{"gene":"EFNA3","run_date":"2026-04-28T17:46:03","timeline":{"discoveries":[{"year":2014,"finding":"Hypoxia induces HIF-mediated expression of novel long noncoding RNAs from the EFNA3 locus, which cause Ephrin-A3 protein accumulation (without changing coding EFNA3 mRNA levels), and both the lncRNAs and Ephrin-A3 increase the metastatic potential of breast cancer cells by enhancing extravasation","method":"lncRNA identification, HIF reporter assays, protein level measurements under hypoxia, in vivo extravasation/metastasis assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 — single lab with multiple methods including in vivo functional validation; mechanistic link between lncRNA and protein accumulation shown","pmids":["25023702"],"is_preprint":false},{"year":2020,"finding":"EFNA3 is a direct target of miR-210-3p; downregulation of Ephrin-A3 protein in HUVECs activates the PI3K/AKT pathway, promoting angiogenesis, while upregulation of EFNA3 suppresses PI3K/AKT signaling and inhibits HUVEC migration and proliferation","method":"Luciferase reporter assay (target validation), miR-210-3p mimic/inhibitor transfection, Western blot for phosphorylated AKT, tube formation assay, exosome transfer experiments","journal":"BioMed research international","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal methods in single lab; target validation by luciferase assay with functional pathway readout","pmids":["32695810"],"is_preprint":false},{"year":2022,"finding":"miR-210-3p (upregulated by HIF-1α under hypoxia) downregulates EFNA3 expression and thereby enhances phosphorylation of the PI3K/AKT pathway to promote angiogenesis","method":"miRNA sequencing, luciferase reporter assay, Western blot for PI3K/AKT phosphorylation, HUVEC functional assays, in vivo calvarial bone defect model","journal":"Acta biomaterialia","confidence":"Medium","confidence_rationale":"Tier 2 — multiple methods including in vivo validation; consistent with independent replications of miR-210-3p/EFNA3/PI3K axis","pmids":["35850484"],"is_preprint":false},{"year":2013,"finding":"EFNA3 is a direct target of miR-210; miR-210 regulates EFNA3 mRNA and protein expression in MPNST cells, and EFNA3-mediated signaling promotes proliferation and invasion of malignant peripheral nerve sheath tumor cells","method":"Luciferase reporter assay, qRT-PCR, Western blot, cell viability/colony formation/invasion assays with miR-210 overexpression and inhibition","journal":"Oncology research","confidence":"Medium","confidence_rationale":"Tier 2 — luciferase target validation plus loss/gain of function with defined cellular phenotypes","pmids":["24512729"],"is_preprint":false},{"year":2022,"finding":"lncRNA HOTTIP promotes EFNA3 transcription by recruiting the chromatin architectural protein CTCF to the EFNA3 promoter, and EFNA3 in turn drives airway inflammatory responses in asthma","method":"RNA pull-down, RNA immunoprecipitation, luciferase reporter assay, chromatin immunoprecipitation, in vivo OVA-asthma mouse model with EFNA3 knockdown","journal":"American journal of translational research","confidence":"Medium","confidence_rationale":"Tier 2 — multiple biochemical methods (ChIP, RIP, luciferase) with in vivo validation in single lab","pmids":["36628218"],"is_preprint":false},{"year":2022,"finding":"hsa_circ_0007478 acts as a miR-765 sponge (competing endogenous RNA), upregulating EFNA3 expression; EFNA3 in turn regulates NLRP3 inflammasome activation, IL-1β levels, and lipid metabolism/foam cell formation in ox-LDL-stimulated macrophages","method":"microarray, qRT-PCR, siRNA knockdown, miR-765 mimic transfection, luciferase reporter assay for miR-765/EFNA3 interaction, NLRP3/IL-1β readouts","journal":"Chemico-biological interactions","confidence":"Medium","confidence_rationale":"Tier 2-3 — target validation by luciferase plus functional cellular assays in single lab","pmids":["36191606"],"is_preprint":false},{"year":2023,"finding":"miR-423-5p targets and inhibits EFNA3 expression; hucMSC-derived extracellular vesicles deliver miR-423-5p to suppress EFNA3 in endothelial cells, thereby promoting HUVEC migration and angiogenesis; EFNA3 overexpression reverses these pro-angiogenic effects","method":"EV isolation and characterization, miR-423-5p mimic transfection, EFNA3 overexpression rescue, HUVEC migration/tube formation assays, in vivo rat MI model with capillary density measurement","journal":"Postepy w kardiologii interwencyjnej","confidence":"Medium","confidence_rationale":"Tier 2-3 — rescue experiment plus in vivo model in single lab","pmids":["36967852"],"is_preprint":false},{"year":2018,"finding":"lncRNA EFNA3 acts as a sponge for miR-101a in PC-12 cells under hypoxia; sequestration of miR-101a by lncRNA EFNA3 de-represses ROCK2, which activates Wnt/β-catenin and suppresses JAK/STAT pathways to exert neuroprotective effects","method":"shRNA knockdown of lncRNA EFNA3, RNA pull-down, RNA immunoprecipitation, luciferase activity assay, qRT-PCR, Western blot for ROCK2, Wnt/β-catenin and JAK/STAT pathway components","journal":"Journal of cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2-3 — multiple biochemical methods validating lncRNA-miRNA-mRNA axis with pathway readouts; single lab","pmids":["30125989"],"is_preprint":false},{"year":2024,"finding":"hMAGEA2 binds to the EFNA3 promoter region and transcriptionally activates EFNA3; elevated EFNA3 drives Ras/Braf/MEK/Erk1/2 phosphorylation to promote prostate cancer proliferation, migration, and invasion","method":"Dual-luciferase reporter assay for EFNA3 promoter binding, Western blot for ERK1/2 phosphorylation, hMAGEA2 knockdown cell lines, CCK-8/colony formation/transwell assays","journal":"Anticancer research","confidence":"Medium","confidence_rationale":"Tier 2-3 — luciferase assay for transcriptional regulation plus downstream pathway validation; single lab","pmids":["38925815"],"is_preprint":false},{"year":2025,"finding":"EphA3 physically interacts with EFNA3 (confirmed by co-immunoprecipitation); EphA3/EFNA3 reverse signaling promotes epithelial-to-mesenchymal transition (EMT) by activating ERK1/2 signaling, driving colorectal cancer metastasis","method":"Co-immunoprecipitation, EFNA3 knockdown/overexpression, transwell/wound healing/colony formation assays, subcutaneous and spleen injection tumor models in nude mice, Western blot for EMT and ERK1/2 markers","journal":"Digestive diseases and sciences","confidence":"Medium","confidence_rationale":"Tier 2 — direct binding shown by Co-IP, functional validation in vitro and in vivo with pathway readout; single lab","pmids":["40928719"],"is_preprint":false},{"year":2025,"finding":"NSUN5 (an m5C RNA methyltransferase) promotes m5C modification of EFNA3 mRNA, stabilizing EFNA3; elevated EFNA3 drives aerobic glycolysis in liver hepatocellular carcinoma cells, and EFNA3 overexpression rescues glycolysis suppressed by NSUN5 knockdown","method":"Methylated RNA immunoprecipitation, dual-luciferase reporter assay, NSUN5 knockdown, EFNA3 overexpression rescue, glycolysis measurements in vitro and xenograft tumor model in vivo","journal":"BMC cancer","confidence":"Medium","confidence_rationale":"Tier 2 — MeRIP for m5C modification plus rescue experiments with in vivo validation; single lab","pmids":["40730949"],"is_preprint":false},{"year":2022,"finding":"lncRNA LINC01270 acts as a competing endogenous RNA (ceRNA) for miR-326, thereby positively regulating EFNA3 expression; LINC01270/miR-326/EFNA3 axis promotes gastric cancer cell proliferation, migration, and invasion","method":"Luciferase reporter assay, RNA pull-down, qRT-PCR, Western blot, CCK-8/colony formation/transwell assays, rescue experiments with miR-326 inhibitor or EFNA3 overexpression","journal":"Bioengineered","confidence":"Low","confidence_rationale":"Tier 3 — standard ceRNA validation approach, single lab, no novel mechanistic depth beyond axis description","pmids":["35345980"],"is_preprint":false},{"year":2023,"finding":"EFNA3 is a direct target of miR-365; miR-365-mediated suppression of EFNA3 inhibits nucleus pulposus cell apoptosis, reduces MMP-13 expression, and preserves extracellular matrix (collagen II, aggrecan) in intervertebral disc degeneration","method":"Luciferase reporter assay, miR-365 mimic/inhibitor transfection, immunofluorescence, flow cytometry apoptosis assay, in vivo rat IDD model with NP cell injection","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2-3 — luciferase target validation with in vivo confirmation; single lab","pmids":["38009813"],"is_preprint":false},{"year":2024,"finding":"Recombinant EFNA3 (rEFNA3) administered topically promotes vaginal epithelial expression of desmosomal cadherins DSG1 and DSC1 in a biphasic dose-dependent manner and partially restores vaginal epithelial barrier function lost after DMPA (progestin) treatment","method":"Topical administration of recombinant EFNA3 in mice, Western blot/gene expression for DSG1/DSC1, epithelial barrier function assay, HSV-2 infection morbidity/mortality challenge","journal":"bioRxiv (preprint)","confidence":"Low","confidence_rationale":"Tier 3 — preprint, single lab, in vivo functional phenotype but mechanism linking EFNA3 to desmosomal cadherin transcription not yet biochemically resolved","pmids":["bio_10.1101_2024.10.29.620915"],"is_preprint":true},{"year":2024,"finding":"EFNA3, produced by basal cells of the mammary epithelium, targets luminal cells and enhances oxidative phosphorylation (OXPHOS) to provide energy that promotes collective epithelial migration and branching morphogenesis; inhibition of EFNA3 slows breast cancer metastasis","method":"Cell-type-specific EFNA3 expression analysis, OXPHOS measurements, in vivo mammary gland branching morphogenesis assay, EFNA3 inhibition in cancer metastasis models","journal":"bioRxiv (preprint)","confidence":"Low","confidence_rationale":"Tier 3 — preprint, novel mechanism proposed with in vivo data but not yet peer-reviewed; single lab","pmids":["bio_10.1101_2024.10.18.619009"],"is_preprint":true},{"year":2026,"finding":"EFNA3 activates the PI3K/AKT/mTOR signaling pathway, suppresses autophagy, and promotes breast cancer cell proliferation, EMT, and metastasis; EFNA3 knockdown induces autophagy and inhibits tumor growth in xenograft models","method":"EFNA3 knockdown/overexpression, Western blot for PI3K/AKT/mTOR phosphorylation, LC3 staining, transmission electron microscopy for autophagy, xenograft mouse model","journal":"The international journal of biochemistry & cell biology","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal methods (TEM, LC3, Western blot pathway analysis, in vivo) in single lab","pmids":["41763291"],"is_preprint":false},{"year":1996,"finding":"EFNA3 (LERK-3/EPLG3) is a GPI-anchored membrane protein that functions as a ligand for Eph-related receptor tyrosine kinases (hek and elk); its gene maps to human chromosome 1q21-q22 and mouse chromosome 3","method":"Southern hybridization of human×rodent somatic cell hybrids, fluorescence in situ hybridization, Southern blot of interspecific backcross mice, structural characterization (GPI anchor vs transmembrane)","journal":"Genomics","confidence":"High","confidence_rationale":"Tier 1-2 — foundational characterization of protein class (GPI-anchored RTK ligand) and chromosomal assignment; replicated by multiple independent approaches","pmids":["8660976"],"is_preprint":false}],"current_model":"EFNA3 encodes a GPI-anchored ephrin ligand that engages Eph receptor tyrosine kinases (including EphA3) to trigger bidirectional signaling; in the forward/reverse signaling context it activates ERK1/2 and PI3K/AKT/mTOR pathways, suppresses autophagy, promotes EMT and metastasis, and regulates angiogenesis, while its expression is controlled transcriptionally by HIF-mediated lncRNAs under hypoxia, by the transcription factor CTCF (recruited by lncRNA HOTTIP), by hMAGEA2 binding its promoter, and post-transcriptionally by m5C methylation (via NSUN5) as well as by multiple miRNAs (miR-210-3p, miR-423-5p, miR-326, miR-365, miR-765) that repress EFNA3 to modulate downstream PI3K/AKT and ERK signaling in contexts ranging from angiogenesis and cancer metastasis to intervertebral disc homeostasis and epithelial barrier integrity."},"narrative":{"teleology":[{"year":1996,"claim":"The molecular identity of EFNA3 was established as a GPI-anchored ligand for Eph receptor tyrosine kinases, placing it within the ephrin-A family and providing the chromosomal assignment (1q21-q22).","evidence":"Southern hybridization of somatic cell hybrids, FISH, and structural characterization of GPI linkage","pmids":["8660976"],"confidence":"High","gaps":["No cognate receptor specificity profile determined beyond hek/elk","No functional signaling readout measured","No tissue-specific expression pattern characterized"]},{"year":2014,"claim":"The question of how EFNA3 expression is controlled under pathophysiological conditions was addressed by showing that hypoxia-induced, HIF-dependent lncRNAs transcribed from the EFNA3 locus cause Ephrin-A3 protein accumulation and enhance metastatic extravasation, establishing EFNA3 as a hypoxia-responsive effector of metastasis.","evidence":"lncRNA identification, HIF reporter assays, protein measurements under hypoxia, and in vivo extravasation assays in breast cancer models","pmids":["25023702"],"confidence":"Medium","gaps":["Mechanism by which lncRNA increases protein without changing coding mRNA levels is not resolved","No identification of the downstream receptor engaged during extravasation"]},{"year":2013,"claim":"EFNA3 was identified as a direct target of miR-210, establishing the first post-transcriptional regulatory axis controlling EFNA3 and linking its expression to tumor cell proliferation and invasion.","evidence":"Luciferase reporter assay for miR-210/EFNA3 3′-UTR, qRT-PCR, Western blot, and functional assays in MPNST cells","pmids":["24512729"],"confidence":"Medium","gaps":["Downstream signaling pathway through which EFNA3 drives MPNST proliferation not identified","No receptor engagement demonstrated in this system"]},{"year":2020,"claim":"The downstream signaling consequence of EFNA3 suppression was resolved: miR-210-3p-mediated downregulation of EFNA3 activates PI3K/AKT signaling in endothelial cells to promote angiogenesis, establishing EFNA3 as a tonic suppressor of the PI3K/AKT pathway.","evidence":"Luciferase reporter validation, miR-210-3p mimic/inhibitor, Western blot for phospho-AKT, tube formation assays in HUVECs","pmids":["32695810"],"confidence":"Medium","gaps":["Whether EFNA3 inhibits PI3K/AKT through a specific Eph receptor or an alternative mechanism is unknown","No structural or biochemical basis for EFNA3-mediated AKT suppression"]},{"year":2022,"claim":"The miR-210-3p/EFNA3/PI3K-AKT axis was independently replicated in a bone regeneration context, and additional miRNA regulators (miR-765, miR-326) were shown to converge on EFNA3 to modulate inflammasome activation and cancer proliferation, broadening the functional repertoire of EFNA3 regulation.","evidence":"In vivo calvarial bone defect model with HIF-1α/miR-210-3p/EFNA3 axis (PMID:35850484); circRNA/miR-765/EFNA3/NLRP3 axis in macrophages (PMID:36191606); LINC01270/miR-326/EFNA3 axis in gastric cancer (PMID:35345980)","pmids":["35850484","36191606","35345980"],"confidence":"Medium","gaps":["Mechanism by which EFNA3 activates NLRP3 inflammasome is not defined","LINC01270/miR-326 axis is single-lab without replication","No direct EFNA3-receptor interaction demonstrated in macrophage or gastric cancer systems"]},{"year":2022,"claim":"A new layer of transcriptional regulation was uncovered: lncRNA HOTTIP recruits the chromatin architectural factor CTCF to the EFNA3 promoter, activating EFNA3 transcription and driving airway inflammation in asthma.","evidence":"RNA pull-down, RNA immunoprecipitation, ChIP, luciferase reporter, and OVA-induced asthma mouse model with EFNA3 knockdown","pmids":["36628218"],"confidence":"Medium","gaps":["Which Eph receptor transduces EFNA3 signaling in airway epithelium is unknown","No independent replication of HOTTIP-CTCF-EFNA3 axis"]},{"year":2023,"claim":"EFNA3 was shown to promote apoptosis and extracellular matrix degradation in nucleus pulposus cells, with miR-365-mediated suppression of EFNA3 protecting against intervertebral disc degeneration, extending EFNA3 function to musculoskeletal homeostasis.","evidence":"Luciferase reporter, miR-365 mimic/inhibitor, flow cytometry, immunofluorescence, rat IDD model","pmids":["38009813"],"confidence":"Medium","gaps":["Downstream pathway linking EFNA3 to MMP-13 expression and apoptosis not identified","Single lab with no independent confirmation"]},{"year":2023,"claim":"The miR-423-5p/EFNA3 axis was identified as a second endothelial angiogenesis-regulatory circuit, with extracellular vesicle delivery of miR-423-5p suppressing EFNA3 to promote vascularization after myocardial infarction.","evidence":"EV isolation, miR-423-5p mimic, EFNA3 overexpression rescue, HUVEC functional assays, rat MI model with capillary density measurement","pmids":["36967852"],"confidence":"Medium","gaps":["Specific Eph receptor interaction mediating EFNA3 anti-angiogenic effect not resolved","Single lab, no independent replication"]},{"year":2024,"claim":"The transcription factor hMAGEA2 was shown to directly bind the EFNA3 promoter and activate transcription, with elevated EFNA3 driving Ras/Braf/MEK/ERK1/2 signaling to promote prostate cancer aggressiveness, identifying a new transcriptional activator and the MAPK cascade as a major EFNA3 effector pathway.","evidence":"Dual-luciferase reporter for promoter binding, Western blot for ERK1/2 phosphorylation, hMAGEA2 knockdown, proliferation/invasion assays","pmids":["38925815"],"confidence":"Medium","gaps":["Whether hMAGEA2 binds EFNA3 promoter directly or through a co-factor is not resolved biochemically","No receptor engagement shown in prostate cancer cells"]},{"year":2025,"claim":"The first direct physical interaction between EFNA3 and EphA3 was confirmed, and reverse signaling through EFNA3 was shown to activate ERK1/2 to drive EMT and colorectal cancer metastasis, establishing a receptor-ligand pair and directionality of signaling.","evidence":"Co-immunoprecipitation, EFNA3 knockdown/overexpression, EMT and ERK1/2 Western blot, subcutaneous and spleen injection tumor models in nude mice","pmids":["40928719"],"confidence":"Medium","gaps":["Reverse signaling mechanism through a GPI-anchored ligand (which lacks cytoplasmic domain) is not biochemically resolved — likely requires co-receptor","Single Co-IP without reciprocal validation explicitly described"]},{"year":2025,"claim":"EFNA3 mRNA was found to be stabilized by NSUN5-mediated m5C modification, and stabilized EFNA3 promotes aerobic glycolysis in hepatocellular carcinoma, revealing an epitranscriptomic layer of regulation.","evidence":"MeRIP for m5C, dual-luciferase reporter, NSUN5 knockdown with EFNA3 rescue, glycolysis measurements in vitro and xenograft model","pmids":["40730949"],"confidence":"Medium","gaps":["Specific m5C site(s) on EFNA3 mRNA not mapped at single-nucleotide resolution","How EFNA3 protein mechanistically promotes glycolysis is undefined"]},{"year":2026,"claim":"EFNA3 was shown to activate PI3K/AKT/mTOR signaling, suppress autophagy, and promote EMT and metastasis in breast cancer, integrating its roles in proliferation, survival, and metabolic reprogramming into a unified oncogenic signaling model.","evidence":"EFNA3 knockdown/overexpression, Western blot for PI3K/AKT/mTOR phosphorylation, LC3 staining, TEM for autophagosomes, xenograft mouse model","pmids":["41763291"],"confidence":"Medium","gaps":["Whether autophagy suppression is a direct consequence of mTOR activation or involves additional EFNA3-dependent mechanisms is unclear","Receptor mediating PI3K/AKT/mTOR activation in breast cancer not identified"]},{"year":null,"claim":"How EFNA3, a GPI-anchored protein lacking a cytoplasmic domain, transduces reverse signals to activate ERK1/2 and PI3K/AKT/mTOR pathways remains mechanistically unresolved — the identity of the co-receptor or transmembrane adaptor mediating intracellular signal propagation is unknown.","evidence":"","pmids":[],"confidence":"Low","gaps":["Co-receptor or transmembrane adaptor for reverse signaling not identified","No structural model of EFNA3-EphA3 complex exists","Relative contributions of forward versus reverse signaling in each disease context remain unquantified"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0048018","term_label":"receptor ligand activity","supporting_discovery_ids":[16,9]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,2,15]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[16,9]}],"pathway":[{"term_id":"GO:0005576","term_label":"extracellular region","supporting_discovery_ids":[16]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[1,2,8,9,15]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[0,3,8,9,11,15]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[15]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[1,2,6]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[4,5]}],"complexes":[],"partners":["EPHA3","NSUN5","CTCF"],"other_free_text":[]},"mechanistic_narrative":"EFNA3 encodes a GPI-anchored ligand for Eph receptor tyrosine kinases that mediates bidirectional signaling to regulate angiogenesis, epithelial-to-mesenchymal transition, autophagy, and cellular metabolism [PMID:8660976, PMID:40928719, PMID:41763291]. Upon engagement with EphA3, EFNA3 reverse signaling activates ERK1/2 to drive EMT and metastasis in colorectal cancer, while in breast cancer it activates PI3K/AKT/mTOR signaling to suppress autophagy and promote proliferation [PMID:40928719, PMID:41763291]. EFNA3 expression is transcriptionally regulated by hypoxia-induced lncRNAs from its own locus, by CTCF recruited via lncRNA HOTTIP, and by hMAGEA2, and is post-transcriptionally controlled by multiple miRNAs (miR-210-3p, miR-423-5p, miR-326, miR-365, miR-765) and by NSUN5-mediated m5C mRNA methylation that stabilizes the transcript [PMID:25023702, PMID:36628218, PMID:38925815, PMID:32695810, PMID:40730949]. Downregulation of EFNA3 by miR-210-3p or miR-423-5p relieves its tonic suppression of PI3K/AKT signaling in endothelial cells, thereby promoting angiogenesis [PMID:32695810, PMID:35850484, PMID:36967852]."},"prefetch_data":{"uniprot":{"accession":"P52797","full_name":"Ephrin-A3","aliases":["EFL-2","EHK1 ligand","EHK1-L","EPH-related receptor tyrosine kinase ligand 3","LERK-3"],"length_aa":238,"mass_kda":26.4,"function":"Cell surface GPI-bound ligand for Eph receptors, a family of receptor tyrosine kinases which are crucial for migration, repulsion and adhesion during neuronal, vascular and epithelial development. Binds promiscuously Eph receptors residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling (By similarity)","subcellular_location":"Cell membrane","url":"https://www.uniprot.org/uniprotkb/P52797/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/EFNA3","classification":"Not Classified","n_dependent_lines":74,"n_total_lines":1208,"dependency_fraction":0.061258278145695365},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/EFNA3","total_profiled":1310},"omim":[{"mim_id":"612982","title":"MICRO RNA 210; MIR210","url":"https://www.omim.org/entry/612982"},{"mim_id":"611123","title":"EPHRIN RECEPTOR EphA10; EPHA10","url":"https://www.omim.org/entry/611123"},{"mim_id":"602756","title":"EPHRIN A2; EFNA2","url":"https://www.omim.org/entry/602756"},{"mim_id":"601535","title":"EPHRIN A5; EFNA5","url":"https://www.omim.org/entry/601535"},{"mim_id":"601381","title":"EPHRIN A3; EFNA3","url":"https://www.omim.org/entry/601381"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"esophagus","ntpm":29.0},{"tissue":"skin 1","ntpm":94.6}],"url":"https://www.proteinatlas.org/search/EFNA3"},"hgnc":{"alias_symbol":["LERK3","Ehk1-L"],"prev_symbol":["EPLG3"]},"alphafold":{"accession":"P52797","domains":[{"cath_id":"2.60.40.420","chopping":"31-170","consensus_level":"high","plddt":87.9933,"start":31,"end":170}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P52797","model_url":"https://alphafold.ebi.ac.uk/files/AF-P52797-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P52797-F1-predicted_aligned_error_v6.png","plddt_mean":73.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=EFNA3","jax_strain_url":"https://www.jax.org/strain/search?query=EFNA3"},"sequence":{"accession":"P52797","fasta_url":"https://rest.uniprot.org/uniprotkb/P52797.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P52797/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P52797"}},"corpus_meta":[{"pmid":"25023702","id":"PMC_25023702","title":"EFNA3 long noncoding RNAs induced by hypoxia promote metastatic dissemination.","date":"2014","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/25023702","citation_count":94,"is_preprint":false},{"pmid":"32695810","id":"PMC_32695810","title":"OSCC Exosomes Regulate miR-210-3p Targeting EFNA3 to Promote Oral Cancer Angiogenesis through the PI3K/AKT Pathway.","date":"2020","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/32695810","citation_count":78,"is_preprint":false},{"pmid":"35850484","id":"PMC_35850484","title":"Small extracellular vesicles derived from hypoxic mesenchymal stem cells promote vascularized bone regeneration through the miR-210-3p/EFNA3/PI3K pathway.","date":"2022","source":"Acta biomaterialia","url":"https://pubmed.ncbi.nlm.nih.gov/35850484","citation_count":78,"is_preprint":false},{"pmid":"24512729","id":"PMC_24512729","title":"MicroRNA-210 promotes proliferation and invasion of peripheral nerve sheath tumor cells targeting EFNA3.","date":"2013","source":"Oncology research","url":"https://pubmed.ncbi.nlm.nih.gov/24512729","citation_count":48,"is_preprint":false},{"pmid":"29131373","id":"PMC_29131373","title":"Differentially expressed miRNA-210 during follicular-luteal transition regulates pre-ovulatory granulosa cell function targeting HRas and EFNA3.","date":"2018","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29131373","citation_count":19,"is_preprint":false},{"pmid":"16466970","id":"PMC_16466970","title":"Expression analysis of the Epha1 receptor tyrosine kinase and its high-affinity ligands Efna1 and Efna3 during early mouse development.","date":"2006","source":"Gene expression patterns : GEP","url":"https://pubmed.ncbi.nlm.nih.gov/16466970","citation_count":16,"is_preprint":false},{"pmid":"36191606","id":"PMC_36191606","title":"Hsa_circ_0007478 aggravates NLRP3 inflammasome activation and lipid metabolism imbalance in ox-LDL-stimulated macrophage via miR-765/EFNA3 axis.","date":"2022","source":"Chemico-biological interactions","url":"https://pubmed.ncbi.nlm.nih.gov/36191606","citation_count":14,"is_preprint":false},{"pmid":"8660976","id":"PMC_8660976","title":"The genes encoding the eph-related receptor tyrosine kinase ligands LERK-1 (EPLG1, Epl1), LERK-3 (EPLG3, Epl3), and LERK-4 (EPLG4, Epl4) are clustered on human chromosome 1 and mouse chromosome 3.","date":"1996","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/8660976","citation_count":13,"is_preprint":false},{"pmid":"38630320","id":"PMC_38630320","title":"Artesunate attenuates the tumorigenesis of choroidal melanoma via inhibiting EFNA3 through Stat3/Akt signaling pathway.","date":"2024","source":"Journal of cancer research and clinical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/38630320","citation_count":10,"is_preprint":false},{"pmid":"38009813","id":"PMC_38009813","title":"microRNA-365 attenuated intervertebral disc degeneration through modulating nucleus pulposus cell apoptosis and extracellular matrix degradation by targeting EFNA3.","date":"2023","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38009813","citation_count":8,"is_preprint":false},{"pmid":"36967852","id":"PMC_36967852","title":"Extracellular vesicles derived from human umbilical cord mesenchymal stem cells stimulate angiogenesis in myocardial infarction via the microRNA-423-5p/EFNA3 axis.","date":"2023","source":"Postepy w kardiologii interwencyjnej = Advances in interventional cardiology","url":"https://pubmed.ncbi.nlm.nih.gov/36967852","citation_count":8,"is_preprint":false},{"pmid":"35345980","id":"PMC_35345980","title":"LncRNA LINC01270 aggravates the progression of gastric cancer through modulation of miR-326/EFNA3 axis.","date":"2022","source":"Bioengineered","url":"https://pubmed.ncbi.nlm.nih.gov/35345980","citation_count":6,"is_preprint":false},{"pmid":"36628218","id":"PMC_36628218","title":"Long non-coding RNA HOTTIP induces inflammation in asthma by promoting EFNA3 transcription by CCCTC-binding factor.","date":"2022","source":"American journal of translational research","url":"https://pubmed.ncbi.nlm.nih.gov/36628218","citation_count":6,"is_preprint":false},{"pmid":"30125989","id":"PMC_30125989","title":"Deletion of long noncoding RNA EFNA3 aggravates hypoxia-induced injury in PC-12 cells by upregulation of miR-101a.","date":"2018","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/30125989","citation_count":6,"is_preprint":false},{"pmid":"40730949","id":"PMC_40730949","title":"NSUN5 accelerates the progression of liver hepatocellular carcinoma by m5C-EFNA3-mediated glycolysis.","date":"2025","source":"BMC cancer","url":"https://pubmed.ncbi.nlm.nih.gov/40730949","citation_count":4,"is_preprint":false},{"pmid":"35706812","id":"PMC_35706812","title":"The 1q21.3 region driver gene EFNA3 promotes disease progression via inhibition of lung adenocarcinoma cell apoptosis.","date":"2022","source":"Translational cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/35706812","citation_count":2,"is_preprint":false},{"pmid":"40928719","id":"PMC_40928719","title":"EphA3/EFNA3 Reverse Signalling Promotes Epithelial-to-Mesenchymal Transition via ERK Pathway to Facilitate Colorectal Cancer Metastasis.","date":"2025","source":"Digestive diseases and sciences","url":"https://pubmed.ncbi.nlm.nih.gov/40928719","citation_count":0,"is_preprint":false},{"pmid":"38925815","id":"PMC_38925815","title":"hMAGEA2 Accelerates the Progression of Prostate Cancer via the EFNA3-Erk1/2 Signaling Pathway.","date":"2024","source":"Anticancer research","url":"https://pubmed.ncbi.nlm.nih.gov/38925815","citation_count":0,"is_preprint":false},{"pmid":"41763291","id":"PMC_41763291","title":"EFNA3-mediated autophagy suppression drives breast cancer proliferation, EMT and metastasis via PI3K/AKT/mTOR axis.","date":"2026","source":"The international journal of biochemistry & cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/41763291","citation_count":0,"is_preprint":false},{"pmid":"42004975","id":"PMC_42004975","title":"Integrated multi-omics and machine learning identify EFNA3 as a key biomarker of tumor invasion.","date":"2026","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/42004975","citation_count":0,"is_preprint":false},{"pmid":"41307306","id":"PMC_41307306","title":"Comprehensive analysis of Ephrin ligand and receptor expression reveals exclusive domains during nephrogenesis for epha4/epha7 and efna3.","date":"2025","source":"The International journal of developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/41307306","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.10.29.620915","title":"Exogenous ephrin-A3 administration restores vaginal epithelial barrier function in progestin-treated mice","date":"2024-11-03","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.29.620915","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.10.18.619009","title":"Basal EFNA3 Facilitates Luminal-Driving Mammary Epithelial Migration and Cancer Metastasis by Promoting OXPHOS","date":"2024-10-21","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.18.619009","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13655,"output_tokens":4279,"usd":0.052575},"stage2":{"model":"claude-opus-4-6","input_tokens":7739,"output_tokens":3527,"usd":0.190305},"total_usd":0.24288,"stage1_batch_id":"msgbatch_0118RScg3WGaGkaZRtWZbtce","stage2_batch_id":"msgbatch_01Cpfzvtbj42aqp5oYZ5Te2s","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"Hypoxia induces HIF-mediated expression of novel long noncoding RNAs from the EFNA3 locus, which cause Ephrin-A3 protein accumulation (without changing coding EFNA3 mRNA levels), and both the lncRNAs and Ephrin-A3 increase the metastatic potential of breast cancer cells by enhancing extravasation\",\n      \"method\": \"lncRNA identification, HIF reporter assays, protein level measurements under hypoxia, in vivo extravasation/metastasis assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — single lab with multiple methods including in vivo functional validation; mechanistic link between lncRNA and protein accumulation shown\",\n      \"pmids\": [\"25023702\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"EFNA3 is a direct target of miR-210-3p; downregulation of Ephrin-A3 protein in HUVECs activates the PI3K/AKT pathway, promoting angiogenesis, while upregulation of EFNA3 suppresses PI3K/AKT signaling and inhibits HUVEC migration and proliferation\",\n      \"method\": \"Luciferase reporter assay (target validation), miR-210-3p mimic/inhibitor transfection, Western blot for phosphorylated AKT, tube formation assay, exosome transfer experiments\",\n      \"journal\": \"BioMed research international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods in single lab; target validation by luciferase assay with functional pathway readout\",\n      \"pmids\": [\"32695810\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"miR-210-3p (upregulated by HIF-1α under hypoxia) downregulates EFNA3 expression and thereby enhances phosphorylation of the PI3K/AKT pathway to promote angiogenesis\",\n      \"method\": \"miRNA sequencing, luciferase reporter assay, Western blot for PI3K/AKT phosphorylation, HUVEC functional assays, in vivo calvarial bone defect model\",\n      \"journal\": \"Acta biomaterialia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple methods including in vivo validation; consistent with independent replications of miR-210-3p/EFNA3/PI3K axis\",\n      \"pmids\": [\"35850484\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"EFNA3 is a direct target of miR-210; miR-210 regulates EFNA3 mRNA and protein expression in MPNST cells, and EFNA3-mediated signaling promotes proliferation and invasion of malignant peripheral nerve sheath tumor cells\",\n      \"method\": \"Luciferase reporter assay, qRT-PCR, Western blot, cell viability/colony formation/invasion assays with miR-210 overexpression and inhibition\",\n      \"journal\": \"Oncology research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — luciferase target validation plus loss/gain of function with defined cellular phenotypes\",\n      \"pmids\": [\"24512729\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"lncRNA HOTTIP promotes EFNA3 transcription by recruiting the chromatin architectural protein CTCF to the EFNA3 promoter, and EFNA3 in turn drives airway inflammatory responses in asthma\",\n      \"method\": \"RNA pull-down, RNA immunoprecipitation, luciferase reporter assay, chromatin immunoprecipitation, in vivo OVA-asthma mouse model with EFNA3 knockdown\",\n      \"journal\": \"American journal of translational research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple biochemical methods (ChIP, RIP, luciferase) with in vivo validation in single lab\",\n      \"pmids\": [\"36628218\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"hsa_circ_0007478 acts as a miR-765 sponge (competing endogenous RNA), upregulating EFNA3 expression; EFNA3 in turn regulates NLRP3 inflammasome activation, IL-1β levels, and lipid metabolism/foam cell formation in ox-LDL-stimulated macrophages\",\n      \"method\": \"microarray, qRT-PCR, siRNA knockdown, miR-765 mimic transfection, luciferase reporter assay for miR-765/EFNA3 interaction, NLRP3/IL-1β readouts\",\n      \"journal\": \"Chemico-biological interactions\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — target validation by luciferase plus functional cellular assays in single lab\",\n      \"pmids\": [\"36191606\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"miR-423-5p targets and inhibits EFNA3 expression; hucMSC-derived extracellular vesicles deliver miR-423-5p to suppress EFNA3 in endothelial cells, thereby promoting HUVEC migration and angiogenesis; EFNA3 overexpression reverses these pro-angiogenic effects\",\n      \"method\": \"EV isolation and characterization, miR-423-5p mimic transfection, EFNA3 overexpression rescue, HUVEC migration/tube formation assays, in vivo rat MI model with capillary density measurement\",\n      \"journal\": \"Postepy w kardiologii interwencyjnej\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — rescue experiment plus in vivo model in single lab\",\n      \"pmids\": [\"36967852\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"lncRNA EFNA3 acts as a sponge for miR-101a in PC-12 cells under hypoxia; sequestration of miR-101a by lncRNA EFNA3 de-represses ROCK2, which activates Wnt/β-catenin and suppresses JAK/STAT pathways to exert neuroprotective effects\",\n      \"method\": \"shRNA knockdown of lncRNA EFNA3, RNA pull-down, RNA immunoprecipitation, luciferase activity assay, qRT-PCR, Western blot for ROCK2, Wnt/β-catenin and JAK/STAT pathway components\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — multiple biochemical methods validating lncRNA-miRNA-mRNA axis with pathway readouts; single lab\",\n      \"pmids\": [\"30125989\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"hMAGEA2 binds to the EFNA3 promoter region and transcriptionally activates EFNA3; elevated EFNA3 drives Ras/Braf/MEK/Erk1/2 phosphorylation to promote prostate cancer proliferation, migration, and invasion\",\n      \"method\": \"Dual-luciferase reporter assay for EFNA3 promoter binding, Western blot for ERK1/2 phosphorylation, hMAGEA2 knockdown cell lines, CCK-8/colony formation/transwell assays\",\n      \"journal\": \"Anticancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — luciferase assay for transcriptional regulation plus downstream pathway validation; single lab\",\n      \"pmids\": [\"38925815\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"EphA3 physically interacts with EFNA3 (confirmed by co-immunoprecipitation); EphA3/EFNA3 reverse signaling promotes epithelial-to-mesenchymal transition (EMT) by activating ERK1/2 signaling, driving colorectal cancer metastasis\",\n      \"method\": \"Co-immunoprecipitation, EFNA3 knockdown/overexpression, transwell/wound healing/colony formation assays, subcutaneous and spleen injection tumor models in nude mice, Western blot for EMT and ERK1/2 markers\",\n      \"journal\": \"Digestive diseases and sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct binding shown by Co-IP, functional validation in vitro and in vivo with pathway readout; single lab\",\n      \"pmids\": [\"40928719\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NSUN5 (an m5C RNA methyltransferase) promotes m5C modification of EFNA3 mRNA, stabilizing EFNA3; elevated EFNA3 drives aerobic glycolysis in liver hepatocellular carcinoma cells, and EFNA3 overexpression rescues glycolysis suppressed by NSUN5 knockdown\",\n      \"method\": \"Methylated RNA immunoprecipitation, dual-luciferase reporter assay, NSUN5 knockdown, EFNA3 overexpression rescue, glycolysis measurements in vitro and xenograft tumor model in vivo\",\n      \"journal\": \"BMC cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — MeRIP for m5C modification plus rescue experiments with in vivo validation; single lab\",\n      \"pmids\": [\"40730949\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"lncRNA LINC01270 acts as a competing endogenous RNA (ceRNA) for miR-326, thereby positively regulating EFNA3 expression; LINC01270/miR-326/EFNA3 axis promotes gastric cancer cell proliferation, migration, and invasion\",\n      \"method\": \"Luciferase reporter assay, RNA pull-down, qRT-PCR, Western blot, CCK-8/colony formation/transwell assays, rescue experiments with miR-326 inhibitor or EFNA3 overexpression\",\n      \"journal\": \"Bioengineered\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — standard ceRNA validation approach, single lab, no novel mechanistic depth beyond axis description\",\n      \"pmids\": [\"35345980\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"EFNA3 is a direct target of miR-365; miR-365-mediated suppression of EFNA3 inhibits nucleus pulposus cell apoptosis, reduces MMP-13 expression, and preserves extracellular matrix (collagen II, aggrecan) in intervertebral disc degeneration\",\n      \"method\": \"Luciferase reporter assay, miR-365 mimic/inhibitor transfection, immunofluorescence, flow cytometry apoptosis assay, in vivo rat IDD model with NP cell injection\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — luciferase target validation with in vivo confirmation; single lab\",\n      \"pmids\": [\"38009813\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Recombinant EFNA3 (rEFNA3) administered topically promotes vaginal epithelial expression of desmosomal cadherins DSG1 and DSC1 in a biphasic dose-dependent manner and partially restores vaginal epithelial barrier function lost after DMPA (progestin) treatment\",\n      \"method\": \"Topical administration of recombinant EFNA3 in mice, Western blot/gene expression for DSG1/DSC1, epithelial barrier function assay, HSV-2 infection morbidity/mortality challenge\",\n      \"journal\": \"bioRxiv (preprint)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — preprint, single lab, in vivo functional phenotype but mechanism linking EFNA3 to desmosomal cadherin transcription not yet biochemically resolved\",\n      \"pmids\": [\"bio_10.1101_2024.10.29.620915\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"EFNA3, produced by basal cells of the mammary epithelium, targets luminal cells and enhances oxidative phosphorylation (OXPHOS) to provide energy that promotes collective epithelial migration and branching morphogenesis; inhibition of EFNA3 slows breast cancer metastasis\",\n      \"method\": \"Cell-type-specific EFNA3 expression analysis, OXPHOS measurements, in vivo mammary gland branching morphogenesis assay, EFNA3 inhibition in cancer metastasis models\",\n      \"journal\": \"bioRxiv (preprint)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — preprint, novel mechanism proposed with in vivo data but not yet peer-reviewed; single lab\",\n      \"pmids\": [\"bio_10.1101_2024.10.18.619009\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"EFNA3 activates the PI3K/AKT/mTOR signaling pathway, suppresses autophagy, and promotes breast cancer cell proliferation, EMT, and metastasis; EFNA3 knockdown induces autophagy and inhibits tumor growth in xenograft models\",\n      \"method\": \"EFNA3 knockdown/overexpression, Western blot for PI3K/AKT/mTOR phosphorylation, LC3 staining, transmission electron microscopy for autophagy, xenograft mouse model\",\n      \"journal\": \"The international journal of biochemistry & cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (TEM, LC3, Western blot pathway analysis, in vivo) in single lab\",\n      \"pmids\": [\"41763291\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"EFNA3 (LERK-3/EPLG3) is a GPI-anchored membrane protein that functions as a ligand for Eph-related receptor tyrosine kinases (hek and elk); its gene maps to human chromosome 1q21-q22 and mouse chromosome 3\",\n      \"method\": \"Southern hybridization of human×rodent somatic cell hybrids, fluorescence in situ hybridization, Southern blot of interspecific backcross mice, structural characterization (GPI anchor vs transmembrane)\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — foundational characterization of protein class (GPI-anchored RTK ligand) and chromosomal assignment; replicated by multiple independent approaches\",\n      \"pmids\": [\"8660976\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"EFNA3 encodes a GPI-anchored ephrin ligand that engages Eph receptor tyrosine kinases (including EphA3) to trigger bidirectional signaling; in the forward/reverse signaling context it activates ERK1/2 and PI3K/AKT/mTOR pathways, suppresses autophagy, promotes EMT and metastasis, and regulates angiogenesis, while its expression is controlled transcriptionally by HIF-mediated lncRNAs under hypoxia, by the transcription factor CTCF (recruited by lncRNA HOTTIP), by hMAGEA2 binding its promoter, and post-transcriptionally by m5C methylation (via NSUN5) as well as by multiple miRNAs (miR-210-3p, miR-423-5p, miR-326, miR-365, miR-765) that repress EFNA3 to modulate downstream PI3K/AKT and ERK signaling in contexts ranging from angiogenesis and cancer metastasis to intervertebral disc homeostasis and epithelial barrier integrity.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"EFNA3 encodes a GPI-anchored ligand for Eph receptor tyrosine kinases that mediates bidirectional signaling to regulate angiogenesis, epithelial-to-mesenchymal transition, autophagy, and cellular metabolism [PMID:8660976, PMID:40928719, PMID:41763291]. Upon engagement with EphA3, EFNA3 reverse signaling activates ERK1/2 to drive EMT and metastasis in colorectal cancer, while in breast cancer it activates PI3K/AKT/mTOR signaling to suppress autophagy and promote proliferation [PMID:40928719, PMID:41763291]. EFNA3 expression is transcriptionally regulated by hypoxia-induced lncRNAs from its own locus, by CTCF recruited via lncRNA HOTTIP, and by hMAGEA2, and is post-transcriptionally controlled by multiple miRNAs (miR-210-3p, miR-423-5p, miR-326, miR-365, miR-765) and by NSUN5-mediated m5C mRNA methylation that stabilizes the transcript [PMID:25023702, PMID:36628218, PMID:38925815, PMID:32695810, PMID:40730949]. Downregulation of EFNA3 by miR-210-3p or miR-423-5p relieves its tonic suppression of PI3K/AKT signaling in endothelial cells, thereby promoting angiogenesis [PMID:32695810, PMID:35850484, PMID:36967852].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"The molecular identity of EFNA3 was established as a GPI-anchored ligand for Eph receptor tyrosine kinases, placing it within the ephrin-A family and providing the chromosomal assignment (1q21-q22).\",\n      \"evidence\": \"Southern hybridization of somatic cell hybrids, FISH, and structural characterization of GPI linkage\",\n      \"pmids\": [\"8660976\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No cognate receptor specificity profile determined beyond hek/elk\", \"No functional signaling readout measured\", \"No tissue-specific expression pattern characterized\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"The question of how EFNA3 expression is controlled under pathophysiological conditions was addressed by showing that hypoxia-induced, HIF-dependent lncRNAs transcribed from the EFNA3 locus cause Ephrin-A3 protein accumulation and enhance metastatic extravasation, establishing EFNA3 as a hypoxia-responsive effector of metastasis.\",\n      \"evidence\": \"lncRNA identification, HIF reporter assays, protein measurements under hypoxia, and in vivo extravasation assays in breast cancer models\",\n      \"pmids\": [\"25023702\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which lncRNA increases protein without changing coding mRNA levels is not resolved\", \"No identification of the downstream receptor engaged during extravasation\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"EFNA3 was identified as a direct target of miR-210, establishing the first post-transcriptional regulatory axis controlling EFNA3 and linking its expression to tumor cell proliferation and invasion.\",\n      \"evidence\": \"Luciferase reporter assay for miR-210/EFNA3 3′-UTR, qRT-PCR, Western blot, and functional assays in MPNST cells\",\n      \"pmids\": [\"24512729\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Downstream signaling pathway through which EFNA3 drives MPNST proliferation not identified\", \"No receptor engagement demonstrated in this system\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"The downstream signaling consequence of EFNA3 suppression was resolved: miR-210-3p-mediated downregulation of EFNA3 activates PI3K/AKT signaling in endothelial cells to promote angiogenesis, establishing EFNA3 as a tonic suppressor of the PI3K/AKT pathway.\",\n      \"evidence\": \"Luciferase reporter validation, miR-210-3p mimic/inhibitor, Western blot for phospho-AKT, tube formation assays in HUVECs\",\n      \"pmids\": [\"32695810\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether EFNA3 inhibits PI3K/AKT through a specific Eph receptor or an alternative mechanism is unknown\", \"No structural or biochemical basis for EFNA3-mediated AKT suppression\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"The miR-210-3p/EFNA3/PI3K-AKT axis was independently replicated in a bone regeneration context, and additional miRNA regulators (miR-765, miR-326) were shown to converge on EFNA3 to modulate inflammasome activation and cancer proliferation, broadening the functional repertoire of EFNA3 regulation.\",\n      \"evidence\": \"In vivo calvarial bone defect model with HIF-1α/miR-210-3p/EFNA3 axis (PMID:35850484); circRNA/miR-765/EFNA3/NLRP3 axis in macrophages (PMID:36191606); LINC01270/miR-326/EFNA3 axis in gastric cancer (PMID:35345980)\",\n      \"pmids\": [\"35850484\", \"36191606\", \"35345980\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which EFNA3 activates NLRP3 inflammasome is not defined\", \"LINC01270/miR-326 axis is single-lab without replication\", \"No direct EFNA3-receptor interaction demonstrated in macrophage or gastric cancer systems\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"A new layer of transcriptional regulation was uncovered: lncRNA HOTTIP recruits the chromatin architectural factor CTCF to the EFNA3 promoter, activating EFNA3 transcription and driving airway inflammation in asthma.\",\n      \"evidence\": \"RNA pull-down, RNA immunoprecipitation, ChIP, luciferase reporter, and OVA-induced asthma mouse model with EFNA3 knockdown\",\n      \"pmids\": [\"36628218\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Which Eph receptor transduces EFNA3 signaling in airway epithelium is unknown\", \"No independent replication of HOTTIP-CTCF-EFNA3 axis\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"EFNA3 was shown to promote apoptosis and extracellular matrix degradation in nucleus pulposus cells, with miR-365-mediated suppression of EFNA3 protecting against intervertebral disc degeneration, extending EFNA3 function to musculoskeletal homeostasis.\",\n      \"evidence\": \"Luciferase reporter, miR-365 mimic/inhibitor, flow cytometry, immunofluorescence, rat IDD model\",\n      \"pmids\": [\"38009813\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Downstream pathway linking EFNA3 to MMP-13 expression and apoptosis not identified\", \"Single lab with no independent confirmation\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"The miR-423-5p/EFNA3 axis was identified as a second endothelial angiogenesis-regulatory circuit, with extracellular vesicle delivery of miR-423-5p suppressing EFNA3 to promote vascularization after myocardial infarction.\",\n      \"evidence\": \"EV isolation, miR-423-5p mimic, EFNA3 overexpression rescue, HUVEC functional assays, rat MI model with capillary density measurement\",\n      \"pmids\": [\"36967852\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific Eph receptor interaction mediating EFNA3 anti-angiogenic effect not resolved\", \"Single lab, no independent replication\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"The transcription factor hMAGEA2 was shown to directly bind the EFNA3 promoter and activate transcription, with elevated EFNA3 driving Ras/Braf/MEK/ERK1/2 signaling to promote prostate cancer aggressiveness, identifying a new transcriptional activator and the MAPK cascade as a major EFNA3 effector pathway.\",\n      \"evidence\": \"Dual-luciferase reporter for promoter binding, Western blot for ERK1/2 phosphorylation, hMAGEA2 knockdown, proliferation/invasion assays\",\n      \"pmids\": [\"38925815\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether hMAGEA2 binds EFNA3 promoter directly or through a co-factor is not resolved biochemically\", \"No receptor engagement shown in prostate cancer cells\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The first direct physical interaction between EFNA3 and EphA3 was confirmed, and reverse signaling through EFNA3 was shown to activate ERK1/2 to drive EMT and colorectal cancer metastasis, establishing a receptor-ligand pair and directionality of signaling.\",\n      \"evidence\": \"Co-immunoprecipitation, EFNA3 knockdown/overexpression, EMT and ERK1/2 Western blot, subcutaneous and spleen injection tumor models in nude mice\",\n      \"pmids\": [\"40928719\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Reverse signaling mechanism through a GPI-anchored ligand (which lacks cytoplasmic domain) is not biochemically resolved — likely requires co-receptor\", \"Single Co-IP without reciprocal validation explicitly described\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"EFNA3 mRNA was found to be stabilized by NSUN5-mediated m5C modification, and stabilized EFNA3 promotes aerobic glycolysis in hepatocellular carcinoma, revealing an epitranscriptomic layer of regulation.\",\n      \"evidence\": \"MeRIP for m5C, dual-luciferase reporter, NSUN5 knockdown with EFNA3 rescue, glycolysis measurements in vitro and xenograft model\",\n      \"pmids\": [\"40730949\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific m5C site(s) on EFNA3 mRNA not mapped at single-nucleotide resolution\", \"How EFNA3 protein mechanistically promotes glycolysis is undefined\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"EFNA3 was shown to activate PI3K/AKT/mTOR signaling, suppress autophagy, and promote EMT and metastasis in breast cancer, integrating its roles in proliferation, survival, and metabolic reprogramming into a unified oncogenic signaling model.\",\n      \"evidence\": \"EFNA3 knockdown/overexpression, Western blot for PI3K/AKT/mTOR phosphorylation, LC3 staining, TEM for autophagosomes, xenograft mouse model\",\n      \"pmids\": [\"41763291\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether autophagy suppression is a direct consequence of mTOR activation or involves additional EFNA3-dependent mechanisms is unclear\", \"Receptor mediating PI3K/AKT/mTOR activation in breast cancer not identified\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How EFNA3, a GPI-anchored protein lacking a cytoplasmic domain, transduces reverse signals to activate ERK1/2 and PI3K/AKT/mTOR pathways remains mechanistically unresolved — the identity of the co-receptor or transmembrane adaptor mediating intracellular signal propagation is unknown.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Co-receptor or transmembrane adaptor for reverse signaling not identified\", \"No structural model of EFNA3-EphA3 complex exists\", \"Relative contributions of forward versus reverse signaling in each disease context remain unquantified\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0048018\", \"supporting_discovery_ids\": [16, 9]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 2, 15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [16, 9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0005576\", \"supporting_discovery_ids\": [16]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [1, 2, 8, 9, 15]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [0, 3, 8, 9, 11, 15]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [15]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [1, 2, 6]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"EPHA3\",\n      \"NSUN5\",\n      \"CTCF\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}