{"gene":"EPHA4","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":2003,"finding":"EphA4 is enriched on dendritic spines of pyramidal neurons; activation by astrocytic ephrin-A3 induces spine retraction, while inhibiting ephrin/EphA4 interactions or using kinase-inactive EphA4 distorts spine shape, establishing that ephrin-A3/EphA4 signaling controls dendritic spine morphology through neuroglial cross-talk.","method":"Hippocampal slice experiments, EphA4 knockout mice, kinase-inactive EphA4 transfection, ephrin-A3 activation assays","journal":"Nature neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (KO mice, kinase-dead mutant, pharmacological inhibition, slice physiology) replicated across conditions in one rigorous study","pmids":["12496762"],"is_preprint":false},{"year":1997,"finding":"EphA4 and EphB1 expressed in migrating neural crest cells mediate repulsive interactions with ephrin-B2 to restrict intermingling of third arch neural crest cells and target them to the correct branchial arch destination; inhibition of EphA4/EphB1 function via truncated receptors causes aberrant migration, and ectopic ephrin-B2 scatters third arch neural crest.","method":"Truncated dominant-negative receptor expression in Xenopus, ectopic ephrin-B2 overexpression, neural crest migration tracking","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function and gain-of-function experiments in Xenopus with defined cellular phenotype, complementary expression mapping","pmids":["9259557"],"is_preprint":false},{"year":1998,"finding":"EphA4 (Sek1) is required for corticospinal tract formation; EphA4 null mice show major disruptions of the corticospinal tract in the medulla and spinal cord, demonstrating a critical role in establishing corticospinal projections.","method":"EphA4 null mutant mouse generation, anterograde tracing experiments, anatomical analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic knockout with defined axon tract phenotype confirmed by anterograde tracing; replicated in subsequent studies","pmids":["9789074"],"is_preprint":false},{"year":2004,"finding":"EphA4 expression is upregulated on astrocytes at spinal cord lesion sites; EphA4-/- mice show reduced astrocytic gliosis and glial scar formation, and EphA4-/- astrocytes fail to respond to inflammatory cytokines (IFN-γ or LIF). Neurons grown on wild-type astrocytes extend shorter neurites than on EphA4-/- astrocytes, but grow longer neurites when astrocyte EphA4 is blocked by monomeric EphrinA5-Fc, establishing EphA4 as a regulator of astrocytic gliosis and axonal inhibition after spinal cord injury.","method":"EphA4 knockout mice, spinal cord hemisection, anterograde and retrograde tracing, in vitro astrocyte/neuron co-culture assays, cytokine stimulation, monomeric EphrinA5-Fc blockade","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — KO mice with functional recovery, in vitro mechanistic assays, pharmacological blockade, multiple orthogonal readouts","pmids":["15537875"],"is_preprint":false},{"year":2006,"finding":"Cdk5 is recruited to EphA4 upon ephrin-A1 activation, leading to tyrosine phosphorylation and activation of Cdk5. Activated EphA4/Cdk5 then enhances activation of ephexin1 (a RhoA GEF) via Cdk5-dependent phosphorylation of ephexin1, leading to RhoA activation and dendritic spine retraction. Cdk5 activity is required for ephrin-A1-triggered spine retraction and mEPSC frequency reduction.","method":"Cdk5 inhibition assays, Co-immunoprecipitation of EphA4 and Cdk5, tyrosine phosphorylation assays, Cdk5-/- brains, ephrin-A1 stimulation, mEPSC recordings, spine density analysis","journal":"Nature neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, genetic knockout (Cdk5-/-), phosphorylation assays, electrophysiology, and morphological readouts in one study","pmids":["17143272"],"is_preprint":false},{"year":2009,"finding":"EphA4 in postsynaptic CA1 neurons and ephrin-A3 in astrocytes modulate LTP at the CA3-CA1 synapse by regulating glial glutamate transporter abundance; lack of EphA4 increases glial glutamate transporters, and ephrin-A3 modulates transporter currents in astrocytes. Pharmacological inhibition of glial glutamate transporters rescues LTP defects in EphA4 and ephrin-A3 mutant mice.","method":"EphA4 and ephrin-A3 mutant mice, LTP recordings, glutamate transporter current measurements, pharmacological transporter inhibition, transgenic ephrin-A3 overexpression","journal":"Nature neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic mutants, pharmacological rescue, electrophysiology, multiple orthogonal methods across two mutant lines","pmids":["19734893"],"is_preprint":false},{"year":2000,"finding":"EphA4 expressed at higher levels in dorsal versus ventral limb motor axons is required for dorsal/ventral pathway selection; in EphA4 mutant mice, presumptive dorsal motor axons fail to enter the dorsal compartment of the limb and instead join the ventral nerve, resulting in absence of the peroneal nerve.","method":"EphA4 gene inactivation (knockout mouse), limb innervation analysis, immunolabeling of EphA4 protein in dorsal vs. ventral axons","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO with defined axon guidance phenotype confirmed by protein expression differential; replicated by subsequent cooperation studies","pmids":["10887087"],"is_preprint":false},{"year":2001,"finding":"EphA4 kinase activity is required for corticospinal tract (CST) formation (receptor function), whereas anterior commissure (AC) formation is rescued by kinase-dead EphA4, indicating EphA4 acts as a ligand (kinase-independent) for AC. The cytoplasmic SAM domain is not required for either function.","method":"Knock-in mice expressing kinase-dead or reduced-kinase EphA4 mutants, SAM domain deletion mutants, axon tract tracing","journal":"Neuron","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — structure-function mutagenesis in vivo with multiple mutant alleles and defined phenotypic readouts for two distinct axon tracts","pmids":["11182082"],"is_preprint":false},{"year":2007,"finding":"Alpha2-chimaerin, a Rac-specific GTPase-activating protein, binds activated EphA4 via its SH2 domain and mediates EphA4-triggered axonal growth cone collapse by enhancing its GAP activity toward Rac1. Alpha2-chimaerin mutant mice phenocopy EphA4 kinase-dead mice with hopping gait and aberrant midline axon guidance, establishing alpha2-chimaerin as an essential downstream effector of EphA4.","method":"Co-immunoprecipitation, SH2 domain interaction assay, in vitro GAP activity assay, tyrosine phosphorylation assay, alpha2-chimaerin knockout mice, growth cone collapse assay, locomotor analysis","journal":"Neuron / PNAS","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — biochemical interaction and activity assays combined with genetic KO phenocopying EphA4 mutants, replicated independently by two groups (PMIDs 17785182 and 17785183)","pmids":["17785182","17785183","17911252"],"is_preprint":false},{"year":2009,"finding":"Crystal structure of EphA4 ligand-binding domain (LBD) in complex with ephrin-B2 reveals a loose fit of the ephrin-B2 G-H loop in the EphA4 binding channel. Residues Gln12 and Glu14 of EphA4 make surface contacts critical for ephrin-B class (interclass) binding but not ephrin-A binding; mutation of these residues reduces affinity for ephrin-B ligands ~10-fold without affecting ephrin-A affinity, explaining EphA4's unique pan-ephrin binding promiscuity.","method":"X-ray crystallography, site-directed mutagenesis, binding affinity measurements, NMR characterization","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure combined with mutagenesis and quantitative binding assays in a single study","pmids":["19875447"],"is_preprint":false},{"year":2013,"finding":"High-resolution structures of the complete EphA4 ectodomain and its complex with ephrin-A5 reveal how ligand binding promotes conformational changes in the EphA4 LBD to form higher-order signaling clusters. A previously undescribed receptor-receptor interaction between the EphA4 LBD and membrane-proximal fibronectin domains is functionally important for efficient receptor activation, demonstrated by structure-based mutagenesis.","method":"X-ray crystallography of full EphA4 ectodomain and ephrin-A5 complex, structure-based mutagenesis, receptor activation assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Moderate — high-resolution crystal structures combined with mutagenesis and functional activation assays","pmids":["23959867"],"is_preprint":false},{"year":2010,"finding":"EphA4 activation results in decrease of synaptic and surface GluR1 (AMPA receptor subunit) via the ubiquitin-proteasome system (UPS). EphA4, upon ligand-dependent activation and tyrosine phosphorylation, associates with the ubiquitin ligase APC(Cdh1); APC(Cdh1) directly targets GluR1 for proteasomal degradation. Cdh1 depletion abolishes EphA4-dependent GluR1 downregulation and prevents mEPSC amplitude reduction during homeostatic plasticity.","method":"Co-immunoprecipitation of EphA4 with APC/Cdh1, in vitro proteasomal degradation assay, Cdh1 knockdown in neurons, mEPSC recordings, surface GluR1 imaging","journal":"Nature neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, in vitro reconstitution of degradation, shRNA knockdown with electrophysiological readout, multiple orthogonal methods","pmids":["21186356"],"is_preprint":false},{"year":2007,"finding":"EphA4 activation by ephrin-A3 in hippocampal slices inhibits beta1-integrin signaling: decreases tyrosine phosphorylation of FAK, Pyk2, and Cas, and reduces Cas association with Fyn and Crk. Inhibition of beta1-integrin or Cas function mimics EphA4-induced spine morphological changes, and preventing beta1-integrin inactivation blocks EphA4 effects on spines.","method":"Hippocampal slice ephrin-A3 stimulation, phosphorylation assays, Co-immunoprecipitation, integrin activity assay in neuronal cells, dominant-negative constructs","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — biochemical signaling assays combined with functional rescue/block experiments and morphological readouts in a single study","pmids":["17875741"],"is_preprint":false},{"year":2003,"finding":"EphA4 associates with Vsm-RhoGEF (a VSMC-specific RhoA GEF) in quiescent vascular smooth muscle cells. Upon ephrin-A1 stimulation, EphA4 phosphorylates Vsm-RhoGEF on tyrosine, enhancing its GEF activity toward RhoA. Dominant-negative Vsm-RhoGEF or RNAi depletion blocks ephrin-A1-induced actin stress fiber assembly in VSMCs.","method":"Co-immunoprecipitation (EphA4-Vsm-RhoGEF), tyrosine phosphorylation assays, GEF activity assay, dominant-negative overexpression, siRNA knockdown, actin staining","journal":"Circulation research","confidence":"High","confidence_rationale":"Tier 2 / Moderate — biochemical interaction, enzymatic activity measurement, and functional rescue experiments with two independent methods (dominant-negative and RNAi)","pmids":["12775584"],"is_preprint":false},{"year":2007,"finding":"EphA4 interacts with the PDZ domain of spine-associated RapGAP (SPAR) via its C-terminus, mediating EphA4-dependent inactivation of Rap1 and Rap2. SPAR-mediated Rap1 inactivation (but not Rap2) is critical for ephrin-A-dependent growth cone collapse and decreased integrin-mediated adhesion in neuronal cells.","method":"Co-immunoprecipitation of EphA4-SPAR, Rap GTPase activity assays, dominant-negative SPAR, growth cone collapse assay, integrin adhesion assay","journal":"The Journal of neuroscience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and functional downstream assays in a single lab, single study","pmids":["18094260"],"is_preprint":false},{"year":2007,"finding":"EphA4 activation by ephrin stimulation recruits and activates PLCgamma1 through an SH2 domain interaction requiring EphA4 juxtamembrane tyrosines. PLC activity is required for ephrin-induced spine retraction, and EphA4/PLC signaling modulates the association of cofilin with the plasma membrane, linking EphA4 signaling to actin depolymerization and spine restructuring.","method":"PLCgamma1 recruitment assay, SH2 domain interaction, juxtamembrane tyrosine mutagenesis, PLC inhibitors, cofilin membrane fractionation, hippocampal slice spine morphology","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — mutagenesis of active residues, biochemical recruitment assays, pharmacological inhibition, and morphological readout in a single study with multiple orthogonal methods","pmids":["17494698"],"is_preprint":false},{"year":2005,"finding":"EphA4 promotes cell adhesion within rhombomeres (in addition to mediating repulsion between rhombomeres); in mosaic zebrafish embryos, EphA4-depleted cells sort away from EphA4-expressing cells, supporting a differential cell adhesion mechanism parallel to repulsion in driving rhombomere boundary formation.","method":"Antisense morpholino knockdown in zebrafish, mosaic embryo analysis, cell sorting assays","journal":"Current biology : CB","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — morpholino loss-of-function in zebrafish with mosaic analysis, single lab","pmids":["15797022"],"is_preprint":false},{"year":1998,"finding":"Krox-20 transcription factor directly activates EphA4 transcription in rhombomeres 3 and 5 through eight Krox-20 binding sites within a 470 bp enhancer element; mutation of these sites abolishes r3/r5-specific enhancer activity, and ectopic Krox-20 drives ectopic enhancer activation.","method":"Transgenic mouse enhancer analysis, Krox-20 binding site mutagenesis, ectopic Krox-20 expression, luciferase reporter assays","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — direct binding site mutagenesis, transgenic reporters, and ectopic expression experiments in a single study","pmids":["9425139"],"is_preprint":false},{"year":2006,"finding":"GDNF/Ret and ephrin-A/EphA4 signaling cooperate in the same binary motor axon guidance decision (dorsal vs ventral limb); Ret and EphA4 double-mutant mice show enhanced misrouting of LMC(l) axons compared to single mutants, demonstrating epistatic cooperation between these two guidance systems.","method":"Gdnf, Ret, and EphA4 single and double mutant mouse analysis, limb motor axon tracing","journal":"Neuron","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with double-mutant analysis and axon tracing, well-controlled","pmids":["16600854"],"is_preprint":false},{"year":2005,"finding":"Trans-activation between EphA4 and FGFRs is mediated by direct protein-protein interactions between the juxtamembrane domain of FGFR1-4 and the N-terminal kinase domain of EphA4. FGFR activation leads to tyrosine phosphorylation of kinase-negative EphA4, and EphA4 activation phosphorylates kinase-negative FGFR1; both receptors mutually potentiate FRS2alpha phosphorylation and MAPK activation.","method":"Yeast two-hybrid, Co-immunoprecipitation, kinase-negative receptor trans-phosphorylation assays, MAPK activation assays, ephrin-A1/FGF co-stimulation","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — yeast two-hybrid, biochemical Co-IP, trans-phosphorylation with kinase-negative mutants; multiple methods in one study","pmids":["16365308"],"is_preprint":false},{"year":2014,"finding":"Soluble amyloid-beta oligomers (AβOs) activate EphA4 in hippocampal neurons and synaptoneurosomes; EphA4 depletion or a small-molecule inhibitor (rhynchophylline, identified by molecular docking to the EphA4 LBD) blocks AβO-induced EphA4 activation and reverses suppression of LTP in APP/PS1 transgenic mice, establishing EphA4 as a mediator of Aβ-induced synaptic dysfunction.","method":"EphA4 knockdown in CA1, APP/PS1 transgenic mice, LTP recordings, molecular docking, rhynchophylline administration, EphA4 phosphorylation assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Moderate — genetic depletion and pharmacological inhibition with LTP electrophysiological readout in transgenic AD model, multiple convergent approaches","pmids":["24958880"],"is_preprint":false},{"year":2014,"finding":"EphA4 is upstream of c-Abl kinase activation by amyloid-beta oligomers in hippocampal neurons; AβO-induced EphA4 tyrosine phosphorylation is required for c-Abl activation (no c-Abl activation detected in EphA4-KO neurons exposed to AβOs). EphA4/c-Abl signaling mediates dendritic spine reduction, LTP blockade, and neuronal apoptosis caused by AβOs.","method":"EphA4 knockout neurons, sh-EphA4 transfection, c-Abl activity assays, EphA4 antagonist peptide (KYL), c-Abl inhibitor (STI), LTP recordings, spine density analysis","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Moderate — genetic KO, shRNA, two pharmacological inhibitors, and multiple functional readouts converge on same pathway","pmids":["24658113"],"is_preprint":false},{"year":2006,"finding":"Mesp2 transcription factor directly binds to E-box-containing enhancer sequences of Epha4 and activates its transcription in the anterior presomitic mesoderm; forced Mesp2 expression activates EphA4 expression and represses caudal gene Uncx4.1 in somitic cells.","method":"Enhancer deletion analysis, luciferase reporter assays, transgenic mice, Mesp2 chromatin immunoprecipitation / direct binding assay, ectopic Mesp2 expression","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — direct binding demonstrated, transgenic and reporter assays, gain-of-function in vivo in a single study","pmids":["16728472"],"is_preprint":false},{"year":2007,"finding":"EphA4 is localized predominantly on the plasma membrane of axon terminals and dendritic spines (25-40% of terminals and 9-19% of spines labeled) at asymmetric/excitatory synapses in adult rat hippocampus, with dual pre- and postsynaptic localization supporting roles in synaptic plasticity.","method":"Electron microscopic immunocytochemistry (immunoperoxidase and immunogold labeling) in adult rat hippocampus","journal":"The Journal of comparative neurology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — high-resolution electron microscopy with two immunolabeling methods in one study; localization without direct functional link in this paper","pmids":["17299751"],"is_preprint":false},{"year":2013,"finding":"EphA4 forward signaling (ephrin-A5/EphA4) is required for targeting type I spiral ganglion neuron afferents to inner hair cells in the cochlea; in EphA4 forward signaling-deficient mice, type I projections aberrantly invade the outer hair cell area. Downstream effectors ephexin-1, cofilin, and myosin light chain kinase act downstream of EphA4 to induce type I neuron growth cone collapse.","method":"EphA4 and ephrin-A5 knockout mice, conditional EphA4 mutants, growth cone collapse assay with ephexin-1/cofilin/MLCK pathway analysis, cochlear innervation analysis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Moderate — conditional genetic mutants, pathway epistasis, and growth cone collapse assay with downstream effector analysis","pmids":["23385583"],"is_preprint":false},{"year":2015,"finding":"EphA4 forward signaling in pancreatic alpha-cells maintains a dense F-actin network that tonically inhibits glucagon secretion; alpha-cell-specific EphA4-/- mice exhibit abnormal glucagon dynamics and less dense F-actin. Stimulation of EphA4 inhibits glucagon secretion while inhibition enhances it, and restoration of EphA4 forward signaling in sorted alpha-cells rescues normal basal glucagon secretion and glucose inhibition of secretion.","method":"Alpha-cell-specific EphA4 knockout mice, glucagon secretion assays, EphA4 stimulation/inhibition in islets, sorted alpha-cells, F-actin density measurements","journal":"Diabetes","confidence":"High","confidence_rationale":"Tier 2 / Moderate — cell-type-specific KO, functional secretion assays, rescue experiments, mechanistic link to F-actin","pmids":["26251403"],"is_preprint":false},{"year":2008,"finding":"EphA4 forms a heteroreceptor complex with FGFR1 in glioma cells; EphA4 overexpression enhances FGF2-mediated MAPK and Akt phosphorylation, and increases active Rac1 and Cdc42, promoting cell proliferation and migration.","method":"Co-immunoprecipitation (EphA4-FGFR1), MAPK/Akt phosphorylation assays, Rac1/Cdc42 pull-down (GTP-bound), overexpression in U251 glioma cells","journal":"Molecular cancer therapeutics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP of endogenous complex, multiple downstream signaling readouts, single lab","pmids":["18790757"],"is_preprint":false},{"year":2018,"finding":"Axonal ephrin-A1 activates EphA4 on oligodendrocytes to trigger the ephexin1-RhoA-ROCK-myosin 2 signaling cascade, causing inhibition of oligodendrocyte process extension and reduced myelination. EphA4 knockdown or inhibition at multiple levels of this pathway increases the number of myelin sheaths per oligodendrocyte.","method":"Axon-mimicking microfibers, zebrafish myelination model, EphA4 knockdown, pathway inhibitors (ROCK, myosin 2), ephexin1 assays, myelin sheath counting","journal":"Glia","confidence":"High","confidence_rationale":"Tier 2 / Moderate — two experimental systems (in vitro microfibers + in vivo zebrafish), genetic knockdown, and pharmacological inhibition at multiple pathway levels","pmids":["29350423"],"is_preprint":false},{"year":2017,"finding":"SORLA (SORL1) directly interacts with EphA4 and attenuates ephrinA1-induced EphA4 clustering and activation; SORLA transgenic mice show decreased EphA4 activation and redistribution to postsynaptic densities, with milder LTP and memory deficits induced by Aβ oligomers. Active EphA4 levels are elevated in human AD brains inversely correlated with SORLA/EphA4 association.","method":"Co-immunoprecipitation (SORLA-EphA4), SORLA transgenic mice, EphA4 clustering assay, LTP recordings, human AD brain analysis","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 / Moderate — biochemical interaction, transgenic mouse physiology, and human tissue correlation in a single study with multiple methods","pmids":["29114064"],"is_preprint":false},{"year":2014,"finding":"EphA4 shedding (ectodomain cleavage) in limb mesenchyme regulates spinal motor axon guidance: blocking EphA4 cleavage increases full-length EphA4 in limb mesenchyme, which via cis-attenuation reduces effective ephrin-A concentration available to trigger EphA4 forward signaling in motor axons, causing guidance defects. Cleavage-resistant EphA4 on neurons is as effective as wild-type for redirecting motor axons.","method":"Cleavage-resistant EphA4 knock-in mice, in vitro cell detachment assays, motor axon tracing, conditional EphA4 cleavage ablation in limb mesenchyme","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — knock-in genetic models with tissue-specific conditional analysis and functional axon tracing readouts","pmids":["25264256"],"is_preprint":false},{"year":2020,"finding":"EphA4 in vascular endothelial cells suppresses pial collateral remodeling and cerebral blood flow recovery after ischemic stroke; endothelial-specific EphA4 deletion (EphA4fl/fl/Tie2-Cre and EphA4fl/fl/VeCadherin-CreERT2) enhances arteriogenic response. EphA4 negatively regulates Tie2 receptor signaling in endothelial cells through p-Akt modulation.","method":"Endothelial-specific EphA4 conditional knockout mice (two Cre lines), vessel painting, CBF measurement, Akt phosphorylation assays, peptide inhibition of EphA4","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 / Strong — two independent conditional KO models, functional vascular readout, biochemical pathway analysis, and pharmacological confirmation","pmids":["31689239"],"is_preprint":false},{"year":2009,"finding":"EphA4 forward signaling, specifically requiring EphA4 kinase activity, promotes proliferation of cortical progenitor cells during corticogenesis; EphA4-/- cortex has fewer cells and less cell division. EphA4 and ephrin-B1 (expressed in cortical progenitors) bind and initiate signaling, and ephrin-B1 overexpression stimulates division of neighboring cells via EphA4 forward signaling.","method":"EphA4-/- mice, in vivo EphA4 overexpression/knockdown in progenitors, cell division assays, binding assay (EphA4-ephrin-B1), cortical area measurements","journal":"Development (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO plus in vivo gain/loss-of-function and direct binding assay in a single study, single lab","pmids":["19542359"],"is_preprint":false},{"year":2013,"finding":"EphrinB3-induced EphA4 forward signaling guides both ascending Zic2+/EphA4+ spinal neuron axons and descending corticospinal tract axons using the same molecular mechanism; conditional EphA4 mutant analysis reveals that dorsal funiculus development depends on EphA4 in Zic2+ spinal neurons, not in descending CST axons.","method":"Conditional EphA4 knockout mice (Zic2-Cre and other Cre lines), axon tract tracing, anatomical analysis","journal":"Neuron","confidence":"High","confidence_rationale":"Tier 2 / Moderate — conditional genetic approach disambiguating cell-type-specific roles with axon tracing","pmids":["24360544"],"is_preprint":false},{"year":2007,"finding":"EphA4 signaling in Xenopus blastulae induces reversible, cell-autonomous loss of adhesion; this is rescued by Nckbeta (Grb4) interaction with EphA4. EphA4 activates xPAK1 in an Nck-dependent manner; xPAK1 GTPase-binding domain sequesters active Cdc42, causing RhoA-GTP downregulation and loss of cell-cell adhesion.","method":"Xenopus blastula injection, dominant-negative and constitutively active GTPase constructs, xPAK1 activation assay, epistasis analysis, Cdc42/Rac/RhoA activity assays","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis analysis and GTPase activity measurements in Xenopus, single lab","pmids":["17215521"],"is_preprint":false},{"year":2002,"finding":"In early Xenopus embryos, EphA4 catalytic activity inhibits RhoA GTPase (in contrast to activation in neuronal cells); constitutively active XRhoA rescues EphA4-induced loss of cell-cell adhesion, and overexpression of ephexin blocks EphA4-induced dissociation, suggesting an ephexin-dependent or independent pathway to Rho depending on cell context.","method":"Chimeric EPP receptor expression in Xenopus embryos, constitutively active XRhoA rescue, Rho GTPase inhibitor injection, ephexin overexpression","journal":"Differentiation; research in biological diversity","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis with constitutively active GTPase rescue and pharmacological inhibition in Xenopus, single lab","pmids":["11963655"],"is_preprint":false},{"year":2014,"finding":"Crystal structure of a cyclic peptide antagonist (APY) bound to the EphA4 ligand-binding domain shows efficient occupation of the ephrin-binding pocket with a 'closed' loop conformation. Structure-guided optimization yielded APY-βAla8.am with nanomolar EphA4 affinity; this peptide potently inhibits ephrin-induced EphA4 activation in cells and EphA4-dependent neuronal growth cone collapse with high EphA4 selectivity.","method":"X-ray crystallography of peptide-EphA4 LBD complex, structure-guided mutagenesis, binding affinity assay, cell-based EphA4 activation assay, growth cone collapse assay","journal":"ACS chemical biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structures of two peptide-receptor complexes combined with functional cellular assays in a single study","pmids":["25268696"],"is_preprint":false},{"year":2014,"finding":"EphA4 deficiency in osteoclasts activates beta3-integrin signaling through reduced phosphorylation of tyr-747, which increases binding of stimulatory talin and reduces binding of inhibitory Dok1 to beta3-integrin, in turn activating Vav3 and osteoclast bone resorption activity. EphA4 is thus a negative regulator of osteoclastic activity via this integrin-signaling pathway.","method":"EphA4 null mice (bone analysis), siRNA knockdown in RAW/C4 cells, EfnA4-Fc stimulation, beta3-integrin phosphorylation assays, talin/Dok1 Co-IP with beta3-integrin, Vav3 activation assay, bone resorption assay","journal":"Journal of bone and mineral research","confidence":"High","confidence_rationale":"Tier 2 / Moderate — KO mouse, RNAi, activation ligand, and multiple biochemical assays converge on same mechanistic pathway","pmids":["23983218"],"is_preprint":false},{"year":2016,"finding":"EphA4 is an upstream negative regulator of efferocytosis in macrophages/microglia after brain injury; EphA4 loss enhances efferocytosis by increasing p-ERK and p-Stat6 activity, which upregulates MERTK and Gas6 expression. ERK and Stat6 inhibitors abrogate the efferocytosis enhancement in EphA4 KO cells, establishing an EphA4→ERK/Stat6→MERTK signaling axis.","method":"Bone marrow chimeric EphA4 KO mice, TBI model, in vitro efferocytosis assay, phosphoarray, ERK/Stat6 selective inhibitors, MERTK/Gas6 mRNA analysis, single-cell RNAseq","journal":"Journal of neuroinflammation","confidence":"High","confidence_rationale":"Tier 2 / Moderate — genetic KO, pharmacological inhibition of downstream effectors, in vitro and in vivo convergence on the same pathway","pmids":["37941008"],"is_preprint":false},{"year":2017,"finding":"EphA4 acts upstream of Sipa1l3 during eye development in Xenopus; EphA4 deficiency phenocopies Sipa1l3 loss, and rescue experiments show EphA4 is upstream of Sipa1l3. Both proteins inhibit canonical Wnt/beta-catenin signaling (EphA4/Sipa1l3 loss upregulates axin2); inhibiting Wnt/beta-catenin or activating non-canonical Wnt rescues the EphA4-depletion eye phenotype.","method":"Xenopus morpholino knockdown, direct interaction assay (EphA4-Sipa1l3), genetic epistasis (rescue experiments), Wnt pathway reporter (axin2), pathway inhibition/activation rescue","journal":"Development (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct interaction and epistasis in Xenopus, single lab, pathway placement supported by rescue experiments","pmids":["27993984"],"is_preprint":false},{"year":2022,"finding":"EphA4 promotes proliferation of oligodendrocyte precursor cells (OPCs) but reduces maturation to oligodendrocytes and decreases myelin-associated proteins after ischemic stroke; conditional OPC-specific EphA4 knockout improves remyelination and functional recovery. This effect is mediated by the Ephexin-1/RhoA/ROCK signaling pathway.","method":"PDGFRα-EphA4-shRNA, LV-EphA4 overexpression, EphA4fl/fl/AAV-PDGFRα-Cre conditional KO, MCAO/R ischemia model, OGD/R in vitro, myelin protein analysis, Ephexin-1/RhoA/ROCK pathway assays","journal":"Glia","confidence":"High","confidence_rationale":"Tier 2 / Moderate — conditional KO and knockdown/overexpression in two experimental models with pathway epistasis demonstration","pmids":["35762396"],"is_preprint":false},{"year":2017,"finding":"EphA4 acts as a dependence receptor: in the absence of its ligand ephrin-B3, EphA4 triggers apoptosis in glioblastoma cells. Ephrin-B3 overexpression in GBM inhibits EphA4 pro-apoptotic activity; Ephrin-B3 silencing reduces tumor vascularization and growth in xenograft mice.","method":"Ephrin-B3 silencing (siRNA), xenograft GBM mouse model, apoptosis assays, in vitro endothelial cell survival assay, human GBM biopsy analysis","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional siRNA, xenograft model, and in vitro assays in one study; dependence receptor mechanism inferred from ligand-removal apoptosis","pmids":["28423606"],"is_preprint":false}],"current_model":"EphA4 is a receptor tyrosine kinase that upon binding A- or B-class ephrin ligands (with unique pan-ephrin promiscuity enabled by distinct LBD surface contacts) undergoes clustering and kinase activation to trigger multiple downstream signaling cascades—including ephexin1/RhoA, alpha2-chimaerin/Rac1, PLCgamma1/cofilin, SPAR/Rap GTPases, Cdk5, APC(Cdh1)/GluR1, and beta1-integrin pathways—that regulate dendritic spine morphology, synaptic plasticity (LTP, AMPA receptor homeostasis), axon guidance (corticospinal, limb motor, commissural tracts), neuroglial interactions (astrocyte-mediated glutamate transport, myelination, gliosis), and diverse cell biological processes including cell adhesion, vascular remodeling, osteoclast activity, glucagon secretion, and neuroinflammation resolution."},"narrative":{"mechanistic_narrative":"EphA4 is a receptor tyrosine kinase that, upon binding A- and B-class ephrins, clusters and activates a tyrosine-kinase cascade to control cell repulsion, adhesion, cytoskeletal remodeling, and synaptic function across the nervous system and beyond [PMID:12496762, PMID:9259557, PMID:19875447]. Its unusual pan-ephrin promiscuity is structurally explained: ephrin-A5 binding drives conformational change and higher-order clustering reinforced by an LBD–fibronectin receptor-receptor contact, while LBD residues Gln12/Glu14 provide interclass ephrin-B binding [PMID:19875447, PMID:23959867]. Activated EphA4 channels signaling principally into Rho-family GTPase regulation—recruiting Cdk5 to activate the RhoA-GEF ephexin1 [PMID:17143272], engaging the Rac-GAP alpha2-chimaerin via its SH2 domain [PMID:17785182, PMID:17785183, PMID:17911252], and acting through SPAR/Rap1 and PLCgamma1/cofilin—to drive growth-cone collapse, dendritic spine retraction, and actin reorganization [PMID:18094260, PMID:17494698]. In parallel, ligand-activated EphA4 recruits the ubiquitin ligase APC(Cdh1) to degrade GluR1 and downregulates beta1-integrin signaling, linking it to AMPA-receptor homeostasis and synaptic plasticity [PMID:21186356, PMID:17875741]. At the circuit level EphA4 directs axon guidance of corticospinal, limb-motor, and commissural tracts—requiring kinase activity for some tracts but acting kinase-independently (as a ligand) for the anterior commissure—and patterns neural crest and rhombomere/somite boundaries downstream of Krox-20 and Mesp2 [PMID:9789074, PMID:10887087, PMID:11182082, PMID:9425139, PMID:16728472]. EphA4 additionally regulates astrocytic gliosis after injury, glial glutamate transport during LTP, oligodendrocyte myelination via ephexin1/RhoA/ROCK, and is a mediator of amyloid-beta oligomer-induced synaptic dysfunction through c-Abl, antagonized by SORLA [PMID:15537875, PMID:19734893, PMID:24958880, PMID:24658113, PMID:29350423, PMID:29114064]. Outside the nervous system it negatively regulates osteoclast bone resorption, endothelial collateral remodeling, glucagon secretion, and macrophage efferocytosis [PMID:26251403, PMID:31689239, PMID:23983218, PMID:37941008].","teleology":[{"year":1997,"claim":"Established EphA4 as a repulsive guidance receptor governing positional sorting, answering how migrating cells reach correct destinations.","evidence":"Dominant-negative receptor and ectopic ephrin-B2 in Xenopus neural crest","pmids":["9259557"],"confidence":"High","gaps":["Downstream signaling not defined","Mammalian relevance not tested in this study"]},{"year":1998,"claim":"Genetic knockout defined EphA4 as essential for corticospinal tract formation and revealed direct transcriptional control by Krox-20 in rhombomeres, linking patterning to receptor expression.","evidence":"EphA4 null mice with anterograde tracing; Krox-20 binding-site mutagenesis and transgenic reporters","pmids":["9789074","9425139"],"confidence":"High","gaps":["Did not separate kinase-dependent from kinase-independent function","Effector pathways unresolved"]},{"year":2000,"claim":"Showed EphA4 dosage encodes binary axon pathfinding decisions, explaining dorsal/ventral limb motor selection.","evidence":"EphA4 knockout limb innervation analysis with differential protein expression","pmids":["10887087"],"confidence":"High","gaps":["Co-acting guidance systems not yet integrated","Mechanism of dorsal-specific enrichment unknown"]},{"year":2001,"claim":"Demonstrated EphA4 can signal both as a kinase-active receptor and as a kinase-independent ligand, resolving how one molecule guides distinct tracts.","evidence":"Kinase-dead and SAM-deletion knock-in mice with tract tracing","pmids":["11182082"],"confidence":"High","gaps":["Reverse-signaling partner for AC not identified","Structural basis of kinase-independent mode unclear"]},{"year":2003,"claim":"Connected EphA4 to dendritic spine morphology via neuroglial cross-talk, establishing a postsynaptic role and a Rho-GEF mechanism in vascular cells.","evidence":"Hippocampal slices with KO mice and kinase-dead mutant; Co-IP and GEF assays of Vsm-RhoGEF in VSMCs","pmids":["12496762","12775584"],"confidence":"High","gaps":["Full effector chain to actin not yet mapped","VSMC and neuronal mechanisms not unified"]},{"year":2006,"claim":"Identified Cdk5 recruitment to EphA4 as the trigger for ephexin1/RhoA activation and spine retraction, defining a core kinase-effector module; Mesp2 added a second direct transcriptional input.","evidence":"Reciprocal Co-IP, Cdk5-/- brains, phosphorylation and electrophysiology; Mesp2 binding and reporter assays","pmids":["17143272","16728472"],"confidence":"High","gaps":["Spatial control of Cdk5 recruitment unknown","Crosstalk between ephexin1 and other GEFs unresolved"]},{"year":2007,"claim":"Mapped parallel downstream effectors—alpha2-chimaerin/Rac1, PLCgamma1/cofilin, SPAR/Rap, and beta1-integrin inactivation—that mediate growth-cone collapse and spine remodeling, and showed FGFR trans-activation.","evidence":"SH2-domain interaction, GAP/GEF activity assays, KO mice phenocopying, juxtamembrane mutagenesis, yeast two-hybrid and trans-phosphorylation","pmids":["17785182","17785183","17911252","17494698","18094260","17875741","16365308"],"confidence":"High","gaps":["Hierarchy among parallel effectors not established","Context-dependent effector selection unexplained"]},{"year":2009,"claim":"Defined the structural basis of pan-ephrin promiscuity and linked EphA4 to LTP via glial glutamate transport and cortical progenitor proliferation.","evidence":"EphA4-ephrin-B2 crystal structure with mutagenesis; ephrin-A3/EphA4 mutant LTP recordings; cortical progenitor gain/loss of function","pmids":["19875447","19734893","19542359"],"confidence":"High","gaps":["Cluster assembly mechanism still incomplete in 2009","Progenitor effector pathway not defined"]},{"year":2010,"claim":"Revealed that EphA4 drives AMPA-receptor homeostasis by recruiting APC(Cdh1) to degrade GluR1, connecting receptor activation to proteostatic control of synaptic strength.","evidence":"Reciprocal Co-IP, in vitro proteasomal degradation, Cdh1 knockdown with mEPSC recordings","pmids":["21186356"],"confidence":"High","gaps":["How phosphorylated EphA4 selects APC(Cdh1) unknown","Other proteasomal substrates not identified"]},{"year":2013,"claim":"Resolved the full ectodomain architecture and clustering mechanism, and used conditional and forward-signaling-specific models to assign cell-autonomous guidance roles in cochlea and spinal cord.","evidence":"Full ectodomain and ephrin-A5 complex crystallography with mutagenesis; conditional EphA4 mutants with tract/innervation tracing","pmids":["23959867","23385583","24360544"],"confidence":"High","gaps":["Stoichiometry of physiological clusters in vivo unknown","Link between cluster size and effector output unmapped"]},{"year":2014,"claim":"Implicated EphA4 as a mediator of amyloid-beta oligomer synaptic toxicity via c-Abl, identified small-molecule and peptide antagonists, and showed ectodomain shedding tunes ligand availability.","evidence":"EphA4-KO neurons and APP/PS1 mice with LTP; molecular docking and rhynchophylline; cyclic peptide co-crystal structures; cleavage-resistant knock-in mice","pmids":["24958880","24658113","25268696","25264256"],"confidence":"High","gaps":["In vivo therapeutic efficacy of antagonists not established","Sheddase identity and regulation unresolved"]},{"year":2017,"claim":"Extended EphA4 function to dependence-receptor apoptosis in glioblastoma, SORLA-mediated negative regulation in AD, and Sipa1l3/Wnt control in eye development.","evidence":"Ephrin-B3 silencing with GBM xenografts; SORLA Co-IP, transgenic mice and human AD brain; Xenopus epistasis with Wnt reporters","pmids":["28423606","29114064","27993984"],"confidence":"Medium","gaps":["Dependence-receptor death effectors not defined","SORLA regulatory mechanism on clustering incompletely resolved"]},{"year":2020,"claim":"Defined non-neuronal physiological roles: endothelial EphA4 suppresses collateral remodeling via Tie2/Akt, alpha-cell EphA4 tonically inhibits glucagon through F-actin, osteoclast EphA4 restrains bone resorption via beta3-integrin, and macrophage EphA4 limits efferocytosis through ERK/Stat6/MERTK.","evidence":"Cell-type-specific conditional KO mice with functional and biochemical pathway assays across vascular, pancreatic, bone, and immune systems","pmids":["31689239","26251403","23983218","37941008"],"confidence":"High","gaps":["Ligands driving each peripheral context not fully defined","Shared versus distinct effector logic across tissues unclear"]},{"year":2022,"claim":"Established that EphA4 in oligodendrocyte lineage cells restrains maturation and myelination via ephexin1/RhoA/ROCK, identifying it as a remyelination target after stroke.","evidence":"OPC-specific conditional KO, knockdown/overexpression in MCAO/R and OGD/R models with pathway epistasis","pmids":["35762396","29350423"],"confidence":"High","gaps":["Axonal versus glial ligand source not isolated","Translation to chronic demyelination untested"]},{"year":null,"claim":"How distinct ephrin ligands and cluster geometries are decoded into selection among the many parallel effector pathways (Cdk5/ephexin1, alpha2-chimaerin, PLCgamma1, SPAR/Rap, APC(Cdh1), integrin) in a cell-type-specific manner remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No unified model linking cluster state to effector choice","Quantitative effector competition not measured","Context determinants of kinase-dependent versus dependence-receptor outputs unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[4,8,13,19]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[4,13,19]},{"term_id":"GO:0098631","term_label":"cell adhesion mediator activity","supporting_discovery_ids":[16,33]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[0,9,10]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[5,30,36]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[23]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[23]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[4,8,15,19]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[2,6,7,17,22,31]},{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[0,5,11,20]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[11]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[20,21,28,40]}],"complexes":[],"partners":["EFNA3","CDK5","NGEF","CHN1","PLCG1","FGFR1","SORL1","FCHSD"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P54764","full_name":"Ephrin type-A receptor 4","aliases":["EPH-like kinase 8","EK8","hEK8","Tyrosine-protein kinase TYRO1","Tyrosine-protein kinase receptor SEK"],"length_aa":986,"mass_kda":109.9,"function":"Receptor tyrosine kinase which binds membrane-bound ephrin 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. Highly promiscuous, it has the unique property among Eph receptors to bind and to be physiologically activated by both GPI-anchored ephrin-A and transmembrane ephrin-B ligands including EFNA1 and EFNB3. Upon activation by ephrin ligands, modulates cell morphology and integrin-dependent cell adhesion through regulation of the Rac, Rap and Rho GTPases activity. Plays an important role in the development of the nervous system controlling different steps of axonal guidance including the establishment of the corticospinal projections. May also control the segregation of motor and sensory axons during neuromuscular circuit development. In addition to its role in axonal guidance plays a role in synaptic plasticity. Activated by EFNA1 phosphorylates CDK5 at 'Tyr-15' which in turn phosphorylates NGEF regulating RHOA and dendritic spine morphogenesis. In the nervous system, also plays a role in repair after injury preventing axonal regeneration and in angiogenesis playing a role in central nervous system vascular formation. Additionally, its promiscuity makes it available to participate in a variety of cell-cell signaling regulating for instance the development of the thymic epithelium. During development of the cochlear organ of Corti, regulates pillar cell separation by forming a ternary complex with ADAM10 and CADH1 which facilitates the cleavage of CADH1 by ADAM10 and disruption of adherens junctions (By similarity). Phosphorylates CAPRIN1, promoting CAPRIN1-dependent formation of a membraneless compartment (By similarity)","subcellular_location":"Cell membrane; Cell projection, axon; Cell projection, dendrite; Postsynaptic density membrane; Early endosome; Cell junction, adherens junction","url":"https://www.uniprot.org/uniprotkb/P54764/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/EPHA4","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/EPHA4","total_profiled":1310},"omim":[{"mim_id":"620431","title":"FLYWCH-TYPE ZINC FINGER PROTEIN 1; FLYWCH1","url":"https://www.omim.org/entry/620431"},{"mim_id":"608504","title":"RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 15; ARHGEF15","url":"https://www.omim.org/entry/608504"},{"mim_id":"604930","title":"NCK ADAPTOR PROTEIN 2; NCK2","url":"https://www.omim.org/entry/604930"},{"mim_id":"602297","title":"EPHRIN B3; EFNB3","url":"https://www.omim.org/entry/602297"},{"mim_id":"602190","title":"EPHRIN RECEPTOR EphA7; EPHA7","url":"https://www.omim.org/entry/602190"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":23.6}],"url":"https://www.proteinatlas.org/search/EPHA4"},"hgnc":{"alias_symbol":["Hek8"],"prev_symbol":["TYRO1"]},"alphafold":{"accession":"P54764","domains":[{"cath_id":"2.60.120.260","chopping":"29-203","consensus_level":"high","plddt":89.2692,"start":29,"end":203},{"cath_id":"2.60.40.1770","chopping":"206-262","consensus_level":"medium","plddt":92.2212,"start":206,"end":262},{"cath_id":"2.60.40.10","chopping":"331-434","consensus_level":"high","plddt":91.0904,"start":331,"end":434},{"cath_id":"2.60.40.10","chopping":"446-531","consensus_level":"high","plddt":91.0194,"start":446,"end":531},{"cath_id":"3.30.200.20","chopping":"602-699","consensus_level":"high","plddt":86.8497,"start":602,"end":699},{"cath_id":"1.10.510.10","chopping":"704-769_786-887","consensus_level":"high","plddt":91.2629,"start":704,"end":887},{"cath_id":"1.10.150.50","chopping":"909-980","consensus_level":"high","plddt":82.4174,"start":909,"end":980}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P54764","model_url":"https://alphafold.ebi.ac.uk/files/AF-P54764-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P54764-F1-predicted_aligned_error_v6.png","plddt_mean":83.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=EPHA4","jax_strain_url":"https://www.jax.org/strain/search?query=EPHA4"},"sequence":{"accession":"P54764","fasta_url":"https://rest.uniprot.org/uniprotkb/P54764.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P54764/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P54764"}},"corpus_meta":[{"pmid":"12496762","id":"PMC_12496762","title":"Control 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by astrocytic ephrin-A3 induces spine retraction, while inhibiting ephrin/EphA4 interactions or using kinase-inactive EphA4 distorts spine shape, establishing that ephrin-A3/EphA4 signaling controls dendritic spine morphology through neuroglial cross-talk.\",\n      \"method\": \"Hippocampal slice experiments, EphA4 knockout mice, kinase-inactive EphA4 transfection, ephrin-A3 activation assays\",\n      \"journal\": \"Nature neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (KO mice, kinase-dead mutant, pharmacological inhibition, slice physiology) replicated across conditions in one rigorous study\",\n      \"pmids\": [\"12496762\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"EphA4 and EphB1 expressed in migrating neural crest cells mediate repulsive interactions with ephrin-B2 to restrict intermingling of third arch neural crest cells and target them to the correct branchial arch destination; inhibition of EphA4/EphB1 function via truncated receptors causes aberrant migration, and ectopic ephrin-B2 scatters third arch neural crest.\",\n      \"method\": \"Truncated dominant-negative receptor expression in Xenopus, ectopic ephrin-B2 overexpression, neural crest migration tracking\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function and gain-of-function experiments in Xenopus with defined cellular phenotype, complementary expression mapping\",\n      \"pmids\": [\"9259557\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"EphA4 (Sek1) is required for corticospinal tract formation; EphA4 null mice show major disruptions of the corticospinal tract in the medulla and spinal cord, demonstrating a critical role in establishing corticospinal projections.\",\n      \"method\": \"EphA4 null mutant mouse generation, anterograde tracing experiments, anatomical analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic knockout with defined axon tract phenotype confirmed by anterograde tracing; replicated in subsequent studies\",\n      \"pmids\": [\"9789074\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"EphA4 expression is upregulated on astrocytes at spinal cord lesion sites; EphA4-/- mice show reduced astrocytic gliosis and glial scar formation, and EphA4-/- astrocytes fail to respond to inflammatory cytokines (IFN-γ or LIF). Neurons grown on wild-type astrocytes extend shorter neurites than on EphA4-/- astrocytes, but grow longer neurites when astrocyte EphA4 is blocked by monomeric EphrinA5-Fc, establishing EphA4 as a regulator of astrocytic gliosis and axonal inhibition after spinal cord injury.\",\n      \"method\": \"EphA4 knockout mice, spinal cord hemisection, anterograde and retrograde tracing, in vitro astrocyte/neuron co-culture assays, cytokine stimulation, monomeric EphrinA5-Fc blockade\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — KO mice with functional recovery, in vitro mechanistic assays, pharmacological blockade, multiple orthogonal readouts\",\n      \"pmids\": [\"15537875\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Cdk5 is recruited to EphA4 upon ephrin-A1 activation, leading to tyrosine phosphorylation and activation of Cdk5. Activated EphA4/Cdk5 then enhances activation of ephexin1 (a RhoA GEF) via Cdk5-dependent phosphorylation of ephexin1, leading to RhoA activation and dendritic spine retraction. Cdk5 activity is required for ephrin-A1-triggered spine retraction and mEPSC frequency reduction.\",\n      \"method\": \"Cdk5 inhibition assays, Co-immunoprecipitation of EphA4 and Cdk5, tyrosine phosphorylation assays, Cdk5-/- brains, ephrin-A1 stimulation, mEPSC recordings, spine density analysis\",\n      \"journal\": \"Nature neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, genetic knockout (Cdk5-/-), phosphorylation assays, electrophysiology, and morphological readouts in one study\",\n      \"pmids\": [\"17143272\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"EphA4 in postsynaptic CA1 neurons and ephrin-A3 in astrocytes modulate LTP at the CA3-CA1 synapse by regulating glial glutamate transporter abundance; lack of EphA4 increases glial glutamate transporters, and ephrin-A3 modulates transporter currents in astrocytes. Pharmacological inhibition of glial glutamate transporters rescues LTP defects in EphA4 and ephrin-A3 mutant mice.\",\n      \"method\": \"EphA4 and ephrin-A3 mutant mice, LTP recordings, glutamate transporter current measurements, pharmacological transporter inhibition, transgenic ephrin-A3 overexpression\",\n      \"journal\": \"Nature neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic mutants, pharmacological rescue, electrophysiology, multiple orthogonal methods across two mutant lines\",\n      \"pmids\": [\"19734893\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"EphA4 expressed at higher levels in dorsal versus ventral limb motor axons is required for dorsal/ventral pathway selection; in EphA4 mutant mice, presumptive dorsal motor axons fail to enter the dorsal compartment of the limb and instead join the ventral nerve, resulting in absence of the peroneal nerve.\",\n      \"method\": \"EphA4 gene inactivation (knockout mouse), limb innervation analysis, immunolabeling of EphA4 protein in dorsal vs. ventral axons\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO with defined axon guidance phenotype confirmed by protein expression differential; replicated by subsequent cooperation studies\",\n      \"pmids\": [\"10887087\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"EphA4 kinase activity is required for corticospinal tract (CST) formation (receptor function), whereas anterior commissure (AC) formation is rescued by kinase-dead EphA4, indicating EphA4 acts as a ligand (kinase-independent) for AC. The cytoplasmic SAM domain is not required for either function.\",\n      \"method\": \"Knock-in mice expressing kinase-dead or reduced-kinase EphA4 mutants, SAM domain deletion mutants, axon tract tracing\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — structure-function mutagenesis in vivo with multiple mutant alleles and defined phenotypic readouts for two distinct axon tracts\",\n      \"pmids\": [\"11182082\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Alpha2-chimaerin, a Rac-specific GTPase-activating protein, binds activated EphA4 via its SH2 domain and mediates EphA4-triggered axonal growth cone collapse by enhancing its GAP activity toward Rac1. Alpha2-chimaerin mutant mice phenocopy EphA4 kinase-dead mice with hopping gait and aberrant midline axon guidance, establishing alpha2-chimaerin as an essential downstream effector of EphA4.\",\n      \"method\": \"Co-immunoprecipitation, SH2 domain interaction assay, in vitro GAP activity assay, tyrosine phosphorylation assay, alpha2-chimaerin knockout mice, growth cone collapse assay, locomotor analysis\",\n      \"journal\": \"Neuron / PNAS\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — biochemical interaction and activity assays combined with genetic KO phenocopying EphA4 mutants, replicated independently by two groups (PMIDs 17785182 and 17785183)\",\n      \"pmids\": [\"17785182\", \"17785183\", \"17911252\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Crystal structure of EphA4 ligand-binding domain (LBD) in complex with ephrin-B2 reveals a loose fit of the ephrin-B2 G-H loop in the EphA4 binding channel. Residues Gln12 and Glu14 of EphA4 make surface contacts critical for ephrin-B class (interclass) binding but not ephrin-A binding; mutation of these residues reduces affinity for ephrin-B ligands ~10-fold without affecting ephrin-A affinity, explaining EphA4's unique pan-ephrin binding promiscuity.\",\n      \"method\": \"X-ray crystallography, site-directed mutagenesis, binding affinity measurements, NMR characterization\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure combined with mutagenesis and quantitative binding assays in a single study\",\n      \"pmids\": [\"19875447\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"High-resolution structures of the complete EphA4 ectodomain and its complex with ephrin-A5 reveal how ligand binding promotes conformational changes in the EphA4 LBD to form higher-order signaling clusters. A previously undescribed receptor-receptor interaction between the EphA4 LBD and membrane-proximal fibronectin domains is functionally important for efficient receptor activation, demonstrated by structure-based mutagenesis.\",\n      \"method\": \"X-ray crystallography of full EphA4 ectodomain and ephrin-A5 complex, structure-based mutagenesis, receptor activation assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — high-resolution crystal structures combined with mutagenesis and functional activation assays\",\n      \"pmids\": [\"23959867\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"EphA4 activation results in decrease of synaptic and surface GluR1 (AMPA receptor subunit) via the ubiquitin-proteasome system (UPS). EphA4, upon ligand-dependent activation and tyrosine phosphorylation, associates with the ubiquitin ligase APC(Cdh1); APC(Cdh1) directly targets GluR1 for proteasomal degradation. Cdh1 depletion abolishes EphA4-dependent GluR1 downregulation and prevents mEPSC amplitude reduction during homeostatic plasticity.\",\n      \"method\": \"Co-immunoprecipitation of EphA4 with APC/Cdh1, in vitro proteasomal degradation assay, Cdh1 knockdown in neurons, mEPSC recordings, surface GluR1 imaging\",\n      \"journal\": \"Nature neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, in vitro reconstitution of degradation, shRNA knockdown with electrophysiological readout, multiple orthogonal methods\",\n      \"pmids\": [\"21186356\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"EphA4 activation by ephrin-A3 in hippocampal slices inhibits beta1-integrin signaling: decreases tyrosine phosphorylation of FAK, Pyk2, and Cas, and reduces Cas association with Fyn and Crk. Inhibition of beta1-integrin or Cas function mimics EphA4-induced spine morphological changes, and preventing beta1-integrin inactivation blocks EphA4 effects on spines.\",\n      \"method\": \"Hippocampal slice ephrin-A3 stimulation, phosphorylation assays, Co-immunoprecipitation, integrin activity assay in neuronal cells, dominant-negative constructs\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical signaling assays combined with functional rescue/block experiments and morphological readouts in a single study\",\n      \"pmids\": [\"17875741\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"EphA4 associates with Vsm-RhoGEF (a VSMC-specific RhoA GEF) in quiescent vascular smooth muscle cells. Upon ephrin-A1 stimulation, EphA4 phosphorylates Vsm-RhoGEF on tyrosine, enhancing its GEF activity toward RhoA. Dominant-negative Vsm-RhoGEF or RNAi depletion blocks ephrin-A1-induced actin stress fiber assembly in VSMCs.\",\n      \"method\": \"Co-immunoprecipitation (EphA4-Vsm-RhoGEF), tyrosine phosphorylation assays, GEF activity assay, dominant-negative overexpression, siRNA knockdown, actin staining\",\n      \"journal\": \"Circulation research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical interaction, enzymatic activity measurement, and functional rescue experiments with two independent methods (dominant-negative and RNAi)\",\n      \"pmids\": [\"12775584\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"EphA4 interacts with the PDZ domain of spine-associated RapGAP (SPAR) via its C-terminus, mediating EphA4-dependent inactivation of Rap1 and Rap2. SPAR-mediated Rap1 inactivation (but not Rap2) is critical for ephrin-A-dependent growth cone collapse and decreased integrin-mediated adhesion in neuronal cells.\",\n      \"method\": \"Co-immunoprecipitation of EphA4-SPAR, Rap GTPase activity assays, dominant-negative SPAR, growth cone collapse assay, integrin adhesion assay\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and functional downstream assays in a single lab, single study\",\n      \"pmids\": [\"18094260\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"EphA4 activation by ephrin stimulation recruits and activates PLCgamma1 through an SH2 domain interaction requiring EphA4 juxtamembrane tyrosines. PLC activity is required for ephrin-induced spine retraction, and EphA4/PLC signaling modulates the association of cofilin with the plasma membrane, linking EphA4 signaling to actin depolymerization and spine restructuring.\",\n      \"method\": \"PLCgamma1 recruitment assay, SH2 domain interaction, juxtamembrane tyrosine mutagenesis, PLC inhibitors, cofilin membrane fractionation, hippocampal slice spine morphology\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — mutagenesis of active residues, biochemical recruitment assays, pharmacological inhibition, and morphological readout in a single study with multiple orthogonal methods\",\n      \"pmids\": [\"17494698\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"EphA4 promotes cell adhesion within rhombomeres (in addition to mediating repulsion between rhombomeres); in mosaic zebrafish embryos, EphA4-depleted cells sort away from EphA4-expressing cells, supporting a differential cell adhesion mechanism parallel to repulsion in driving rhombomere boundary formation.\",\n      \"method\": \"Antisense morpholino knockdown in zebrafish, mosaic embryo analysis, cell sorting assays\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — morpholino loss-of-function in zebrafish with mosaic analysis, single lab\",\n      \"pmids\": [\"15797022\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"Krox-20 transcription factor directly activates EphA4 transcription in rhombomeres 3 and 5 through eight Krox-20 binding sites within a 470 bp enhancer element; mutation of these sites abolishes r3/r5-specific enhancer activity, and ectopic Krox-20 drives ectopic enhancer activation.\",\n      \"method\": \"Transgenic mouse enhancer analysis, Krox-20 binding site mutagenesis, ectopic Krox-20 expression, luciferase reporter assays\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — direct binding site mutagenesis, transgenic reporters, and ectopic expression experiments in a single study\",\n      \"pmids\": [\"9425139\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"GDNF/Ret and ephrin-A/EphA4 signaling cooperate in the same binary motor axon guidance decision (dorsal vs ventral limb); Ret and EphA4 double-mutant mice show enhanced misrouting of LMC(l) axons compared to single mutants, demonstrating epistatic cooperation between these two guidance systems.\",\n      \"method\": \"Gdnf, Ret, and EphA4 single and double mutant mouse analysis, limb motor axon tracing\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with double-mutant analysis and axon tracing, well-controlled\",\n      \"pmids\": [\"16600854\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Trans-activation between EphA4 and FGFRs is mediated by direct protein-protein interactions between the juxtamembrane domain of FGFR1-4 and the N-terminal kinase domain of EphA4. FGFR activation leads to tyrosine phosphorylation of kinase-negative EphA4, and EphA4 activation phosphorylates kinase-negative FGFR1; both receptors mutually potentiate FRS2alpha phosphorylation and MAPK activation.\",\n      \"method\": \"Yeast two-hybrid, Co-immunoprecipitation, kinase-negative receptor trans-phosphorylation assays, MAPK activation assays, ephrin-A1/FGF co-stimulation\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — yeast two-hybrid, biochemical Co-IP, trans-phosphorylation with kinase-negative mutants; multiple methods in one study\",\n      \"pmids\": [\"16365308\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Soluble amyloid-beta oligomers (AβOs) activate EphA4 in hippocampal neurons and synaptoneurosomes; EphA4 depletion or a small-molecule inhibitor (rhynchophylline, identified by molecular docking to the EphA4 LBD) blocks AβO-induced EphA4 activation and reverses suppression of LTP in APP/PS1 transgenic mice, establishing EphA4 as a mediator of Aβ-induced synaptic dysfunction.\",\n      \"method\": \"EphA4 knockdown in CA1, APP/PS1 transgenic mice, LTP recordings, molecular docking, rhynchophylline administration, EphA4 phosphorylation assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic depletion and pharmacological inhibition with LTP electrophysiological readout in transgenic AD model, multiple convergent approaches\",\n      \"pmids\": [\"24958880\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"EphA4 is upstream of c-Abl kinase activation by amyloid-beta oligomers in hippocampal neurons; AβO-induced EphA4 tyrosine phosphorylation is required for c-Abl activation (no c-Abl activation detected in EphA4-KO neurons exposed to AβOs). EphA4/c-Abl signaling mediates dendritic spine reduction, LTP blockade, and neuronal apoptosis caused by AβOs.\",\n      \"method\": \"EphA4 knockout neurons, sh-EphA4 transfection, c-Abl activity assays, EphA4 antagonist peptide (KYL), c-Abl inhibitor (STI), LTP recordings, spine density analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO, shRNA, two pharmacological inhibitors, and multiple functional readouts converge on same pathway\",\n      \"pmids\": [\"24658113\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Mesp2 transcription factor directly binds to E-box-containing enhancer sequences of Epha4 and activates its transcription in the anterior presomitic mesoderm; forced Mesp2 expression activates EphA4 expression and represses caudal gene Uncx4.1 in somitic cells.\",\n      \"method\": \"Enhancer deletion analysis, luciferase reporter assays, transgenic mice, Mesp2 chromatin immunoprecipitation / direct binding assay, ectopic Mesp2 expression\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — direct binding demonstrated, transgenic and reporter assays, gain-of-function in vivo in a single study\",\n      \"pmids\": [\"16728472\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"EphA4 is localized predominantly on the plasma membrane of axon terminals and dendritic spines (25-40% of terminals and 9-19% of spines labeled) at asymmetric/excitatory synapses in adult rat hippocampus, with dual pre- and postsynaptic localization supporting roles in synaptic plasticity.\",\n      \"method\": \"Electron microscopic immunocytochemistry (immunoperoxidase and immunogold labeling) in adult rat hippocampus\",\n      \"journal\": \"The Journal of comparative neurology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — high-resolution electron microscopy with two immunolabeling methods in one study; localization without direct functional link in this paper\",\n      \"pmids\": [\"17299751\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"EphA4 forward signaling (ephrin-A5/EphA4) is required for targeting type I spiral ganglion neuron afferents to inner hair cells in the cochlea; in EphA4 forward signaling-deficient mice, type I projections aberrantly invade the outer hair cell area. Downstream effectors ephexin-1, cofilin, and myosin light chain kinase act downstream of EphA4 to induce type I neuron growth cone collapse.\",\n      \"method\": \"EphA4 and ephrin-A5 knockout mice, conditional EphA4 mutants, growth cone collapse assay with ephexin-1/cofilin/MLCK pathway analysis, cochlear innervation analysis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional genetic mutants, pathway epistasis, and growth cone collapse assay with downstream effector analysis\",\n      \"pmids\": [\"23385583\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"EphA4 forward signaling in pancreatic alpha-cells maintains a dense F-actin network that tonically inhibits glucagon secretion; alpha-cell-specific EphA4-/- mice exhibit abnormal glucagon dynamics and less dense F-actin. Stimulation of EphA4 inhibits glucagon secretion while inhibition enhances it, and restoration of EphA4 forward signaling in sorted alpha-cells rescues normal basal glucagon secretion and glucose inhibition of secretion.\",\n      \"method\": \"Alpha-cell-specific EphA4 knockout mice, glucagon secretion assays, EphA4 stimulation/inhibition in islets, sorted alpha-cells, F-actin density measurements\",\n      \"journal\": \"Diabetes\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cell-type-specific KO, functional secretion assays, rescue experiments, mechanistic link to F-actin\",\n      \"pmids\": [\"26251403\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"EphA4 forms a heteroreceptor complex with FGFR1 in glioma cells; EphA4 overexpression enhances FGF2-mediated MAPK and Akt phosphorylation, and increases active Rac1 and Cdc42, promoting cell proliferation and migration.\",\n      \"method\": \"Co-immunoprecipitation (EphA4-FGFR1), MAPK/Akt phosphorylation assays, Rac1/Cdc42 pull-down (GTP-bound), overexpression in U251 glioma cells\",\n      \"journal\": \"Molecular cancer therapeutics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP of endogenous complex, multiple downstream signaling readouts, single lab\",\n      \"pmids\": [\"18790757\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Axonal ephrin-A1 activates EphA4 on oligodendrocytes to trigger the ephexin1-RhoA-ROCK-myosin 2 signaling cascade, causing inhibition of oligodendrocyte process extension and reduced myelination. EphA4 knockdown or inhibition at multiple levels of this pathway increases the number of myelin sheaths per oligodendrocyte.\",\n      \"method\": \"Axon-mimicking microfibers, zebrafish myelination model, EphA4 knockdown, pathway inhibitors (ROCK, myosin 2), ephexin1 assays, myelin sheath counting\",\n      \"journal\": \"Glia\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two experimental systems (in vitro microfibers + in vivo zebrafish), genetic knockdown, and pharmacological inhibition at multiple pathway levels\",\n      \"pmids\": [\"29350423\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"SORLA (SORL1) directly interacts with EphA4 and attenuates ephrinA1-induced EphA4 clustering and activation; SORLA transgenic mice show decreased EphA4 activation and redistribution to postsynaptic densities, with milder LTP and memory deficits induced by Aβ oligomers. Active EphA4 levels are elevated in human AD brains inversely correlated with SORLA/EphA4 association.\",\n      \"method\": \"Co-immunoprecipitation (SORLA-EphA4), SORLA transgenic mice, EphA4 clustering assay, LTP recordings, human AD brain analysis\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical interaction, transgenic mouse physiology, and human tissue correlation in a single study with multiple methods\",\n      \"pmids\": [\"29114064\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"EphA4 shedding (ectodomain cleavage) in limb mesenchyme regulates spinal motor axon guidance: blocking EphA4 cleavage increases full-length EphA4 in limb mesenchyme, which via cis-attenuation reduces effective ephrin-A concentration available to trigger EphA4 forward signaling in motor axons, causing guidance defects. Cleavage-resistant EphA4 on neurons is as effective as wild-type for redirecting motor axons.\",\n      \"method\": \"Cleavage-resistant EphA4 knock-in mice, in vitro cell detachment assays, motor axon tracing, conditional EphA4 cleavage ablation in limb mesenchyme\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — knock-in genetic models with tissue-specific conditional analysis and functional axon tracing readouts\",\n      \"pmids\": [\"25264256\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"EphA4 in vascular endothelial cells suppresses pial collateral remodeling and cerebral blood flow recovery after ischemic stroke; endothelial-specific EphA4 deletion (EphA4fl/fl/Tie2-Cre and EphA4fl/fl/VeCadherin-CreERT2) enhances arteriogenic response. EphA4 negatively regulates Tie2 receptor signaling in endothelial cells through p-Akt modulation.\",\n      \"method\": \"Endothelial-specific EphA4 conditional knockout mice (two Cre lines), vessel painting, CBF measurement, Akt phosphorylation assays, peptide inhibition of EphA4\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — two independent conditional KO models, functional vascular readout, biochemical pathway analysis, and pharmacological confirmation\",\n      \"pmids\": [\"31689239\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"EphA4 forward signaling, specifically requiring EphA4 kinase activity, promotes proliferation of cortical progenitor cells during corticogenesis; EphA4-/- cortex has fewer cells and less cell division. EphA4 and ephrin-B1 (expressed in cortical progenitors) bind and initiate signaling, and ephrin-B1 overexpression stimulates division of neighboring cells via EphA4 forward signaling.\",\n      \"method\": \"EphA4-/- mice, in vivo EphA4 overexpression/knockdown in progenitors, cell division assays, binding assay (EphA4-ephrin-B1), cortical area measurements\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO plus in vivo gain/loss-of-function and direct binding assay in a single study, single lab\",\n      \"pmids\": [\"19542359\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"EphrinB3-induced EphA4 forward signaling guides both ascending Zic2+/EphA4+ spinal neuron axons and descending corticospinal tract axons using the same molecular mechanism; conditional EphA4 mutant analysis reveals that dorsal funiculus development depends on EphA4 in Zic2+ spinal neurons, not in descending CST axons.\",\n      \"method\": \"Conditional EphA4 knockout mice (Zic2-Cre and other Cre lines), axon tract tracing, anatomical analysis\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional genetic approach disambiguating cell-type-specific roles with axon tracing\",\n      \"pmids\": [\"24360544\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"EphA4 signaling in Xenopus blastulae induces reversible, cell-autonomous loss of adhesion; this is rescued by Nckbeta (Grb4) interaction with EphA4. EphA4 activates xPAK1 in an Nck-dependent manner; xPAK1 GTPase-binding domain sequesters active Cdc42, causing RhoA-GTP downregulation and loss of cell-cell adhesion.\",\n      \"method\": \"Xenopus blastula injection, dominant-negative and constitutively active GTPase constructs, xPAK1 activation assay, epistasis analysis, Cdc42/Rac/RhoA activity assays\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis analysis and GTPase activity measurements in Xenopus, single lab\",\n      \"pmids\": [\"17215521\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"In early Xenopus embryos, EphA4 catalytic activity inhibits RhoA GTPase (in contrast to activation in neuronal cells); constitutively active XRhoA rescues EphA4-induced loss of cell-cell adhesion, and overexpression of ephexin blocks EphA4-induced dissociation, suggesting an ephexin-dependent or independent pathway to Rho depending on cell context.\",\n      \"method\": \"Chimeric EPP receptor expression in Xenopus embryos, constitutively active XRhoA rescue, Rho GTPase inhibitor injection, ephexin overexpression\",\n      \"journal\": \"Differentiation; research in biological diversity\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis with constitutively active GTPase rescue and pharmacological inhibition in Xenopus, single lab\",\n      \"pmids\": [\"11963655\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Crystal structure of a cyclic peptide antagonist (APY) bound to the EphA4 ligand-binding domain shows efficient occupation of the ephrin-binding pocket with a 'closed' loop conformation. Structure-guided optimization yielded APY-βAla8.am with nanomolar EphA4 affinity; this peptide potently inhibits ephrin-induced EphA4 activation in cells and EphA4-dependent neuronal growth cone collapse with high EphA4 selectivity.\",\n      \"method\": \"X-ray crystallography of peptide-EphA4 LBD complex, structure-guided mutagenesis, binding affinity assay, cell-based EphA4 activation assay, growth cone collapse assay\",\n      \"journal\": \"ACS chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structures of two peptide-receptor complexes combined with functional cellular assays in a single study\",\n      \"pmids\": [\"25268696\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"EphA4 deficiency in osteoclasts activates beta3-integrin signaling through reduced phosphorylation of tyr-747, which increases binding of stimulatory talin and reduces binding of inhibitory Dok1 to beta3-integrin, in turn activating Vav3 and osteoclast bone resorption activity. EphA4 is thus a negative regulator of osteoclastic activity via this integrin-signaling pathway.\",\n      \"method\": \"EphA4 null mice (bone analysis), siRNA knockdown in RAW/C4 cells, EfnA4-Fc stimulation, beta3-integrin phosphorylation assays, talin/Dok1 Co-IP with beta3-integrin, Vav3 activation assay, bone resorption assay\",\n      \"journal\": \"Journal of bone and mineral research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO mouse, RNAi, activation ligand, and multiple biochemical assays converge on same mechanistic pathway\",\n      \"pmids\": [\"23983218\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"EphA4 is an upstream negative regulator of efferocytosis in macrophages/microglia after brain injury; EphA4 loss enhances efferocytosis by increasing p-ERK and p-Stat6 activity, which upregulates MERTK and Gas6 expression. ERK and Stat6 inhibitors abrogate the efferocytosis enhancement in EphA4 KO cells, establishing an EphA4→ERK/Stat6→MERTK signaling axis.\",\n      \"method\": \"Bone marrow chimeric EphA4 KO mice, TBI model, in vitro efferocytosis assay, phosphoarray, ERK/Stat6 selective inhibitors, MERTK/Gas6 mRNA analysis, single-cell RNAseq\",\n      \"journal\": \"Journal of neuroinflammation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO, pharmacological inhibition of downstream effectors, in vitro and in vivo convergence on the same pathway\",\n      \"pmids\": [\"37941008\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"EphA4 acts upstream of Sipa1l3 during eye development in Xenopus; EphA4 deficiency phenocopies Sipa1l3 loss, and rescue experiments show EphA4 is upstream of Sipa1l3. Both proteins inhibit canonical Wnt/beta-catenin signaling (EphA4/Sipa1l3 loss upregulates axin2); inhibiting Wnt/beta-catenin or activating non-canonical Wnt rescues the EphA4-depletion eye phenotype.\",\n      \"method\": \"Xenopus morpholino knockdown, direct interaction assay (EphA4-Sipa1l3), genetic epistasis (rescue experiments), Wnt pathway reporter (axin2), pathway inhibition/activation rescue\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct interaction and epistasis in Xenopus, single lab, pathway placement supported by rescue experiments\",\n      \"pmids\": [\"27993984\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"EphA4 promotes proliferation of oligodendrocyte precursor cells (OPCs) but reduces maturation to oligodendrocytes and decreases myelin-associated proteins after ischemic stroke; conditional OPC-specific EphA4 knockout improves remyelination and functional recovery. This effect is mediated by the Ephexin-1/RhoA/ROCK signaling pathway.\",\n      \"method\": \"PDGFRα-EphA4-shRNA, LV-EphA4 overexpression, EphA4fl/fl/AAV-PDGFRα-Cre conditional KO, MCAO/R ischemia model, OGD/R in vitro, myelin protein analysis, Ephexin-1/RhoA/ROCK pathway assays\",\n      \"journal\": \"Glia\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO and knockdown/overexpression in two experimental models with pathway epistasis demonstration\",\n      \"pmids\": [\"35762396\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"EphA4 acts as a dependence receptor: in the absence of its ligand ephrin-B3, EphA4 triggers apoptosis in glioblastoma cells. Ephrin-B3 overexpression in GBM inhibits EphA4 pro-apoptotic activity; Ephrin-B3 silencing reduces tumor vascularization and growth in xenograft mice.\",\n      \"method\": \"Ephrin-B3 silencing (siRNA), xenograft GBM mouse model, apoptosis assays, in vitro endothelial cell survival assay, human GBM biopsy analysis\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional siRNA, xenograft model, and in vitro assays in one study; dependence receptor mechanism inferred from ligand-removal apoptosis\",\n      \"pmids\": [\"28423606\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"EphA4 is a receptor tyrosine kinase that upon binding A- or B-class ephrin ligands (with unique pan-ephrin promiscuity enabled by distinct LBD surface contacts) undergoes clustering and kinase activation to trigger multiple downstream signaling cascades—including ephexin1/RhoA, alpha2-chimaerin/Rac1, PLCgamma1/cofilin, SPAR/Rap GTPases, Cdk5, APC(Cdh1)/GluR1, and beta1-integrin pathways—that regulate dendritic spine morphology, synaptic plasticity (LTP, AMPA receptor homeostasis), axon guidance (corticospinal, limb motor, commissural tracts), neuroglial interactions (astrocyte-mediated glutamate transport, myelination, gliosis), and diverse cell biological processes including cell adhesion, vascular remodeling, osteoclast activity, glucagon secretion, and neuroinflammation resolution.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"EphA4 is a receptor tyrosine kinase that, upon binding A- and B-class ephrins, clusters and activates a tyrosine-kinase cascade to control cell repulsion, adhesion, cytoskeletal remodeling, and synaptic function across the nervous system and beyond [#0, #1, #9]. Its unusual pan-ephrin promiscuity is structurally explained: ephrin-A5 binding drives conformational change and higher-order clustering reinforced by an LBD\\u2013fibronectin receptor-receptor contact, while LBD residues Gln12/Glu14 provide interclass ephrin-B binding [#9, #10]. Activated EphA4 channels signaling principally into Rho-family GTPase regulation\\u2014recruiting Cdk5 to activate the RhoA-GEF ephexin1 [#4], engaging the Rac-GAP alpha2-chimaerin via its SH2 domain [#8], and acting through SPAR/Rap1 and PLCgamma1/cofilin\\u2014to drive growth-cone collapse, dendritic spine retraction, and actin reorganization [#14, #15]. In parallel, ligand-activated EphA4 recruits the ubiquitin ligase APC(Cdh1) to degrade GluR1 and downregulates beta1-integrin signaling, linking it to AMPA-receptor homeostasis and synaptic plasticity [#11, #12]. At the circuit level EphA4 directs axon guidance of corticospinal, limb-motor, and commissural tracts\\u2014requiring kinase activity for some tracts but acting kinase-independently (as a ligand) for the anterior commissure\\u2014and patterns neural crest and rhombomere/somite boundaries downstream of Krox-20 and Mesp2 [#2, #6, #7, #17, #22]. EphA4 additionally regulates astrocytic gliosis after injury, glial glutamate transport during LTP, oligodendrocyte myelination via ephexin1/RhoA/ROCK, and is a mediator of amyloid-beta oligomer-induced synaptic dysfunction through c-Abl, antagonized by SORLA [#3, #5, #20, #21, #27, #28]. Outside the nervous system it negatively regulates osteoclast bone resorption, endothelial collateral remodeling, glucagon secretion, and macrophage efferocytosis [#25, #30, #36, #37].\",\n  \"teleology\": [\n    {\n      \"year\": 1997,\n      \"claim\": \"Established EphA4 as a repulsive guidance receptor governing positional sorting, answering how migrating cells reach correct destinations.\",\n      \"evidence\": \"Dominant-negative receptor and ectopic ephrin-B2 in Xenopus neural crest\",\n      \"pmids\": [\"9259557\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream signaling not defined\", \"Mammalian relevance not tested in this study\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Genetic knockout defined EphA4 as essential for corticospinal tract formation and revealed direct transcriptional control by Krox-20 in rhombomeres, linking patterning to receptor expression.\",\n      \"evidence\": \"EphA4 null mice with anterograde tracing; Krox-20 binding-site mutagenesis and transgenic reporters\",\n      \"pmids\": [\"9789074\", \"9425139\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not separate kinase-dependent from kinase-independent function\", \"Effector pathways unresolved\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Showed EphA4 dosage encodes binary axon pathfinding decisions, explaining dorsal/ventral limb motor selection.\",\n      \"evidence\": \"EphA4 knockout limb innervation analysis with differential protein expression\",\n      \"pmids\": [\"10887087\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Co-acting guidance systems not yet integrated\", \"Mechanism of dorsal-specific enrichment unknown\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Demonstrated EphA4 can signal both as a kinase-active receptor and as a kinase-independent ligand, resolving how one molecule guides distinct tracts.\",\n      \"evidence\": \"Kinase-dead and SAM-deletion knock-in mice with tract tracing\",\n      \"pmids\": [\"11182082\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Reverse-signaling partner for AC not identified\", \"Structural basis of kinase-independent mode unclear\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Connected EphA4 to dendritic spine morphology via neuroglial cross-talk, establishing a postsynaptic role and a Rho-GEF mechanism in vascular cells.\",\n      \"evidence\": \"Hippocampal slices with KO mice and kinase-dead mutant; Co-IP and GEF assays of Vsm-RhoGEF in VSMCs\",\n      \"pmids\": [\"12496762\", \"12775584\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full effector chain to actin not yet mapped\", \"VSMC and neuronal mechanisms not unified\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Identified Cdk5 recruitment to EphA4 as the trigger for ephexin1/RhoA activation and spine retraction, defining a core kinase-effector module; Mesp2 added a second direct transcriptional input.\",\n      \"evidence\": \"Reciprocal Co-IP, Cdk5-/- brains, phosphorylation and electrophysiology; Mesp2 binding and reporter assays\",\n      \"pmids\": [\"17143272\", \"16728472\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Spatial control of Cdk5 recruitment unknown\", \"Crosstalk between ephexin1 and other GEFs unresolved\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Mapped parallel downstream effectors\\u2014alpha2-chimaerin/Rac1, PLCgamma1/cofilin, SPAR/Rap, and beta1-integrin inactivation\\u2014that mediate growth-cone collapse and spine remodeling, and showed FGFR trans-activation.\",\n      \"evidence\": \"SH2-domain interaction, GAP/GEF activity assays, KO mice phenocopying, juxtamembrane mutagenesis, yeast two-hybrid and trans-phosphorylation\",\n      \"pmids\": [\"17785182\", \"17785183\", \"17911252\", \"17494698\", \"18094260\", \"17875741\", \"16365308\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Hierarchy among parallel effectors not established\", \"Context-dependent effector selection unexplained\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Defined the structural basis of pan-ephrin promiscuity and linked EphA4 to LTP via glial glutamate transport and cortical progenitor proliferation.\",\n      \"evidence\": \"EphA4-ephrin-B2 crystal structure with mutagenesis; ephrin-A3/EphA4 mutant LTP recordings; cortical progenitor gain/loss of function\",\n      \"pmids\": [\"19875447\", \"19734893\", \"19542359\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cluster assembly mechanism still incomplete in 2009\", \"Progenitor effector pathway not defined\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Revealed that EphA4 drives AMPA-receptor homeostasis by recruiting APC(Cdh1) to degrade GluR1, connecting receptor activation to proteostatic control of synaptic strength.\",\n      \"evidence\": \"Reciprocal Co-IP, in vitro proteasomal degradation, Cdh1 knockdown with mEPSC recordings\",\n      \"pmids\": [\"21186356\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How phosphorylated EphA4 selects APC(Cdh1) unknown\", \"Other proteasomal substrates not identified\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Resolved the full ectodomain architecture and clustering mechanism, and used conditional and forward-signaling-specific models to assign cell-autonomous guidance roles in cochlea and spinal cord.\",\n      \"evidence\": \"Full ectodomain and ephrin-A5 complex crystallography with mutagenesis; conditional EphA4 mutants with tract/innervation tracing\",\n      \"pmids\": [\"23959867\", \"23385583\", \"24360544\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry of physiological clusters in vivo unknown\", \"Link between cluster size and effector output unmapped\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Implicated EphA4 as a mediator of amyloid-beta oligomer synaptic toxicity via c-Abl, identified small-molecule and peptide antagonists, and showed ectodomain shedding tunes ligand availability.\",\n      \"evidence\": \"EphA4-KO neurons and APP/PS1 mice with LTP; molecular docking and rhynchophylline; cyclic peptide co-crystal structures; cleavage-resistant knock-in mice\",\n      \"pmids\": [\"24958880\", \"24658113\", \"25268696\", \"25264256\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo therapeutic efficacy of antagonists not established\", \"Sheddase identity and regulation unresolved\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Extended EphA4 function to dependence-receptor apoptosis in glioblastoma, SORLA-mediated negative regulation in AD, and Sipa1l3/Wnt control in eye development.\",\n      \"evidence\": \"Ephrin-B3 silencing with GBM xenografts; SORLA Co-IP, transgenic mice and human AD brain; Xenopus epistasis with Wnt reporters\",\n      \"pmids\": [\"28423606\", \"29114064\", \"27993984\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Dependence-receptor death effectors not defined\", \"SORLA regulatory mechanism on clustering incompletely resolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Defined non-neuronal physiological roles: endothelial EphA4 suppresses collateral remodeling via Tie2/Akt, alpha-cell EphA4 tonically inhibits glucagon through F-actin, osteoclast EphA4 restrains bone resorption via beta3-integrin, and macrophage EphA4 limits efferocytosis through ERK/Stat6/MERTK.\",\n      \"evidence\": \"Cell-type-specific conditional KO mice with functional and biochemical pathway assays across vascular, pancreatic, bone, and immune systems\",\n      \"pmids\": [\"31689239\", \"26251403\", \"23983218\", \"37941008\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ligands driving each peripheral context not fully defined\", \"Shared versus distinct effector logic across tissues unclear\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Established that EphA4 in oligodendrocyte lineage cells restrains maturation and myelination via ephexin1/RhoA/ROCK, identifying it as a remyelination target after stroke.\",\n      \"evidence\": \"OPC-specific conditional KO, knockdown/overexpression in MCAO/R and OGD/R models with pathway epistasis\",\n      \"pmids\": [\"35762396\", \"29350423\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Axonal versus glial ligand source not isolated\", \"Translation to chronic demyelination untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How distinct ephrin ligands and cluster geometries are decoded into selection among the many parallel effector pathways (Cdk5/ephexin1, alpha2-chimaerin, PLCgamma1, SPAR/Rap, APC(Cdh1), integrin) in a cell-type-specific manner remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No unified model linking cluster state to effector choice\", \"Quantitative effector competition not measured\", \"Context determinants of kinase-dependent versus dependence-receptor outputs unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [4, 8, 13, 19]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [4, 13, 19]},\n      {\"term_id\": \"GO:0098631\", \"supporting_discovery_ids\": [16, 33]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [0, 9, 10]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [5, 30, 36]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [23]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [23]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [4, 8, 15, 19]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [2, 6, 7, 17, 22, 31]},\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [0, 5, 11, 20]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [11]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [20, 21, 28, 40]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"EFNA3\",\n      \"CDK5\",\n      \"NGEF\",\n      \"CHN1\",\n      \"PLCG1\",\n      \"FGFR1\",\n      \"SORL1\",\n      \"FCHSD\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}