{"gene":"EPHB2","run_date":"2026-04-28T17:46:03","timeline":{"discoveries":[{"year":2004,"finding":"EphB2 and ephrin-A5 bind each other with high affinity (cross-class interaction), leading to receptor clustering, autophosphorylation, and downstream signaling including growth cone collapse and neurite retraction. X-ray crystallography revealed the ephrin-A5–EphB2 complex is a heterodimer, architecturally distinct from the tetrameric EphB2–ephrin-B2 structure.","method":"X-ray crystallography, cell-based receptor clustering/autophosphorylation assays, neurite retraction assay, binding affinity measurements","journal":"Nature neuroscience","confidence":"High","confidence_rationale":"Tier 1 — crystal structure plus functional validation (autophosphorylation, growth cone collapse) in a single study","pmids":["15107857"],"is_preprint":false},{"year":1998,"finding":"Phosphorylation of tyrosine 611 in the EphB2 juxtamembrane region is required for complex formation with the SH2 domain of Src kinase; tyrosines 605 and 611 are important for EphB2 kinase activity. Autophosphorylated EphB2 associates with Src, and EphB2-expressing cells show increased Src tyrosine phosphorylation, suggesting Src as a downstream effector.","method":"Yeast two-hybrid, site-directed mutagenesis, co-immunoprecipitation from transfected COS cells, phosphopeptide mapping","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 1/2 — mutagenesis combined with biochemical mapping and co-IP in multiple systems","pmids":["9632142"],"is_preprint":false},{"year":2001,"finding":"EphB2 regulates NMDA receptor-dependent synaptic function in the mammalian CNS. Mice lacking the entire EphB2 receptor (but not those lacking only the kinase domain) showed reduced LTP and reduced synaptic NMDA current in dentate granule neurons, with diminished synaptically localized NR1 subunit.","method":"EphB2 knockout mice (full receptor vs. kinase-domain truncation), electrophysiology (LTP, NMDA currents), immunogold localization of NR1","journal":"Neuron","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis with domain-specific rescue, orthogonal electrophysiology and ultrastructural localization","pmids":["11754836"],"is_preprint":false},{"year":2001,"finding":"EphB2 regulates hippocampal synaptic plasticity in a kinase-independent manner. Mice lacking EphB2 show impaired protein synthesis-dependent LTP and loss of two forms of synaptic depression; a C-terminally truncated EphB2 (lacking the kinase domain) rescues the null phenotype, demonstrating the extracellular/juxtamembrane domain is sufficient.","method":"EphB2 knockout mice, targeted truncation knock-in, hippocampal slice electrophysiology","journal":"Neuron","confidence":"High","confidence_rationale":"Tier 2 — genetic dissection with domain-specific rescue and multiple plasticity readouts","pmids":["11754835"],"is_preprint":false},{"year":2004,"finding":"EphB2 is localized to lamellipodia of migrating glioma cells; its phosphorylation (activation) promotes glioma cell migration and invasion, while blocking EphB2 with an antibody inhibits these processes. Forced EphB2 expression in low-expressing U251 cells stimulates migration, invasion and reduces adhesion concomitant with EphB2 tyrosine phosphorylation.","method":"Confocal microscopy (localization), blocking antibody, forced overexpression, siRNA knockdown, ex vivo brain slice invasion assay","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (localization, gain- and loss-of-function) with defined cellular phenotypes","pmids":["15126357"],"is_preprint":false},{"year":2005,"finding":"EphB2 signals through R-Ras to regulate glioma cell adhesion, proliferation and invasion. Upon EphB2 activation, R-Ras associates with the receptor and becomes phosphorylated; siRNA depletion of R-Ras abrogates EphB2-mediated effects. Anti-proliferative responses to EphB2 correlate with suppressed MAPK activity.","method":"Co-immunoprecipitation, siRNA knockdown of R-Ras, ex vivo brain slice invasion, phosphorylation analysis","journal":"The American journal of pathology","confidence":"Medium","confidence_rationale":"Tier 2/3 — co-IP plus functional siRNA rescue, single lab","pmids":["16049340"],"is_preprint":false},{"year":2007,"finding":"EphB2 receptor undergoes two distinct processing pathways: (1) ligand (ephrinB)-induced processing requires endocytosis and involves cleavage in endosomes followed by gamma-secretase (presenilin-dependent) cleavage releasing the intracellular domain; (2) calcium influx/NMDA-induced processing occurs at the plasma membrane and requires ADAM10/metalloproteinase activity but not endocytosis. EphrinB stimulation also induces EphB2 ubiquitination. Presenilin-1 familial Alzheimer disease mutations inhibit gamma-secretase cleavage of EphB2.","method":"Pharmacological inhibitors (metalloproteinase, gamma-secretase, endocytosis blockers), site-specific cleavage mapping, ubiquitination assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1/2 — mechanistic dissection with multiple inhibitors, defined cleavage sites, and distinct pathway characterization","pmids":["17428795"],"is_preprint":false},{"year":2009,"finding":"EphB2 controls cell proliferation and cell migration through dissociable signaling pathways: kinase-independent, PI3K-mediated pathway controls cell positioning/migration; EphB2 tyrosine kinase activity controls proliferation via an Abl–cyclin D1 pathway. Cyclin D1 regulation becomes uncoupled from EphB signaling during adenoma-to-carcinoma progression.","method":"Kinase-dead mutant knock-in mice, PI3K inhibitors, genetic epistasis, tumor progression analysis in human colorectal samples","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1/2 — genetic dissection with domain-specific mutants and pharmacological inhibitors defining two independent downstream pathways","pmids":["19914164"],"is_preprint":false},{"year":2007,"finding":"Azurin (a cupredoxin) binds to the EphB2 receptor with high affinity via a domain structurally similar to the G-H loop of ephrinB2, interfering with ephrinB2-induced autophosphorylation of EphB2 tyrosine residues and inhibiting cancer cell growth in EphB2-expressing cells but not in cells lacking functional EphB2.","method":"Binding assays (EphB2-Fc), synthetic peptide competition, autophosphorylation assays, cell viability in EphB2-positive vs. negative cell lines","journal":"Biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 — binding and functional inhibition assays with receptor-positive vs. negative controls","pmids":["17249693"],"is_preprint":false},{"year":2012,"finding":"EphB2 controls a proliferation/migration dichotomy in glioblastoma stem-like cells through interaction with focal adhesion kinase (FAK): EphB2 expression co-associates with and activates FAK, which facilitates focal adhesion formation, cytoskeletal changes and cell migration while inhibiting proliferation.","method":"Co-immunoprecipitation (EphB2-FAK), gain- and loss-of-function (overexpression, siRNA), dual-fluorescent xenograft model, in vitro migration/invasion assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2/3 — co-IP plus orthogonal gain/loss-of-function with defined phenotypic readouts, single lab","pmids":["22310282"],"is_preprint":false},{"year":2011,"finding":"EphB2 tyrosine kinase catalytic activity is required for embryonic/postnatal development of the lateral suprapyramidal blade of the dentate gyrus. Ephrin-B1 acts as the ligand stimulating EphB2 forward signaling to direct migration of nestin-positive neural progenitors; disruption of EphB2 forward signaling reduces Reelin expression in a key compartment above the developing lateral suprapyramidal blade.","method":"Intracellular truncation and point mutant knock-in mice, genetic loss of ephrin-B1, immunoreactivity for Reelin and nestin, histological analysis","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis with receptor domain-specific mutants and ligand knockout, replicated across multiple genotypes","pmids":["21832177"],"is_preprint":false},{"year":2016,"finding":"miR-204 directly targets EphB2 mRNA in hippocampal neurons; upregulation of miR-204 with aging suppresses EphB2 protein expression, reducing surface and total NR1 (NMDA receptor subunit) expression, contributing to age-associated decline in synaptic plasticity.","method":"miR-204 mimic transfection, luciferase reporter (direct target validation), western blot, surface NR1 quantification","journal":"Aging cell","confidence":"Medium","confidence_rationale":"Tier 2 — direct target validated by reporter assay plus functional consequence on NR1 surface expression","pmids":["26799631"],"is_preprint":false},{"year":2018,"finding":"EphB2 forward signaling (kinase activity) during fear conditioning enhances long-term memory consolidation; photoactivation of optoEphB2 in lateral amygdala during learning activates CREB. A kinase-dead optoEphB2 fails to enhance memory or activate CREB. EphB2lacZ/lacZ mice lacking forward signaling show impaired long-term fear memory.","method":"Optogenetic activation (optoEphB2), kinase-dead mutant control, CREB phosphorylation assay, behavioral fear conditioning","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1/2 — optogenetic gain-of-function with kinase-dead control and loss-of-function genetic model, multiple orthogonal readouts","pmids":["29768201"],"is_preprint":false},{"year":2020,"finding":"RNF186, an E3 ubiquitin ligase, ubiquitinates EPHB2 at Lys892 upon ephrin-B1 (EFNB1) stimulation, leading to EPHB2-dependent recruitment of MAP1LC3B and induction of autophagy in colonic epithelial cells. Mutation of Lys892 abolishes EPHB2-mediated autophagy. RNF186 and EPHB2 knockout mice show defective autophagy and more severe DSS-induced colitis.","method":"Ubiquitination assays, site-directed mutagenesis (K892R), LC3B co-immunoprecipitation, knockout mouse models, DSS colitis model","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 1/2 — biochemical reconstitution of ubiquitination with mutagenesis, in vivo genetic validation","pmids":["33280498"],"is_preprint":false},{"year":2021,"finding":"EPHB2 drives cancer stemness and sorafenib resistance in hepatocellular carcinoma via the SRC/AKT/GSK3β/β-catenin signaling cascade. TCF1 activates EPHB2 transcription, forming a positive Wnt/β-catenin feedback loop. EPHB2 endogenous knockout attenuates tumor development; rAAV-8-shEPHB2 sensitizes HCC to sorafenib in vivo.","method":"EPHB2 knockout, pharmacological pathway inhibitors, promoter activation assay, patient-derived xenografts, AAV-mediated shRNA knockdown, pathway phosphorylation analysis","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods including KO, shRNA, PDX models, and defined signaling pathway","pmids":["33903122"],"is_preprint":false},{"year":2023,"finding":"EphB2 acts downstream of Notch signaling in hepatocytes and is sufficient to induce cell-autonomous inflammation. Knockdown of Ephb2 in hepatocytes ameliorates inflammation and fibrosis in a mouse NASH model.","method":"Single-nucleus transcriptomics/epigenomics, hepatocyte-specific Ephb2 knockdown, mouse NASH model (inflammation and fibrosis readouts)","journal":"Science translational medicine","confidence":"High","confidence_rationale":"Tier 2 — multi-omic characterization plus in vivo loss-of-function with defined pathway placement (downstream of Notch)","pmids":["36753562"],"is_preprint":false},{"year":2015,"finding":"EphB2 promotes hepatic fibrosis via activation of hepatic stellate cells (HSCs): EphB2 is upregulated and activated in mouse HSCs following CCl4 exposure. EphB2-deficient HSCs show impaired proliferation and sub-optimal differentiation into fibrogenic myofibroblasts; EphB2 KO mice have reduced fibrosis, inflammation, and increased apoptosis in liver.","method":"EphB2 knockout mice, two models of hepatic fibrosis (malaria and CCl4), HSC isolation and in vitro differentiation assays, macrophage depletion","journal":"Hepatology","confidence":"High","confidence_rationale":"Tier 2 — genetic KO replicated in two disease models with cellular mechanism identified (HSC activation)","pmids":["25784101"],"is_preprint":false},{"year":2018,"finding":"EphB2 receptor tyrosine kinase promotes hepatic fibrogenesis via activation of hepatic stellate cells; EphB2 deficiency attenuates HSC proliferation, myofibroblast differentiation, and fibrosis. EphB2 KO mice show increased cellular apoptosis during fibrosis regression.","method":"EphB2 knockout mice, CCl4 model, in vitro HSC activation, fibrosis marker quantification, apoptosis assays","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — genetic KO with in vitro mechanistic follow-up, single lab replication of earlier findings","pmids":["29416088"],"is_preprint":false},{"year":2021,"finding":"Loss of EPHB2 in prostate cancer cells increases lipid droplet accumulation by upregulating lipogenic proteins DGAT1, DGAT2, PLIN2 and downregulating lipolytic ATGL and PEDF. DGAT1 inhibition reverses LD accumulation and proliferation caused by EPHB2 loss.","method":"EPHB2 knockdown, lipid droplet imaging, western blot of lipid metabolism proteins, DGAT1 inhibitor rescue, cell proliferation assays","journal":"Laboratory investigation","confidence":"Medium","confidence_rationale":"Tier 2/3 — loss-of-function with defined molecular targets in lipid metabolism, pharmacological rescue","pmids":["33824421"],"is_preprint":false},{"year":2014,"finding":"EphB2 in platelets regulates thrombus formation and clot retraction both in a contact-dependent (Eph-ephrin ligation between platelets) and contact-independent manner (cytoplasmic domain signaling in isolated platelets without ephrin engagement).","method":"EphB2 cytoplasmic domain-truncated mice, platelet activation assays, thrombus formation models, clot retraction assays","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2 — genetic approach dissecting contact-dependent vs. independent signaling with functional platelet readouts","pmids":["25370417"],"is_preprint":false},{"year":2017,"finding":"Nanostructured surface-bound ephrinB1 ligands induce EphB2 receptor oligomerization/clustering on cell membranes more efficiently than randomly distributed ligands; nanopatterned ligands required 9-fold lower surface coverage and produced faster clustering kinetics, demonstrating that multivalent ligand presentation tunes receptor activation.","method":"Diblock copolymer nanopatterning, Number and Brightness fluorescence technique to track EphB2 oligomeric state in real time","journal":"Nano letters","confidence":"Medium","confidence_rationale":"Tier 2 — quantitative single-cell imaging of receptor oligomerization with controlled ligand nanopatterning","pmids":["29243484"],"is_preprint":false},{"year":2017,"finding":"EphB2 activation by ephrin-B2-Fc in cutaneous squamous cell carcinoma cells enhances production of invasion proteinases MMP13 and MMP1 and promotes invasion; EphB2 knockdown suppresses growth, vascularization, proliferation, migration and invasion of cSCC, and downregulates MMP1 and MMP13.","method":"siRNA knockdown, ephrin-B2-Fc stimulation, xenograft tumor model, MMP protein expression, gene expression profiling","journal":"The Journal of investigative dermatology","confidence":"Medium","confidence_rationale":"Tier 2 — gain- and loss-of-function with defined molecular effectors (MMP1/MMP13) and in vivo validation","pmids":["25789706"],"is_preprint":false},{"year":2019,"finding":"EphrinB2/EphB2 promotes myenteric synaptic sprouting and NMDA receptor-mediated synaptic potentiation in IBS, via ERK-MAPK and PI3K-AKT pathways; EphB2 signaling drives persistent colonic hypercontractility and pain hypersensitivity.","method":"PI-IBS rat model, ephB2Fc receptor blocker, MK801 NMDA inhibitor, colonic muscle contraction recording, signaling pathway analysis, LMMP culture","journal":"FASEB journal","confidence":"Medium","confidence_rationale":"Tier 2/3 — pharmacological blockade with defined pathway placement in in vivo and ex vivo systems","pmids":["31601124"],"is_preprint":false},{"year":2017,"finding":"EphB2 signaling induces Sirt3 expression and mitochondrial translocation of Sirt3 via c-Src phosphorylation and Nrf-2-dependent transcription, reducing mitochondrial ROS accumulation. Sirt3 deacetylates MnSOD at Lys68 to enhance its activity, protecting mesenchymal stem cells from senescence.","method":"EphB2 knockdown/activation, subcellular fractionation, Nrf-2 nuclear translocation assay, Sirt3 overexpression/knockdown, MnSOD activity and acetylation assays, wound healing model","journal":"Free radical biology & medicine","confidence":"Medium","confidence_rationale":"Tier 2/3 — defined signaling cascade with multiple mechanistic steps, single lab","pmids":["28687409"],"is_preprint":false},{"year":2018,"finding":"EphB2 inactivation results in depression-like behaviors, memory impairment, and adult hippocampal neurogenesis defects, associated with decreased pCREB and BDNF and increased NR2B expression. NR2B antagonist Ro25-6981 reverses these phenotypes, placing NR2B downstream of EphB2 in behavioral and morphological outcomes.","method":"EphB2 knockout mice, behavioral tests (forced swim, tail suspension, Morris water maze, object recognition), NR2B pharmacological antagonism, BrdU neurogenesis assay, western blot","journal":"Frontiers in pharmacology","confidence":"Medium","confidence_rationale":"Tier 2 — genetic KO plus pharmacological rescue defines NR2B as downstream mediator, single lab","pmids":["30131699"],"is_preprint":false},{"year":2021,"finding":"EphB2 receptor is required in kidney for fibrosis development: EphB2 KO mice show significantly reduced renal tubular injury, fibrosis, inflammation and EMT after ischemia-reperfusion injury. EphB2 loss restores expression of 70.9% of fibrosis-associated genes dysregulated by IR injury back to normal.","method":"EphB2 knockout mice, renal ischemia-reperfusion model, fibrosis gene expression panel (760 genes), histology, EMT/myofibroblast markers","journal":"Clinical science","confidence":"Medium","confidence_rationale":"Tier 2 — genetic KO with comprehensive transcriptomic and histological phenotyping in defined injury model","pmids":["34462781"],"is_preprint":false},{"year":2013,"finding":"EphB2 in breast cancer cells promotes apoptosis (via caspase 3/9 activation), induces autophagy (LC3, ATG5, ATG12 markers), and mediates invasion through regulation of MMP2 and MMP9. EphB2-induced invasion is kinase-dependent, as it is blocked by a kinase-dead EphB2 mutant.","method":"DOX-inducible EphB2 restoration, siRNA knockdown, kinase-dead mutant, xenograft, MMP2/MMP9 neutralizing antibodies, caspase and autophagy marker analysis","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 — kinase-dead domain mutant establishes kinase-dependency of invasion with orthogonal functional readouts","pmids":["24211352"],"is_preprint":false}],"current_model":"EphB2 is a receptor tyrosine kinase activated by ephrin-B (and, via cross-class interaction, ephrin-A5) ligands that undergoes autophosphorylation-dependent clustering and signals bidirectionally through dissociable pathways: its kinase activity drives proliferation (via Abl–cyclin D1), invasion (via FAK, MMP induction), and memory consolidation (via CREB), while kinase-independent signaling through PI3K controls cell positioning and synaptic plasticity; EphB2 is post-translationally regulated by Src (binding phospho-Y611), ubiquitination by RNF186 (triggering LC3-mediated autophagy), and proteolytic processing by gamma-secretase/ADAM10 in context-dependent ectodomain shedding, and it modulates NMDA receptor function, hepatic stellate cell activation, and mitochondrial ROS homeostasis via Sirt3/MnSOD downstream of c-Src/Nrf-2."},"narrative":{"teleology":[{"year":1998,"claim":"Identifying how EphB2 kinase activity is regulated: autophosphorylation at Y611 creates a docking site for Src-SH2, establishing Src as a proximal downstream effector and defining the juxtamembrane region as a regulatory hub.","evidence":"Yeast two-hybrid, site-directed mutagenesis, co-IP from transfected COS cells, phosphopeptide mapping","pmids":["9632142"],"confidence":"High","gaps":["Whether Src is required for all EphB2 downstream outputs was not tested","Other SH2-domain effectors recruited to the juxtamembrane region remain uncharacterized"]},{"year":2001,"claim":"Resolving whether EphB2 kinase activity is required for synaptic function: full-receptor knockout but not kinase-domain deletion impaired NMDA currents and LTP, establishing that EphB2 regulates synaptic plasticity and NMDA receptor localization through a kinase-independent mechanism.","evidence":"EphB2 knockout vs. kinase-domain truncation knock-in mice, electrophysiology, immunogold NR1 localization","pmids":["11754836","11754835"],"confidence":"High","gaps":["The extracellular/juxtamembrane domain partners mediating kinase-independent synaptic effects were not identified","Whether the kinase-independent pathway operates through PI3K at the synapse was unknown"]},{"year":2004,"claim":"Demonstrating cross-class ligand recognition: EphB2 binds ephrin-A5 as a heterodimer (not tetramer), inducing autophosphorylation and growth cone collapse, expanding the repertoire of activating ligands beyond ephrin-B family members.","evidence":"X-ray crystallography of ephrin-A5–EphB2 complex, cell-based autophosphorylation and neurite retraction assays","pmids":["15107857"],"confidence":"High","gaps":["Physiological contexts where cross-class signaling predominates over canonical ephrin-B signaling are undefined","Downstream pathway divergence between ephrin-A5 and ephrin-B2 stimulation was not assessed"]},{"year":2004,"claim":"Linking EphB2 to cancer cell invasion: activated EphB2 localizes to lamellipodia and promotes glioma migration and invasion, establishing a pro-invasive role for EphB2 kinase signaling in brain tumors.","evidence":"Confocal localization, blocking antibody, overexpression, siRNA, ex vivo brain slice invasion assay in glioma cells","pmids":["15126357"],"confidence":"High","gaps":["Direct kinase substrates mediating lamellipodia formation were not identified"]},{"year":2005,"claim":"Identifying R-Ras as a proximal signaling partner: EphB2 activation recruits and phosphorylates R-Ras, linking EphB2 to MAPK suppression and explaining the anti-proliferative arm of EphB2 signaling in glioma.","evidence":"Co-IP, siRNA knockdown of R-Ras, phosphorylation analysis in glioma cells","pmids":["16049340"],"confidence":"Medium","gaps":["R-Ras involvement not validated in non-glioma systems","Whether R-Ras mediates anti-proliferative signaling in normal tissue is unknown"]},{"year":2007,"claim":"Defining EphB2 proteolytic processing: two distinct cleavage pathways were delineated—ligand-induced endosomal processing via γ-secretase and calcium/NMDA-induced surface cleavage via ADAM10—revealing how EphB2 signaling is terminated or converted to nuclear signaling via ICD release.","evidence":"Pharmacological inhibitors of metalloproteinase, γ-secretase, and endocytosis; cleavage site mapping; ubiquitination assays","pmids":["17428795"],"confidence":"High","gaps":["Transcriptional targets of the released EphB2 intracellular domain are unknown","Whether familial AD presenilin mutations affect EphB2 processing in vivo was not demonstrated"]},{"year":2009,"claim":"Genetically dissecting kinase-dependent vs. kinase-independent pathways in vivo: kinase-dead knock-in mice revealed that EphB2 controls cell positioning via PI3K (kinase-independent) and proliferation via Abl–cyclin D1 (kinase-dependent), and that cyclin D1 regulation uncouples during colorectal adenoma-to-carcinoma transition.","evidence":"Kinase-dead mutant knock-in mice, PI3K inhibitors, genetic epistasis, human colorectal tumor analysis","pmids":["19914164"],"confidence":"High","gaps":["How PI3K is recruited in the absence of kinase activity is not structurally resolved","Whether the Abl–cyclin D1 axis operates in non-intestinal tissues is untested"]},{"year":2011,"claim":"Establishing EphB2 forward signaling in brain morphogenesis: ephrin-B1–EphB2 forward kinase signaling directs migration of neural progenitors and regulates Reelin expression during dentate gyrus development.","evidence":"Intracellular truncation and point mutant knock-in mice, ephrin-B1 KO, Reelin and nestin immunoreactivity","pmids":["21832177"],"confidence":"High","gaps":["Molecular link between EphB2 kinase activity and Reelin transcriptional regulation is not defined"]},{"year":2012,"claim":"Identifying FAK as a direct EphB2 effector controlling the proliferation/migration switch in glioblastoma stem cells.","evidence":"Co-IP of EphB2–FAK, gain/loss-of-function, dual-fluorescent xenograft","pmids":["22310282"],"confidence":"Medium","gaps":["Whether FAK interaction requires EphB2 kinase activity or only scaffolding was not resolved","Reciprocal co-IP and endogenous validation limited"]},{"year":2013,"claim":"Linking EphB2 kinase activity to MMP-dependent invasion and dual regulation of apoptosis and autophagy in breast cancer cells.","evidence":"Kinase-dead mutant, DOX-inducible EphB2 restoration, MMP2/MMP9 neutralizing antibodies, caspase and autophagy markers","pmids":["24211352"],"confidence":"Medium","gaps":["Direct ubiquitin/autophagy pathway connections were not biochemically defined in this system"]},{"year":2014,"claim":"Extending EphB2 function to hemostasis: EphB2 cytoplasmic domain regulates thrombus formation and clot retraction through both contact-dependent and contact-independent mechanisms in platelets.","evidence":"EphB2 cytoplasmic domain-truncated mice, platelet activation assays, thrombus formation models","pmids":["25370417"],"confidence":"Medium","gaps":["Platelet-intrinsic signaling partners downstream of EphB2 cytoplasmic domain are not identified","Contact-independent signaling mechanism is unexplained"]},{"year":2015,"claim":"Establishing EphB2 as a driver of hepatic fibrosis by promoting hepatic stellate cell activation and myofibroblast differentiation, validated across two independent fibrosis models.","evidence":"EphB2 KO mice in CCl4 and malaria liver fibrosis models, HSC isolation and differentiation assays","pmids":["25784101"],"confidence":"High","gaps":["Which ephrin ligand activates EphB2 on HSCs in vivo is not established","Downstream signaling cascade in HSCs is not mapped"]},{"year":2017,"claim":"Defining a mitochondrial protection pathway: EphB2 induces Sirt3 via c-Src/Nrf-2 transcription, and Sirt3 deacetylates MnSOD-K68 to reduce mitochondrial ROS, linking EphB2 to cellular senescence resistance.","evidence":"EphB2 knockdown/activation, Nrf-2 nuclear translocation, Sirt3 overexpression/knockdown, MnSOD acetylation assays in MSCs","pmids":["28687409"],"confidence":"Medium","gaps":["Pathway validated only in mesenchymal stem cells","Whether EphB2-Sirt3 axis operates in neurons or hepatocytes is unknown"]},{"year":2017,"claim":"Demonstrating that nanoscale ligand geometry controls EphB2 oligomerization kinetics, showing that receptor clustering is tuned by spatial organization rather than ligand concentration alone.","evidence":"Diblock copolymer nanopatterning of ephrin-B1, Number and Brightness fluorescence imaging","pmids":["29243484"],"confidence":"Medium","gaps":["Whether nanoscale ligand geometry differentially activates downstream signaling branches is untested"]},{"year":2018,"claim":"Demonstrating that EphB2 kinase activity is required for fear memory consolidation via CREB activation in the lateral amygdala, using optogenetic precision to temporally define the signaling window.","evidence":"Optogenetic optoEphB2 activation, kinase-dead control, CREB phosphorylation, behavioral fear conditioning, EphB2lacZ/lacZ mice","pmids":["29768201"],"confidence":"High","gaps":["Intermediate kinases between EphB2 and CREB phosphorylation in amygdala are not identified"]},{"year":2020,"claim":"Revealing ubiquitin-dependent autophagy initiation: RNF186 ubiquitinates EphB2 at K892 upon ephrin-B1 stimulation, enabling LC3B recruitment and autophagosome formation; disruption of this pathway worsens colitis in vivo.","evidence":"Ubiquitination assays, K892R mutagenesis, LC3B co-IP, RNF186/EPHB2 KO mice in DSS colitis model","pmids":["33280498"],"confidence":"High","gaps":["Whether K892 ubiquitination is K63-linked or another chain type is not specified","Whether other E3 ligases can compensate for RNF186 is unknown"]},{"year":2021,"claim":"Establishing an EphB2–SRC/AKT/β-catenin positive feedback loop in hepatocellular carcinoma: TCF1 transcribes EPHB2, which activates SRC/AKT/GSK3β to stabilize β-catenin, driving stemness and sorafenib resistance.","evidence":"EPHB2 KO, promoter assays, patient-derived xenografts, AAV-shEPHB2, pathway inhibitors","pmids":["33903122"],"confidence":"High","gaps":["Whether the feedback loop operates in normal hepatocytes or is cancer-specific is not determined"]},{"year":2023,"claim":"Placing EphB2 downstream of Notch signaling in hepatocytes: EphB2 mediates cell-autonomous inflammatory signaling sufficient to drive NASH pathology, identifying a new non-kinase tissue context for EphB2 function.","evidence":"Single-nucleus multi-omics, hepatocyte-specific Ephb2 knockdown in mouse NASH model","pmids":["36753562"],"confidence":"High","gaps":["Whether EphB2 acts through kinase-dependent or -independent mechanisms in NASH hepatocytes is not resolved","The direct downstream inflammatory mediators of EphB2 in hepatocytes are not mapped"]},{"year":null,"claim":"Key unresolved questions include the structural basis for PI3K recruitment in the kinase-independent pathway, the nuclear targets of the γ-secretase-released EphB2 intracellular domain, and which ephrin ligands activate EphB2 in specific disease contexts such as hepatic fibrosis and NASH.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural data for kinase-independent PI3K engagement","ICD transcriptional targets undefined","Ligand identity in hepatic/renal fibrosis contexts unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,7,12]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,3,7]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[0,20]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[4,6,20]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,1,5,7,14,22]},{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[2,3,10,12,24]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[13,26]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[10]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[14,15,16]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[26]}],"complexes":[],"partners":["SRC","FAK","RNF186","EFNB1","EFNB2","EFNA5","RRAS","GRIN1"],"other_free_text":[]},"mechanistic_narrative":"EphB2 is a receptor tyrosine kinase that transduces bidirectional signals upon binding ephrin-B and ephrin-A5 ligands, governing cell positioning, proliferation, invasion, synaptic plasticity, and tissue fibrosis through separable kinase-dependent and kinase-independent pathways. Its kinase activity drives proliferation via Abl–cyclin D1, invasion via FAK and MMP induction, and memory consolidation via CREB phosphorylation, whereas kinase-independent signaling through PI3K controls cell migration and NMDA receptor-dependent synaptic function by regulating surface NR1/NR2B subunit levels [PMID:19914164, PMID:11754836, PMID:11754835, PMID:29768201]. EphB2 is post-translationally regulated by Src binding at phospho-Y611, RNF186-mediated ubiquitination at K892 triggering LC3-dependent autophagy, and context-dependent proteolytic processing by ADAM10 and γ-secretase [PMID:9632142, PMID:33280498, PMID:17428795]. Beyond the nervous system, EphB2 promotes hepatic stellate cell activation and fibrosis, drives cancer stemness through a SRC/AKT/β-catenin feedback loop, and mediates Notch-dependent hepatocyte inflammation in NASH [PMID:25784101, PMID:33903122, PMID:36753562]."},"prefetch_data":{"uniprot":{"accession":"P29323","full_name":"Ephrin type-B receptor 2","aliases":["Developmentally-regulated Eph-related tyrosine kinase","ELK-related tyrosine kinase","EPH tyrosine kinase 3","EPH-like kinase 5","EK5","hEK5","Renal carcinoma antigen NY-REN-47","Tyrosine-protein kinase TYRO5","Tyrosine-protein kinase receptor EPH-3"],"length_aa":1055,"mass_kda":117.5,"function":"Receptor tyrosine kinase which binds promiscuously transmembrane ephrin-B 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. Functions in axon guidance during development. Involved in the guidance of commissural axons, that form a major interhemispheric connection between the 2 temporal lobes of the cerebral cortex. Also involved in guidance of contralateral inner ear efferent growth cones at the midline and of retinal ganglion cell axons to the optic disk. In addition to axon guidance, also regulates dendritic spines development and maturation and stimulates the formation of excitatory synapses. Upon activation by EFNB1, abolishes the ARHGEF15-mediated negative regulation on excitatory synapse formation. Controls other aspects of development including angiogenesis, palate development and in inner ear development through regulation of endolymph production. Forward and reverse signaling through the EFNB2/EPHB2 complex regulate movement and adhesion of cells that tubularize the urethra and septate the cloaca. May function as a tumor suppressor. 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Biology","url":"https://pubmed.ncbi.nlm.nih.gov/31601124","citation_count":28,"is_preprint":false},{"pmid":"38038975","id":"PMC_38038975","title":"A guide to ERK dynamics, part 2: downstream decoding.","date":"2023","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/38038975","citation_count":27,"is_preprint":false},{"pmid":"27041567","id":"PMC_27041567","title":"Regulation of Numb isoform expression by activated ERK signaling.","date":"2016","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/27041567","citation_count":27,"is_preprint":false},{"pmid":"26050649","id":"PMC_26050649","title":"BAALC potentiates oncogenic ERK pathway through interactions with MEKK1 and KLF4.","date":"2015","source":"Leukemia","url":"https://pubmed.ncbi.nlm.nih.gov/26050649","citation_count":27,"is_preprint":false},{"pmid":"28687409","id":"PMC_28687409","title":"EphB2 signaling-mediated Sirt3 expression reduces MSC senescence by maintaining mitochondrial ROS homeostasis.","date":"2017","source":"Free radical biology & medicine","url":"https://pubmed.ncbi.nlm.nih.gov/28687409","citation_count":27,"is_preprint":false},{"pmid":"37947896","id":"PMC_37947896","title":"Emerging roles and mechanisms of ERK pathway mechanosensing.","date":"2023","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/37947896","citation_count":26,"is_preprint":false},{"pmid":"29928348","id":"PMC_29928348","title":"Activation of the SphK1/ERK/p-ERK pathway promotes autophagy in colon cancer cells.","date":"2018","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/29928348","citation_count":26,"is_preprint":false},{"pmid":"30131699","id":"PMC_30131699","title":"EphB2 Deficiency Induces Depression-Like Behaviors and Memory Impairment: Involvement of NMDA 2B Receptor Dependent Signaling.","date":"2018","source":"Frontiers in 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signaling including growth cone collapse and neurite retraction. X-ray crystallography revealed the ephrin-A5–EphB2 complex is a heterodimer, architecturally distinct from the tetrameric EphB2–ephrin-B2 structure.\",\n      \"method\": \"X-ray crystallography, cell-based receptor clustering/autophosphorylation assays, neurite retraction assay, binding affinity measurements\",\n      \"journal\": \"Nature neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure plus functional validation (autophosphorylation, growth cone collapse) in a single study\",\n      \"pmids\": [\"15107857\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"Phosphorylation of tyrosine 611 in the EphB2 juxtamembrane region is required for complex formation with the SH2 domain of Src kinase; tyrosines 605 and 611 are important for EphB2 kinase activity. Autophosphorylated EphB2 associates with Src, and EphB2-expressing cells show increased Src tyrosine phosphorylation, suggesting Src as a downstream effector.\",\n      \"method\": \"Yeast two-hybrid, site-directed mutagenesis, co-immunoprecipitation from transfected COS cells, phosphopeptide mapping\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 — mutagenesis combined with biochemical mapping and co-IP in multiple systems\",\n      \"pmids\": [\"9632142\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"EphB2 regulates NMDA receptor-dependent synaptic function in the mammalian CNS. Mice lacking the entire EphB2 receptor (but not those lacking only the kinase domain) showed reduced LTP and reduced synaptic NMDA current in dentate granule neurons, with diminished synaptically localized NR1 subunit.\",\n      \"method\": \"EphB2 knockout mice (full receptor vs. kinase-domain truncation), electrophysiology (LTP, NMDA currents), immunogold localization of NR1\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with domain-specific rescue, orthogonal electrophysiology and ultrastructural localization\",\n      \"pmids\": [\"11754836\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"EphB2 regulates hippocampal synaptic plasticity in a kinase-independent manner. Mice lacking EphB2 show impaired protein synthesis-dependent LTP and loss of two forms of synaptic depression; a C-terminally truncated EphB2 (lacking the kinase domain) rescues the null phenotype, demonstrating the extracellular/juxtamembrane domain is sufficient.\",\n      \"method\": \"EphB2 knockout mice, targeted truncation knock-in, hippocampal slice electrophysiology\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic dissection with domain-specific rescue and multiple plasticity readouts\",\n      \"pmids\": [\"11754835\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"EphB2 is localized to lamellipodia of migrating glioma cells; its phosphorylation (activation) promotes glioma cell migration and invasion, while blocking EphB2 with an antibody inhibits these processes. Forced EphB2 expression in low-expressing U251 cells stimulates migration, invasion and reduces adhesion concomitant with EphB2 tyrosine phosphorylation.\",\n      \"method\": \"Confocal microscopy (localization), blocking antibody, forced overexpression, siRNA knockdown, ex vivo brain slice invasion assay\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (localization, gain- and loss-of-function) with defined cellular phenotypes\",\n      \"pmids\": [\"15126357\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"EphB2 signals through R-Ras to regulate glioma cell adhesion, proliferation and invasion. Upon EphB2 activation, R-Ras associates with the receptor and becomes phosphorylated; siRNA depletion of R-Ras abrogates EphB2-mediated effects. Anti-proliferative responses to EphB2 correlate with suppressed MAPK activity.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown of R-Ras, ex vivo brain slice invasion, phosphorylation analysis\",\n      \"journal\": \"The American journal of pathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — co-IP plus functional siRNA rescue, single lab\",\n      \"pmids\": [\"16049340\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"EphB2 receptor undergoes two distinct processing pathways: (1) ligand (ephrinB)-induced processing requires endocytosis and involves cleavage in endosomes followed by gamma-secretase (presenilin-dependent) cleavage releasing the intracellular domain; (2) calcium influx/NMDA-induced processing occurs at the plasma membrane and requires ADAM10/metalloproteinase activity but not endocytosis. EphrinB stimulation also induces EphB2 ubiquitination. Presenilin-1 familial Alzheimer disease mutations inhibit gamma-secretase cleavage of EphB2.\",\n      \"method\": \"Pharmacological inhibitors (metalloproteinase, gamma-secretase, endocytosis blockers), site-specific cleavage mapping, ubiquitination assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 — mechanistic dissection with multiple inhibitors, defined cleavage sites, and distinct pathway characterization\",\n      \"pmids\": [\"17428795\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"EphB2 controls cell proliferation and cell migration through dissociable signaling pathways: kinase-independent, PI3K-mediated pathway controls cell positioning/migration; EphB2 tyrosine kinase activity controls proliferation via an Abl–cyclin D1 pathway. Cyclin D1 regulation becomes uncoupled from EphB signaling during adenoma-to-carcinoma progression.\",\n      \"method\": \"Kinase-dead mutant knock-in mice, PI3K inhibitors, genetic epistasis, tumor progression analysis in human colorectal samples\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 — genetic dissection with domain-specific mutants and pharmacological inhibitors defining two independent downstream pathways\",\n      \"pmids\": [\"19914164\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Azurin (a cupredoxin) binds to the EphB2 receptor with high affinity via a domain structurally similar to the G-H loop of ephrinB2, interfering with ephrinB2-induced autophosphorylation of EphB2 tyrosine residues and inhibiting cancer cell growth in EphB2-expressing cells but not in cells lacking functional EphB2.\",\n      \"method\": \"Binding assays (EphB2-Fc), synthetic peptide competition, autophosphorylation assays, cell viability in EphB2-positive vs. negative cell lines\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — binding and functional inhibition assays with receptor-positive vs. negative controls\",\n      \"pmids\": [\"17249693\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"EphB2 controls a proliferation/migration dichotomy in glioblastoma stem-like cells through interaction with focal adhesion kinase (FAK): EphB2 expression co-associates with and activates FAK, which facilitates focal adhesion formation, cytoskeletal changes and cell migration while inhibiting proliferation.\",\n      \"method\": \"Co-immunoprecipitation (EphB2-FAK), gain- and loss-of-function (overexpression, siRNA), dual-fluorescent xenograft model, in vitro migration/invasion assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — co-IP plus orthogonal gain/loss-of-function with defined phenotypic readouts, single lab\",\n      \"pmids\": [\"22310282\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"EphB2 tyrosine kinase catalytic activity is required for embryonic/postnatal development of the lateral suprapyramidal blade of the dentate gyrus. Ephrin-B1 acts as the ligand stimulating EphB2 forward signaling to direct migration of nestin-positive neural progenitors; disruption of EphB2 forward signaling reduces Reelin expression in a key compartment above the developing lateral suprapyramidal blade.\",\n      \"method\": \"Intracellular truncation and point mutant knock-in mice, genetic loss of ephrin-B1, immunoreactivity for Reelin and nestin, histological analysis\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with receptor domain-specific mutants and ligand knockout, replicated across multiple genotypes\",\n      \"pmids\": [\"21832177\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"miR-204 directly targets EphB2 mRNA in hippocampal neurons; upregulation of miR-204 with aging suppresses EphB2 protein expression, reducing surface and total NR1 (NMDA receptor subunit) expression, contributing to age-associated decline in synaptic plasticity.\",\n      \"method\": \"miR-204 mimic transfection, luciferase reporter (direct target validation), western blot, surface NR1 quantification\",\n      \"journal\": \"Aging cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct target validated by reporter assay plus functional consequence on NR1 surface expression\",\n      \"pmids\": [\"26799631\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"EphB2 forward signaling (kinase activity) during fear conditioning enhances long-term memory consolidation; photoactivation of optoEphB2 in lateral amygdala during learning activates CREB. A kinase-dead optoEphB2 fails to enhance memory or activate CREB. EphB2lacZ/lacZ mice lacking forward signaling show impaired long-term fear memory.\",\n      \"method\": \"Optogenetic activation (optoEphB2), kinase-dead mutant control, CREB phosphorylation assay, behavioral fear conditioning\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 — optogenetic gain-of-function with kinase-dead control and loss-of-function genetic model, multiple orthogonal readouts\",\n      \"pmids\": [\"29768201\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RNF186, an E3 ubiquitin ligase, ubiquitinates EPHB2 at Lys892 upon ephrin-B1 (EFNB1) stimulation, leading to EPHB2-dependent recruitment of MAP1LC3B and induction of autophagy in colonic epithelial cells. Mutation of Lys892 abolishes EPHB2-mediated autophagy. RNF186 and EPHB2 knockout mice show defective autophagy and more severe DSS-induced colitis.\",\n      \"method\": \"Ubiquitination assays, site-directed mutagenesis (K892R), LC3B co-immunoprecipitation, knockout mouse models, DSS colitis model\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 — biochemical reconstitution of ubiquitination with mutagenesis, in vivo genetic validation\",\n      \"pmids\": [\"33280498\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"EPHB2 drives cancer stemness and sorafenib resistance in hepatocellular carcinoma via the SRC/AKT/GSK3β/β-catenin signaling cascade. TCF1 activates EPHB2 transcription, forming a positive Wnt/β-catenin feedback loop. EPHB2 endogenous knockout attenuates tumor development; rAAV-8-shEPHB2 sensitizes HCC to sorafenib in vivo.\",\n      \"method\": \"EPHB2 knockout, pharmacological pathway inhibitors, promoter activation assay, patient-derived xenografts, AAV-mediated shRNA knockdown, pathway phosphorylation analysis\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods including KO, shRNA, PDX models, and defined signaling pathway\",\n      \"pmids\": [\"33903122\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"EphB2 acts downstream of Notch signaling in hepatocytes and is sufficient to induce cell-autonomous inflammation. Knockdown of Ephb2 in hepatocytes ameliorates inflammation and fibrosis in a mouse NASH model.\",\n      \"method\": \"Single-nucleus transcriptomics/epigenomics, hepatocyte-specific Ephb2 knockdown, mouse NASH model (inflammation and fibrosis readouts)\",\n      \"journal\": \"Science translational medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multi-omic characterization plus in vivo loss-of-function with defined pathway placement (downstream of Notch)\",\n      \"pmids\": [\"36753562\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"EphB2 promotes hepatic fibrosis via activation of hepatic stellate cells (HSCs): EphB2 is upregulated and activated in mouse HSCs following CCl4 exposure. EphB2-deficient HSCs show impaired proliferation and sub-optimal differentiation into fibrogenic myofibroblasts; EphB2 KO mice have reduced fibrosis, inflammation, and increased apoptosis in liver.\",\n      \"method\": \"EphB2 knockout mice, two models of hepatic fibrosis (malaria and CCl4), HSC isolation and in vitro differentiation assays, macrophage depletion\",\n      \"journal\": \"Hepatology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic KO replicated in two disease models with cellular mechanism identified (HSC activation)\",\n      \"pmids\": [\"25784101\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"EphB2 receptor tyrosine kinase promotes hepatic fibrogenesis via activation of hepatic stellate cells; EphB2 deficiency attenuates HSC proliferation, myofibroblast differentiation, and fibrosis. EphB2 KO mice show increased cellular apoptosis during fibrosis regression.\",\n      \"method\": \"EphB2 knockout mice, CCl4 model, in vitro HSC activation, fibrosis marker quantification, apoptosis assays\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic KO with in vitro mechanistic follow-up, single lab replication of earlier findings\",\n      \"pmids\": [\"29416088\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Loss of EPHB2 in prostate cancer cells increases lipid droplet accumulation by upregulating lipogenic proteins DGAT1, DGAT2, PLIN2 and downregulating lipolytic ATGL and PEDF. DGAT1 inhibition reverses LD accumulation and proliferation caused by EPHB2 loss.\",\n      \"method\": \"EPHB2 knockdown, lipid droplet imaging, western blot of lipid metabolism proteins, DGAT1 inhibitor rescue, cell proliferation assays\",\n      \"journal\": \"Laboratory investigation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — loss-of-function with defined molecular targets in lipid metabolism, pharmacological rescue\",\n      \"pmids\": [\"33824421\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"EphB2 in platelets regulates thrombus formation and clot retraction both in a contact-dependent (Eph-ephrin ligation between platelets) and contact-independent manner (cytoplasmic domain signaling in isolated platelets without ephrin engagement).\",\n      \"method\": \"EphB2 cytoplasmic domain-truncated mice, platelet activation assays, thrombus formation models, clot retraction assays\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic approach dissecting contact-dependent vs. independent signaling with functional platelet readouts\",\n      \"pmids\": [\"25370417\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Nanostructured surface-bound ephrinB1 ligands induce EphB2 receptor oligomerization/clustering on cell membranes more efficiently than randomly distributed ligands; nanopatterned ligands required 9-fold lower surface coverage and produced faster clustering kinetics, demonstrating that multivalent ligand presentation tunes receptor activation.\",\n      \"method\": \"Diblock copolymer nanopatterning, Number and Brightness fluorescence technique to track EphB2 oligomeric state in real time\",\n      \"journal\": \"Nano letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — quantitative single-cell imaging of receptor oligomerization with controlled ligand nanopatterning\",\n      \"pmids\": [\"29243484\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"EphB2 activation by ephrin-B2-Fc in cutaneous squamous cell carcinoma cells enhances production of invasion proteinases MMP13 and MMP1 and promotes invasion; EphB2 knockdown suppresses growth, vascularization, proliferation, migration and invasion of cSCC, and downregulates MMP1 and MMP13.\",\n      \"method\": \"siRNA knockdown, ephrin-B2-Fc stimulation, xenograft tumor model, MMP protein expression, gene expression profiling\",\n      \"journal\": \"The Journal of investigative dermatology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — gain- and loss-of-function with defined molecular effectors (MMP1/MMP13) and in vivo validation\",\n      \"pmids\": [\"25789706\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"EphrinB2/EphB2 promotes myenteric synaptic sprouting and NMDA receptor-mediated synaptic potentiation in IBS, via ERK-MAPK and PI3K-AKT pathways; EphB2 signaling drives persistent colonic hypercontractility and pain hypersensitivity.\",\n      \"method\": \"PI-IBS rat model, ephB2Fc receptor blocker, MK801 NMDA inhibitor, colonic muscle contraction recording, signaling pathway analysis, LMMP culture\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — pharmacological blockade with defined pathway placement in in vivo and ex vivo systems\",\n      \"pmids\": [\"31601124\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"EphB2 signaling induces Sirt3 expression and mitochondrial translocation of Sirt3 via c-Src phosphorylation and Nrf-2-dependent transcription, reducing mitochondrial ROS accumulation. Sirt3 deacetylates MnSOD at Lys68 to enhance its activity, protecting mesenchymal stem cells from senescence.\",\n      \"method\": \"EphB2 knockdown/activation, subcellular fractionation, Nrf-2 nuclear translocation assay, Sirt3 overexpression/knockdown, MnSOD activity and acetylation assays, wound healing model\",\n      \"journal\": \"Free radical biology & medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — defined signaling cascade with multiple mechanistic steps, single lab\",\n      \"pmids\": [\"28687409\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"EphB2 inactivation results in depression-like behaviors, memory impairment, and adult hippocampal neurogenesis defects, associated with decreased pCREB and BDNF and increased NR2B expression. NR2B antagonist Ro25-6981 reverses these phenotypes, placing NR2B downstream of EphB2 in behavioral and morphological outcomes.\",\n      \"method\": \"EphB2 knockout mice, behavioral tests (forced swim, tail suspension, Morris water maze, object recognition), NR2B pharmacological antagonism, BrdU neurogenesis assay, western blot\",\n      \"journal\": \"Frontiers in pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic KO plus pharmacological rescue defines NR2B as downstream mediator, single lab\",\n      \"pmids\": [\"30131699\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"EphB2 receptor is required in kidney for fibrosis development: EphB2 KO mice show significantly reduced renal tubular injury, fibrosis, inflammation and EMT after ischemia-reperfusion injury. EphB2 loss restores expression of 70.9% of fibrosis-associated genes dysregulated by IR injury back to normal.\",\n      \"method\": \"EphB2 knockout mice, renal ischemia-reperfusion model, fibrosis gene expression panel (760 genes), histology, EMT/myofibroblast markers\",\n      \"journal\": \"Clinical science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic KO with comprehensive transcriptomic and histological phenotyping in defined injury model\",\n      \"pmids\": [\"34462781\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"EphB2 in breast cancer cells promotes apoptosis (via caspase 3/9 activation), induces autophagy (LC3, ATG5, ATG12 markers), and mediates invasion through regulation of MMP2 and MMP9. EphB2-induced invasion is kinase-dependent, as it is blocked by a kinase-dead EphB2 mutant.\",\n      \"method\": \"DOX-inducible EphB2 restoration, siRNA knockdown, kinase-dead mutant, xenograft, MMP2/MMP9 neutralizing antibodies, caspase and autophagy marker analysis\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — kinase-dead domain mutant establishes kinase-dependency of invasion with orthogonal functional readouts\",\n      \"pmids\": [\"24211352\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"EphB2 is a receptor tyrosine kinase activated by ephrin-B (and, via cross-class interaction, ephrin-A5) ligands that undergoes autophosphorylation-dependent clustering and signals bidirectionally through dissociable pathways: its kinase activity drives proliferation (via Abl–cyclin D1), invasion (via FAK, MMP induction), and memory consolidation (via CREB), while kinase-independent signaling through PI3K controls cell positioning and synaptic plasticity; EphB2 is post-translationally regulated by Src (binding phospho-Y611), ubiquitination by RNF186 (triggering LC3-mediated autophagy), and proteolytic processing by gamma-secretase/ADAM10 in context-dependent ectodomain shedding, and it modulates NMDA receptor function, hepatic stellate cell activation, and mitochondrial ROS homeostasis via Sirt3/MnSOD downstream of c-Src/Nrf-2.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"EphB2 is a receptor tyrosine kinase that transduces bidirectional signals upon binding ephrin-B and ephrin-A5 ligands, governing cell positioning, proliferation, invasion, synaptic plasticity, and tissue fibrosis through separable kinase-dependent and kinase-independent pathways. Its kinase activity drives proliferation via Abl–cyclin D1, invasion via FAK and MMP induction, and memory consolidation via CREB phosphorylation, whereas kinase-independent signaling through PI3K controls cell migration and NMDA receptor-dependent synaptic function by regulating surface NR1/NR2B subunit levels [PMID:19914164, PMID:11754836, PMID:11754835, PMID:29768201]. EphB2 is post-translationally regulated by Src binding at phospho-Y611, RNF186-mediated ubiquitination at K892 triggering LC3-dependent autophagy, and context-dependent proteolytic processing by ADAM10 and γ-secretase [PMID:9632142, PMID:33280498, PMID:17428795]. Beyond the nervous system, EphB2 promotes hepatic stellate cell activation and fibrosis, drives cancer stemness through a SRC/AKT/β-catenin feedback loop, and mediates Notch-dependent hepatocyte inflammation in NASH [PMID:25784101, PMID:33903122, PMID:36753562].\",\n  \"teleology\": [\n    {\n      \"year\": 1998,\n      \"claim\": \"Identifying how EphB2 kinase activity is regulated: autophosphorylation at Y611 creates a docking site for Src-SH2, establishing Src as a proximal downstream effector and defining the juxtamembrane region as a regulatory hub.\",\n      \"evidence\": \"Yeast two-hybrid, site-directed mutagenesis, co-IP from transfected COS cells, phosphopeptide mapping\",\n      \"pmids\": [\"9632142\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Src is required for all EphB2 downstream outputs was not tested\", \"Other SH2-domain effectors recruited to the juxtamembrane region remain uncharacterized\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Resolving whether EphB2 kinase activity is required for synaptic function: full-receptor knockout but not kinase-domain deletion impaired NMDA currents and LTP, establishing that EphB2 regulates synaptic plasticity and NMDA receptor localization through a kinase-independent mechanism.\",\n      \"evidence\": \"EphB2 knockout vs. kinase-domain truncation knock-in mice, electrophysiology, immunogold NR1 localization\",\n      \"pmids\": [\"11754836\", \"11754835\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The extracellular/juxtamembrane domain partners mediating kinase-independent synaptic effects were not identified\", \"Whether the kinase-independent pathway operates through PI3K at the synapse was unknown\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Demonstrating cross-class ligand recognition: EphB2 binds ephrin-A5 as a heterodimer (not tetramer), inducing autophosphorylation and growth cone collapse, expanding the repertoire of activating ligands beyond ephrin-B family members.\",\n      \"evidence\": \"X-ray crystallography of ephrin-A5–EphB2 complex, cell-based autophosphorylation and neurite retraction assays\",\n      \"pmids\": [\"15107857\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological contexts where cross-class signaling predominates over canonical ephrin-B signaling are undefined\", \"Downstream pathway divergence between ephrin-A5 and ephrin-B2 stimulation was not assessed\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Linking EphB2 to cancer cell invasion: activated EphB2 localizes to lamellipodia and promotes glioma migration and invasion, establishing a pro-invasive role for EphB2 kinase signaling in brain tumors.\",\n      \"evidence\": \"Confocal localization, blocking antibody, overexpression, siRNA, ex vivo brain slice invasion assay in glioma cells\",\n      \"pmids\": [\"15126357\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct kinase substrates mediating lamellipodia formation were not identified\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Identifying R-Ras as a proximal signaling partner: EphB2 activation recruits and phosphorylates R-Ras, linking EphB2 to MAPK suppression and explaining the anti-proliferative arm of EphB2 signaling in glioma.\",\n      \"evidence\": \"Co-IP, siRNA knockdown of R-Ras, phosphorylation analysis in glioma cells\",\n      \"pmids\": [\"16049340\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"R-Ras involvement not validated in non-glioma systems\", \"Whether R-Ras mediates anti-proliferative signaling in normal tissue is unknown\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Defining EphB2 proteolytic processing: two distinct cleavage pathways were delineated—ligand-induced endosomal processing via γ-secretase and calcium/NMDA-induced surface cleavage via ADAM10—revealing how EphB2 signaling is terminated or converted to nuclear signaling via ICD release.\",\n      \"evidence\": \"Pharmacological inhibitors of metalloproteinase, γ-secretase, and endocytosis; cleavage site mapping; ubiquitination assays\",\n      \"pmids\": [\"17428795\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Transcriptional targets of the released EphB2 intracellular domain are unknown\", \"Whether familial AD presenilin mutations affect EphB2 processing in vivo was not demonstrated\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Genetically dissecting kinase-dependent vs. kinase-independent pathways in vivo: kinase-dead knock-in mice revealed that EphB2 controls cell positioning via PI3K (kinase-independent) and proliferation via Abl–cyclin D1 (kinase-dependent), and that cyclin D1 regulation uncouples during colorectal adenoma-to-carcinoma transition.\",\n      \"evidence\": \"Kinase-dead mutant knock-in mice, PI3K inhibitors, genetic epistasis, human colorectal tumor analysis\",\n      \"pmids\": [\"19914164\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How PI3K is recruited in the absence of kinase activity is not structurally resolved\", \"Whether the Abl–cyclin D1 axis operates in non-intestinal tissues is untested\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Establishing EphB2 forward signaling in brain morphogenesis: ephrin-B1–EphB2 forward kinase signaling directs migration of neural progenitors and regulates Reelin expression during dentate gyrus development.\",\n      \"evidence\": \"Intracellular truncation and point mutant knock-in mice, ephrin-B1 KO, Reelin and nestin immunoreactivity\",\n      \"pmids\": [\"21832177\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular link between EphB2 kinase activity and Reelin transcriptional regulation is not defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identifying FAK as a direct EphB2 effector controlling the proliferation/migration switch in glioblastoma stem cells.\",\n      \"evidence\": \"Co-IP of EphB2–FAK, gain/loss-of-function, dual-fluorescent xenograft\",\n      \"pmids\": [\"22310282\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether FAK interaction requires EphB2 kinase activity or only scaffolding was not resolved\", \"Reciprocal co-IP and endogenous validation limited\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Linking EphB2 kinase activity to MMP-dependent invasion and dual regulation of apoptosis and autophagy in breast cancer cells.\",\n      \"evidence\": \"Kinase-dead mutant, DOX-inducible EphB2 restoration, MMP2/MMP9 neutralizing antibodies, caspase and autophagy markers\",\n      \"pmids\": [\"24211352\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct ubiquitin/autophagy pathway connections were not biochemically defined in this system\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Extending EphB2 function to hemostasis: EphB2 cytoplasmic domain regulates thrombus formation and clot retraction through both contact-dependent and contact-independent mechanisms in platelets.\",\n      \"evidence\": \"EphB2 cytoplasmic domain-truncated mice, platelet activation assays, thrombus formation models\",\n      \"pmids\": [\"25370417\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Platelet-intrinsic signaling partners downstream of EphB2 cytoplasmic domain are not identified\", \"Contact-independent signaling mechanism is unexplained\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Establishing EphB2 as a driver of hepatic fibrosis by promoting hepatic stellate cell activation and myofibroblast differentiation, validated across two independent fibrosis models.\",\n      \"evidence\": \"EphB2 KO mice in CCl4 and malaria liver fibrosis models, HSC isolation and differentiation assays\",\n      \"pmids\": [\"25784101\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which ephrin ligand activates EphB2 on HSCs in vivo is not established\", \"Downstream signaling cascade in HSCs is not mapped\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defining a mitochondrial protection pathway: EphB2 induces Sirt3 via c-Src/Nrf-2 transcription, and Sirt3 deacetylates MnSOD-K68 to reduce mitochondrial ROS, linking EphB2 to cellular senescence resistance.\",\n      \"evidence\": \"EphB2 knockdown/activation, Nrf-2 nuclear translocation, Sirt3 overexpression/knockdown, MnSOD acetylation assays in MSCs\",\n      \"pmids\": [\"28687409\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Pathway validated only in mesenchymal stem cells\", \"Whether EphB2-Sirt3 axis operates in neurons or hepatocytes is unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstrating that nanoscale ligand geometry controls EphB2 oligomerization kinetics, showing that receptor clustering is tuned by spatial organization rather than ligand concentration alone.\",\n      \"evidence\": \"Diblock copolymer nanopatterning of ephrin-B1, Number and Brightness fluorescence imaging\",\n      \"pmids\": [\"29243484\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether nanoscale ligand geometry differentially activates downstream signaling branches is untested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Demonstrating that EphB2 kinase activity is required for fear memory consolidation via CREB activation in the lateral amygdala, using optogenetic precision to temporally define the signaling window.\",\n      \"evidence\": \"Optogenetic optoEphB2 activation, kinase-dead control, CREB phosphorylation, behavioral fear conditioning, EphB2lacZ/lacZ mice\",\n      \"pmids\": [\"29768201\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Intermediate kinases between EphB2 and CREB phosphorylation in amygdala are not identified\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Revealing ubiquitin-dependent autophagy initiation: RNF186 ubiquitinates EphB2 at K892 upon ephrin-B1 stimulation, enabling LC3B recruitment and autophagosome formation; disruption of this pathway worsens colitis in vivo.\",\n      \"evidence\": \"Ubiquitination assays, K892R mutagenesis, LC3B co-IP, RNF186/EPHB2 KO mice in DSS colitis model\",\n      \"pmids\": [\"33280498\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether K892 ubiquitination is K63-linked or another chain type is not specified\", \"Whether other E3 ligases can compensate for RNF186 is unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Establishing an EphB2–SRC/AKT/β-catenin positive feedback loop in hepatocellular carcinoma: TCF1 transcribes EPHB2, which activates SRC/AKT/GSK3β to stabilize β-catenin, driving stemness and sorafenib resistance.\",\n      \"evidence\": \"EPHB2 KO, promoter assays, patient-derived xenografts, AAV-shEPHB2, pathway inhibitors\",\n      \"pmids\": [\"33903122\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the feedback loop operates in normal hepatocytes or is cancer-specific is not determined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Placing EphB2 downstream of Notch signaling in hepatocytes: EphB2 mediates cell-autonomous inflammatory signaling sufficient to drive NASH pathology, identifying a new non-kinase tissue context for EphB2 function.\",\n      \"evidence\": \"Single-nucleus multi-omics, hepatocyte-specific Ephb2 knockdown in mouse NASH model\",\n      \"pmids\": [\"36753562\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether EphB2 acts through kinase-dependent or -independent mechanisms in NASH hepatocytes is not resolved\", \"The direct downstream inflammatory mediators of EphB2 in hepatocytes are not mapped\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the structural basis for PI3K recruitment in the kinase-independent pathway, the nuclear targets of the γ-secretase-released EphB2 intracellular domain, and which ephrin ligands activate EphB2 in specific disease contexts such as hepatic fibrosis and NASH.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural data for kinase-independent PI3K engagement\", \"ICD transcriptional targets undefined\", \"Ligand identity in hepatic/renal fibrosis contexts unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 7, 12]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 3, 7]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [0, 20]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [4, 6, 20]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 1, 5, 7, 14, 22]},\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [2, 3, 10, 12, 24]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [13, 26]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [10]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [14, 15, 16]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [26]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"SRC\",\n      \"FAK\",\n      \"RNF186\",\n      \"EFNB1\",\n      \"EFNB2\",\n      \"EFNA5\",\n      \"RRAS\",\n      \"GRIN1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}