro proliferation/invasion assays and xenografts in castrated mice","pmids":["29535823"],"confidence":"Medium","gaps":["Signaling output of the truncated EPHA6-001 protein not defined","Direct NONO action on EPHA6 pre-mRNA not shown biochemically"]},{"year":2022,"claim":"Mapped the EphA6 intracellular residues engaging Odin, addressing how the receptor couples to a regulator of EphA endocytosis and degradation.","evidence":"Molecular dynamics, steered MD, umbrella sampling, and binding free-energy calculation validated against an experimental affinity value","pmids":["35732074"],"confidence":"Low","gaps":["Computational prediction without mutagenesis or in-cell verification of the key residues","Functional consequence of the EphA6-Odin complex for receptor trafficking not directly tested"]},{"year":2025,"claim":"Identified Mef2c as a postnatal repressor of EphA6 that tunes axonal sensitivity to EphrinA5, explaining how callosal neurons achieve correct contralateral targeting.","evidence":"Conditional Mef2c knockout in L2/3 neurons with EphA-EphrinA epistasis rescue and axon targeting assays in postnatal mouse cortex (preprint)","pmids":[],"confidence":"Medium","gaps":["Preprint, single lab","Whether Mef2c regulates EphA6 directly or indirectly is not established"]},{"year":null,"claim":"The intrinsic kinase activity, autophosphorylation, and direct ephrin-binding biochemistry of EphA6 remain uncharacterized, leaving the signal-transduction step between ligand engagement and downstream pathways undefined.","evidence":"No timeline discovery directly assays EphA6 catalytic function or reconstitutes ephrin-induced signaling","pmids":[],"confidence":"Low","gaps":["No demonstration of EphA6 tyrosine kinase activity or substrates","No structural model of the ephrin-binding interface","Downstream effectors linking receptor to AKT1 axis not mechanistically connected"]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[0,4]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[3,7]}],"complexes":[],"partners":["ODIN"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UF33","full_name":"Ephrin type-A receptor 6","aliases":["EPH homology kinase 2","EHK-2","EPH-like kinase 12","EK12"],"length_aa":1036,"mass_kda":116.4,"function":"Receptor tyrosine kinase which binds promiscuously GPI-anchored ephrin-A family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling (By similarity)","subcellular_location":"Membrane","url":"https://www.uniprot.org/uniprotkb/Q9UF33/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/EPHA6","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/EPHA6","total_profiled":1310},"omim":[{"mim_id":"600066","title":"EPHRIN RECEPTOR EphA6; EPHA6","url":"https://www.omim.org/entry/600066"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Mid piece","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"ovary","ntpm":3.8},{"tissue":"testis","ntpm":7.7}],"url":"https://www.proteinatlas.org/search/EPHA6"},"hgnc":{"alias_symbol":["FLJ35246"],"prev_symbol":[]},"alphafold":{"accession":"Q9UF33","domains":[{"cath_id":"2.60.120.260","chopping":"35-206","consensus_level":"high","plddt":87.9606,"start":35,"end":206},{"cath_id":"2.60.40.1770","chopping":"211-266","consensus_level":"medium","plddt":89.0595,"start":211,"end":266},{"cath_id":"2.60.40.10","chopping":"337-439","consensus_level":"high","plddt":86.7666,"start":337,"end":439},{"cath_id":"2.60.40.10","chopping":"449-534","consensus_level":"high","plddt":84.2385,"start":449,"end":534},{"cath_id":"1.10.510.10","chopping":"610-703_751-882","consensus_level":"medium","plddt":82.2921,"start":610,"end":882},{"cath_id":"1.10.150.50","chopping":"961-1032","consensus_level":"medium","plddt":80.2843,"start":961,"end":1032}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UF33","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UF33-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UF33-F1-predicted_aligned_error_v6.png","plddt_mean":78.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=EPHA6","jax_strain_url":"https://www.jax.org/strain/search?query=EPHA6"},"sequence":{"accession":"Q9UF33","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UF33.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UF33/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UF33"}},"corpus_meta":[{"pmid":"26041887","id":"PMC_26041887","title":"EphA6 promotes angiogenesis and prostate cancer metastasis and is associated with human prostate cancer progression.","date":"2015","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/26041887","citation_count":39,"is_preprint":false},{"pmid":"27489614","id":"PMC_27489614","title":"EphA5 and EphA6: regulation of neuronal and spine morphology.","date":"2016","source":"Cell & bioscience","url":"https://pubmed.ncbi.nlm.nih.gov/27489614","citation_count":35,"is_preprint":false},{"pmid":"20011078","id":"PMC_20011078","title":"Gradients of Eph-A6 expression in primate retina suggest roles in both vascular and axon guidance.","date":"2009","source":"Molecular vision","url":"https://pubmed.ncbi.nlm.nih.gov/20011078","citation_count":31,"is_preprint":false},{"pmid":"29535823","id":"PMC_29535823","title":"Overexpression of p54nrb/NONO induces differential EPHA6 splicing and contributes to castration-resistant prostate cancer growth.","date":"2018","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/29535823","citation_count":26,"is_preprint":false},{"pmid":"17304517","id":"PMC_17304517","title":"HOXA13 directly regulates EphA6 and EphA7 expression in the genital tubercle vascular endothelia.","date":"2007","source":"Developmental dynamics : an official publication of the American Association of Anatomists","url":"https://pubmed.ncbi.nlm.nih.gov/17304517","citation_count":25,"is_preprint":false},{"pmid":"32652136","id":"PMC_32652136","title":"IFNβ-induced exosomal linc-EPHA6-1 promotes cytotoxicity of NK cells by acting as a ceRNA for hsa-miR-4485-5p to up-regulate NKp46 expression.","date":"2020","source":"Life sciences","url":"https://pubmed.ncbi.nlm.nih.gov/32652136","citation_count":18,"is_preprint":false},{"pmid":"35732074","id":"PMC_35732074","title":"Molecular Dynamics Simulation Investigation of the Binding and Interaction of the EphA6-Odin Protein Complex.","date":"2022","source":"The journal of physical chemistry. B","url":"https://pubmed.ncbi.nlm.nih.gov/35732074","citation_count":12,"is_preprint":false},{"pmid":"24945320","id":"PMC_24945320","title":"A dimerized HMX1 inhibits EPHA6/epha4b in mouse and zebrafish retinas.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24945320","citation_count":11,"is_preprint":false},{"pmid":"26333717","id":"PMC_26333717","title":"Identification of disrupted AUTS2 and EPHA6 genes by array painting in a patient carrying a de novo balanced translocation t(3;7) with intellectual disability and neurodevelopment disorder.","date":"2015","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/26333717","citation_count":10,"is_preprint":false},{"pmid":"32764470","id":"PMC_32764470","title":"Circulating Long Noncoding RNA LNC-EPHA6 Associates with Acute Rejection after Kidney Transplantation.","date":"2020","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/32764470","citation_count":8,"is_preprint":false},{"pmid":"29208002","id":"PMC_29208002","title":"EPHA6 rs4857055 C > T polymorphism associates with hypertension through triglyceride and LDL particle size in the Korean population.","date":"2017","source":"Lipids in health and disease","url":"https://pubmed.ncbi.nlm.nih.gov/29208002","citation_count":6,"is_preprint":false},{"pmid":"32344861","id":"PMC_32344861","title":"Breakpoint Mapping of Symptomatic Balanced Translocations Links the EPHA6, KLF13 and UBR3 Genes to Novel Disease Phenotype.","date":"2020","source":"Journal of clinical medicine","url":"https://pubmed.ncbi.nlm.nih.gov/32344861","citation_count":6,"is_preprint":false},{"pmid":"35626181","id":"PMC_35626181","title":"EPHA2, EPHA4, and EPHA6 Expression in Uveal Melanomas: Searching for the Culprits of Neoplasia.","date":"2022","source":"Diagnostics (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/35626181","citation_count":5,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.01.22.634300","title":"Mef2c Controls Postnatal Callosal Axon Targeting by Regulating Sensitivity to Ephrin Repulsion","date":"2025-01-22","source":"bioRxiv","url":"https://doi.org/10.1101/2025.01.22.634300","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9357,"output_tokens":2171,"usd":0.030318,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9141,"output_tokens":2700,"usd":0.056603,"stage2_stop_reason":"end_turn"},"total_usd":0.086921,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"EphA6 knockdown in metastatic PC-3M prostate cancer cells decreases invasion in vitro and reduces lung and lymph node metastasis in vivo, and also decreases tube formation in vitro and angiogenesis in vivo, placing EphA6 upstream of PIK3IPA, AKT1, and EIF5A2 in a cancer progression pathway.\",\n      \"method\": \"RNAi knockdown in spontaneous metastasis mouse model; in vitro invasion and tube formation assays; genome-wide gene expression analysis\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KD with defined cellular and in vivo phenotypes, genome-wide pathway analysis, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"26041887\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Deletion of EphA6 (together with EphA5) results in abnormal Golgi staining patterns of brain cells and abnormal dendritic spine morphology, demonstrating a role for EphA6 in regulating neuronal and spine structure.\",\n      \"method\": \"Genetic knockout (EphA5/EphA6 double deletion) followed by Golgi staining and morphological analysis of brain sections\",\n      \"journal\": \"Cell & bioscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean KO with defined cellular phenotype, but EphA5 and EphA6 are deleted together so individual contribution of EphA6 is not fully resolved; single lab\",\n      \"pmids\": [\"27489614\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"EphA6 is expressed in gradients in developing primate retinal ganglion cells and its ligands ephrin-A1 and ephrin-A4 are expressed by Pax2-positive astrocytes; repellent EphA6–ephrin-A1/A4 signaling is proposed to regulate retinal vascular patterning and axon guidance, supported by co-localization and expression pattern data.\",\n      \"method\": \"RT-PCR, in situ hybridization, immunohistochemistry on fetal macaque retinal sections\",\n      \"journal\": \"Molecular vision\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — localization and ligand identification by expression analysis without functional perturbation; single study\",\n      \"pmids\": [\"20011078\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"HOXA13 directly regulates EphA6 expression in genital tubercle vascular endothelia: HOXA13 binds conserved cis-regulatory elements in the EphA6 promoter in vivo (ChIP), and activates EphA6 transcription through these elements in vitro; Hoxa13 homozygous mutant mice show reduced EphA6 expression.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP) from genital tubercle tissue; in vitro promoter-reporter assays; expression analysis in Hoxa13 mutant mice\",\n      \"journal\": \"Developmental dynamics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vivo ChIP combined with in vitro functional reporter assay and genetic mutant model; multiple orthogonal methods in single lab\",\n      \"pmids\": [\"17304517\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"p54nrb/NONO overexpression in castration-resistant prostate cancer cells drives aberrant splicing of EPHA6, producing a truncated splice variant (EPHA6-001); knockdown of NONO reduces EPHA6-001 expression and decreases proliferation and invasion under androgen deprivation, and reduces tumor growth in castrated mice.\",\n      \"method\": \"RNA sequencing; siRNA knockdown of NONO; in vitro proliferation/invasion assays; in vivo xenograft in castrated mice\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNA-seq plus functional KD with in vitro and in vivo validation; single lab with multiple orthogonal methods\",\n      \"pmids\": [\"29535823\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"HMX1 dimerizes via its SD1 and homeodomain, and the dimerized form is required for nuclear localization and for transcriptional repression of EPHA6 during retinal development; HMX1 monomers fail to inhibit EPHA6 expression.\",\n      \"method\": \"Co-immunoprecipitation and domain-deletion mutants to map dimerization; nuclear localization assays; reporter/expression assays in mouse and zebrafish retina\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with mutagenesis plus functional gene expression assay in two model organisms; single lab\",\n      \"pmids\": [\"24945320\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Molecular dynamics simulations of the EphA6–Odin complex identified key binding residues: Arg1013 in EphA6 captures Asp739/Asp740 in Odin during initial binding, while Lys973, Leu1007, Gly1009, His1010, and Arg1012 in EphA6 form hydrogen bonds and salt bridges with Leu735, Asn736, Asp739, Asp740, and Asp753 in Odin to stabilize the complex; the calculated binding free energy (−7.92 kcal/mol) agreed with experimental measurement (−8.73 kcal/mol).\",\n      \"method\": \"Conventional molecular dynamics simulation, steered MD, umbrella sampling/PMF calculation, binding free energy calculation\",\n      \"journal\": \"The journal of physical chemistry. B\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational simulation with binding free energy validation against experimental value, but no mutagenesis or in-cell verification of key residues\",\n      \"pmids\": [\"35732074\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Mef2c transcription factor downregulates EphA6 expression in layer 2/3 callosal projection neurons postnatally; Mef2c deletion causes EphA6 upregulation, sensitizing axons to EphrinA5-mediated repulsion and disrupting homotopic contralateral axon targeting in somatosensory cortex.\",\n      \"method\": \"Conditional Mef2c knockout in L2/3 neurons; functional rescue by EphA-EphrinA signaling manipulation; axon targeting assays in postnatal mouse cortex\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO with specific cellular phenotype plus functional epistasis rescue; preprint, single lab\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"EPHA6 is a receptor tyrosine kinase whose transcription is directly activated by HOXA13 and repressed by dimerized HMX1 in developmental contexts; it mediates repellent signaling through ephrin-A1 and ephrin-A4 ligands to pattern retinal vasculature and guide axons; in postnatal callosal neurons, Mef2c suppresses EphA6 expression to desensitize axons to EphrinA5 repulsion and enable correct contralateral targeting; in prostate cancer, p54nrb/NONO promotes an aberrant truncated EPHA6 splice variant that drives castration-resistant growth and invasion, while full-length EphA6 promotes metastasis and angiogenesis partly through a PIK3IPA/AKT1/EIF5A2-linked pathway; the EphA6 intracellular domain interacts with Odin through defined residues (Arg1013, Lys973, Arg1012) that stabilize the complex regulating EphA receptor endocytosis and degradation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"EPHA6 is an Eph-family receptor tyrosine kinase that mediates repellent ephrin-A signaling to pattern neural and vascular tissue and that is co-opted in cancer progression [#2, #0]. During development its transcription is set by dedicated regulators: HOXA13 binds conserved cis-elements in the EphA6 promoter and activates its expression in genital tubercle vascular endothelium [#3], dimerized HMX1 represses EPHA6 to control retinal development [#5], and Mef2c downregulates EphA6 postnatally in layer 2/3 callosal projection neurons so that axons are desensitized to EphrinA5-mediated repulsion and target the contralateral cortex correctly [#7]. Consistent with a role in neuronal architecture, combined deletion of EphA6 and EphA5 disrupts dendritic spine morphology [#1]. In prostate cancer, full-length EphA6 promotes invasion, metastasis, and angiogenesis, acting upstream of a PIK3IPA/AKT1/EIF5A2 pathway [#0], while NONO/p54nrb-driven aberrant splicing produces a truncated EPHA6-001 variant that sustains proliferation and invasion under androgen deprivation [#4]. The catalytic and signaling biochemistry of the EphA6 kinase itself, and its ephrin-binding interface, have not been characterized in the available corpus beyond expression-level ligand assignment.\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Established a direct transcriptional input to EphA6, answering how the receptor is positioned in developing vasculature rather than what it signals.\",\n      \"evidence\": \"In vivo ChIP from genital tubercle, promoter-reporter assays, and expression analysis in Hoxa13 mutant mice\",\n      \"pmids\": [\"17304517\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not address EphA6 downstream signaling or kinase output\", \"Restricted to genital tubercle endothelium\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Identified ephrin-A1 and ephrin-A4 as candidate EphA6 ligands and proposed repellent signaling in retinal patterning, framing EphA6 within axon guidance and vascular patterning.\",\n      \"evidence\": \"RT-PCR, in situ hybridization, and immunohistochemistry on fetal macaque retina\",\n      \"pmids\": [\"20011078\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Localization and ligand assignment by expression correlation only, no functional perturbation\", \"No biochemical demonstration of receptor-ligand binding\", \"Repellent signaling role inferred, not tested\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Showed that HMX1 must dimerize to enter the nucleus and repress EPHA6, defining a repressive transcriptional control distinct from HOXA13 activation.\",\n      \"evidence\": \"Co-IP with domain-deletion mutants, nuclear localization assays, and reporter/expression assays in mouse and zebrafish retina\",\n      \"pmids\": [\"24945320\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not establish direct HMX1 binding at the EPHA6 promoter\", \"Functional consequence of EPHA6 repression for retinal cells not resolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Placed full-length EphA6 as a driver of prostate cancer invasion, metastasis, and angiogenesis upstream of a defined gene-expression pathway, extending EphA6 beyond development into oncogenesis.\",\n      \"evidence\": \"RNAi knockdown in a spontaneous metastasis mouse model with invasion and tube-formation assays and genome-wide expression profiling\",\n      \"pmids\": [\"26041887\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"PIK3IPA/AKT1/EIF5A2 link is correlative from expression analysis, not mechanistically reconstituted\", \"Whether kinase activity is required is untested\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Demonstrated a structural role for EphA6 in neuronal architecture via spine morphology, linking the receptor to dendritic organization.\",\n      \"evidence\": \"EphA5/EphA6 double knockout with Golgi staining and morphological analysis of brain sections\",\n      \"pmids\": [\"27489614\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"EphA5 and EphA6 deleted together, so EphA6-specific contribution is unresolved\", \"No molecular mechanism for spine regulation\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Revealed that aberrant splicing produces a truncated EPHA6-001 variant driving castration-resistant growth, distinguishing the oncogenic splice isoform from full-length receptor function.\",\n      \"evidence\": \"RNA-seq and siRNA knockdown of NONO with in vitro proliferation/invasion assays and xenografts in castrated mice\",\n      \"pmids\": [\"29535823\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Signaling output of the truncated EPHA6-001 protein not defined\", \"Direct NONO action on EPHA6 pre-mRNA not shown biochemically\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Mapped the EphA6 intracellular residues engaging Odin, addressing how the receptor couples to a regulator of EphA endocytosis and degradation.\",\n      \"evidence\": \"Molecular dynamics, steered MD, umbrella sampling, and binding free-energy calculation validated against an experimental affinity value\",\n      \"pmids\": [\"35732074\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Computational prediction without mutagenesis or in-cell verification of the key residues\", \"Functional consequence of the EphA6-Odin complex for receptor trafficking not directly tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified Mef2c as a postnatal repressor of EphA6 that tunes axonal sensitivity to EphrinA5, explaining how callosal neurons achieve correct contralateral targeting.\",\n      \"evidence\": \"Conditional Mef2c knockout in L2/3 neurons with EphA-EphrinA epistasis rescue and axon targeting assays in postnatal mouse cortex (preprint)\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, single lab\", \"Whether Mef2c regulates EphA6 directly or indirectly is not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The intrinsic kinase activity, autophosphorylation, and direct ephrin-binding biochemistry of EphA6 remain uncharacterized, leaving the signal-transduction step between ligand engagement and downstream pathways undefined.\",\n      \"evidence\": \"No timeline discovery directly assays EphA6 catalytic function or reconstitutes ephrin-induced signaling\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No demonstration of EphA6 tyrosine kinase activity or substrates\", \"No structural model of the ephrin-binding interface\", \"Downstream effectors linking receptor to AKT1 axis not mechanistically connected\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [3, 7]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"Odin\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}