{"gene":"EFNA3","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2014,"finding":"Hypoxia induces HIF-mediated expression of long noncoding RNAs from the EFNA3 locus; these lncRNAs cause Ephrin-A3 protein accumulation (coding EFNA3 mRNA levels remain relatively stable), and sustained expression of both Ephrin-A3 and the EFNA3 lncRNAs increases metastatic potential of breast cancer cells, at least partly by increasing extravasation ability.","method":"HIF pathway manipulation, lncRNA characterization, breast cancer cell functional assays (extravasation), Western blot for protein levels","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — single lab, multiple orthogonal methods (lncRNA characterization, protein level measurement, functional extravasation assays), but mechanistic detail on lncRNA-to-protein link is not fully resolved","pmids":["25023702"],"is_preprint":false},{"year":1996,"finding":"EFNA3 (LERK-3/EPLG3) encodes a GPI-anchored membrane-bound ligand for Eph-related receptor tyrosine kinases (hek and elk), placing it in the GPI-anchored subgroup of ephrin ligands distinct from type-1 transmembrane ephrin members.","method":"Southern hybridization, FISH, genomic mapping, sequence analysis","journal":"Genomics","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct biochemical classification (GPI-anchored vs transmembrane) established by sequence and hybridization analysis, consistent with the broader corpus","pmids":["8660976"],"is_preprint":false},{"year":2020,"finding":"EFNA3 is a direct target of miR-210-3p; ephrinA3 protein levels negatively regulate HUVEC migration and proliferation, and downregulation of ephrinA3 increases phosphorylated AKT, activating the PI3K/AKT pathway, while upregulation of ephrinA3 suppresses PI3K/AKT signaling.","method":"Luciferase reporter assay (miR-210-3p targeting EFNA3 3'UTR), miR-210-3p mimic/inhibitor transfection, Western blot for phospho-AKT, HUVEC migration/tube formation assays","journal":"BioMed research international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — luciferase validation of direct targeting plus functional rescue assays in HUVECs, single lab","pmids":["32695810"],"is_preprint":false},{"year":2013,"finding":"miR-210 directly targets EFNA3 (validated by luciferase reporter assay) and regulates its mRNA and protein expression in MPNST cells; EFNA3 upregulation (when miR-210 is low) promotes proliferation and invasion of peripheral nerve sheath tumor cells.","method":"Luciferase reporter assay, qRT-PCR, Western blot, colony formation, cell cycle analysis, invasion assay","journal":"Oncology research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct target validation by luciferase plus multiple functional readouts, single lab","pmids":["24512729"],"is_preprint":false},{"year":2022,"finding":"miR-210-3p carried in hypoxic MSC-derived small extracellular vesicles suppresses EFNA3 expression and consequently activates the PI3K/AKT pathway to promote angiogenesis; HIF-1α drives miR-210-3p upregulation under hypoxia.","method":"miRNA sequencing, miR-210-3p mimic/inhibitor transfection, Western blot for EFNA3 and phospho-PI3K/AKT, HUVEC functional assays, calvarial bone defect in vivo model","journal":"Acta biomaterialia","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (sequencing, transfection, Western blot, in vivo model), single lab","pmids":["35850484"],"is_preprint":false},{"year":2023,"finding":"miR-423-5p delivered by hucMSC-derived extracellular vesicles inhibits EFNA3 expression; EFNA3 overexpression reverses the pro-angiogenic effects of these EVs on HUVEC migration and tube formation, establishing EFNA3 as a negative regulator of angiogenesis downstream of miR-423-5p.","method":"EV isolation/co-culture, miR-423-5p mimic transfection, EFNA3 overexpression rescue, HUVEC migration/tube formation assays, rat MI in vivo model","journal":"Postepy w kardiologii interwencyjnej","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — rescue experiment with EFNA3 overexpression, multiple assays, in vivo validation, single lab","pmids":["36967852"],"is_preprint":false},{"year":2025,"finding":"EphA3 receptor binds to EFNA3 (confirmed by co-immunoprecipitation); EphA3/EFNA3 reverse signaling activates ERK1/2 signaling and promotes epithelial-to-mesenchymal transition (EMT) to facilitate colorectal cancer metastasis.","method":"Co-immunoprecipitation, EFNA3 knockdown and overexpression, transwell/wound healing assays, subcutaneous and spleen injection tumor models in nude mice, Western blot for EMT markers and phospho-ERK1/2","journal":"Digestive diseases and sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal binding confirmed by Co-IP, functional rescue with overexpression, in vivo validation, single lab","pmids":["40928719"],"is_preprint":false},{"year":2024,"finding":"hMAGEA2 binds to the EFNA3 promoter region and transcriptionally regulates EFNA3 expression (confirmed by luciferase assay); EFNA3 downregulation upon hMAGEA2 knockdown reduces Ras/Braf/MEK/Erk1/2 phosphorylation, placing EFNA3 upstream of the Erk1/2 signaling cascade in prostate cancer.","method":"Luciferase reporter assay (EFNA3 promoter), hMAGEA2 knockdown stable cell lines, Western blot for Erk1/2 pathway components, proliferation/invasion/colony formation assays","journal":"Anticancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — luciferase validates direct promoter binding, pathway knockdown connects EFNA3 to Erk1/2, single lab","pmids":["38925815"],"is_preprint":false},{"year":2022,"finding":"The lncRNA HOTTIP promotes EFNA3 transcription by recruiting CTCF (CCCTC-binding factor) to the EFNA3 promoter; EFNA3 knockdown in vivo reduces OVA-induced airway inflammation in asthmatic mice, demonstrating EFNA3 as a downstream effector of HOTTIP-mediated inflammation.","method":"RNA pull-down, RNA immunoprecipitation, luciferase reporter assay, chromatin immunoprecipitation (ChIP), EFNA3 knockdown in OVA-mouse model, ELISA for inflammatory cytokines","journal":"American journal of translational research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP confirms CTCF recruitment to EFNA3 promoter, multiple orthogonal methods, in vivo validation, single lab","pmids":["36628218"],"is_preprint":false},{"year":2025,"finding":"NSUN5 (an RNA m5C methyltransferase) promotes m5C modification of EFNA3 mRNA, stabilizing EFNA3 expression; EFNA3 overexpression rescues glycolysis inhibition caused by NSUN5 knockdown in liver hepatocellular carcinoma cells, placing EFNA3 downstream of NSUN5-mediated m5C modification in glycolysis regulation.","method":"Methylated RNA immunoprecipitation (MeRIP), dual-luciferase reporter assay, NSUN5 knockdown, EFNA3 overexpression rescue, glycolysis measurement, xenograft tumor model","journal":"BMC cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MeRIP directly detects m5C on EFNA3 mRNA, rescue experiment links EFNA3 to glycolysis, in vivo validation, single lab","pmids":["40730949"],"is_preprint":false},{"year":2022,"finding":"EFNA3 knockdown in lung adenocarcinoma cells (A549 and PC9) reduces cell viability and proliferation, increases apoptosis, and upregulates apoptosis-related proteins Bax and caspase-3, demonstrating that EFNA3 promotes LUAD progression by inhibiting apoptosis.","method":"Lentiviral EFNA3 knockdown, MTT assay, ELISA for proliferation/apoptosis, RT-PCR and Western blot for Bax and caspase-3","journal":"Translational cancer research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — loss-of-function with defined phenotype but no upstream/downstream pathway mechanism beyond apoptosis marker measurement, single lab, single method set","pmids":["35706812"],"is_preprint":false},{"year":2024,"finding":"Topical administration of recombinant EFNA3 promotes vaginal DSG1 (desmoglein-1) expression in a biphasic dose-dependent manner and partially reverses loss of vaginal epithelial barrier function induced by progestin (DMPA) treatment in mice, identifying EFNA3 as a regulator of desmosomal cadherin gene expression in vaginal epithelium.","method":"Recombinant EFNA3 topical administration in mice, DSG1/DSC1 expression measurement, epithelial barrier function assay, HSV-2 infection model","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct in vivo functional rescue with recombinant protein, dose-response validation, multiple readouts; preprint not yet peer-reviewed","pmids":["bio_10.1101_2024.10.29.620915"],"is_preprint":true},{"year":2024,"finding":"Basal mammary epithelial cells produce EFNA3, which acts on luminal cells to enhance oxidative phosphorylation (OXPHOS) and energy production, thereby promoting collective epithelial migration and branching morphogenesis in vivo; inhibition of EFNA3 slows breast cancer metastasis.","method":"Live imaging of collective migration, EFNA3 inhibition/knockdown, OXPHOS measurement, in vivo mammary gland branching morphogenesis assay, breast cancer metastasis model","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo functional validation with EFNA3 inhibition and OXPHOS measurement, multiple assays; preprint not yet peer-reviewed","pmids":["bio_10.1101_2024.10.18.619009"],"is_preprint":true},{"year":2023,"finding":"miR-365 directly targets EFNA3 (validated by luciferase reporter assay); EFNA3 upregulation in nucleus pulposus cells increases apoptosis and catabolic marker (MMP-13) expression while reducing collagen II and aggrecan, demonstrating EFNA3 as a pro-degenerative effector in intervertebral disc degeneration.","method":"Luciferase reporter assay, miR-365 mimic/inhibitor transfection, EFNA3 overexpression, apoptosis assay, immunofluorescence for ECM markers, rat IDD in vivo model","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct target validation by luciferase, EFNA3 overexpression phenotype, in vivo validation, single lab","pmids":["38009813"],"is_preprint":false},{"year":2024,"finding":"EFNA3 promotes choroidal melanoma cell growth and migration through activation of the Stat3/Akt signaling pathway; artesunate inhibits this tumor-promoting effect by downregulating EFNA3.","method":"EFNA3 knockdown, Western blot for Stat3/Akt pathway, clonogenic assay, CCK-8, transwell migration, xenograft tumor model","journal":"Journal of cancer research and clinical oncology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — pathway association by Western blot after knockdown, no direct mechanistic link between EFNA3 and Stat3/Akt established, single lab","pmids":["38630320"],"is_preprint":false},{"year":2026,"finding":"EFNA3 knockdown in breast cancer cells inhibits proliferation, migration, invasion and activates autophagy; mechanistically, EFNA3 activates the PI3K/AKT/mTOR pathway and suppresses autophagy, as confirmed in a xenograft model where EFNA3 knockdown reduces tumor growth, enhances autophagy markers, and reduces PI3K/AKT/mTOR signaling.","method":"EFNA3 knockdown, LC3 staining, TEM for autophagy, Western blot for PI3K/AKT/mTOR pathway, xenograft model, proliferation/apoptosis/invasion assays","journal":"The international journal of biochemistry & cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods including TEM for autophagy and in vivo rescue, single lab","pmids":["41763291"],"is_preprint":false},{"year":2022,"finding":"lncRNA LINC01270 acts as a competing endogenous RNA (ceRNA) by sponging miR-326, thereby positively regulating EFNA3 expression; EFNA3 overexpression rescues the anti-proliferative and anti-invasive effects of LINC01270 knockdown in gastric cancer cells.","method":"Luciferase reporter assay, RNA pull-down assay, LINC01270 knockdown, miR-326 inhibitor, EFNA3 overexpression rescue, CCK-8, colony formation, transwell assay","journal":"Bioengineered","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNA pull-down and luciferase validate ceRNA interaction, rescue experiment confirms EFNA3 as effector, single lab","pmids":["35345980"],"is_preprint":false}],"current_model":"EFNA3 encodes a GPI-anchored ephrin-A ligand that engages Eph receptor tyrosine kinases (notably EphA3) to trigger bidirectional (including reverse) signaling; in tumor contexts, EphA3/EFNA3 reverse signaling activates ERK1/2 to promote EMT and metastasis, EFNA3 activates PI3K/AKT/mTOR signaling to suppress autophagy and promote proliferation, and EFNA3 is subject to transcriptional regulation by HIF-lncRNAs, HOTTIP-recruited CTCF, and hMAGEA2, as well as post-transcriptional suppression by multiple miRNAs (miR-210-3p, miR-423-5p, miR-365, miR-326); additionally, in normal epithelial physiology, basal-cell-derived EFNA3 targets luminal cells to enhance OXPHOS-driven collective migration, and recombinant EFNA3 regulates desmosomal cadherin gene expression to maintain vaginal epithelial barrier function."},"narrative":{"mechanistic_narrative":"EFNA3 (LERK-3/EPLG3) encodes a GPI-anchored, membrane-bound ephrin-A ligand for Eph-related receptor tyrosine kinases, distinguishing it biochemically from the type-1 transmembrane ephrins [PMID:8660976]. In tumor contexts it functions as a pro-progression effector: EphA3 binds EFNA3 and the resulting reverse signaling activates ERK1/2 to drive epithelial-to-mesenchymal transition and metastasis [PMID:40928719], while EFNA3 also engages PI3K/AKT/mTOR signaling to suppress autophagy and sustain proliferation, migration, and invasion [PMID:41763291]. Consistent with a growth-promoting role, EFNA3 inhibits apoptosis in lung adenocarcinoma cells, with knockdown upregulating Bax and caspase-3 [PMID:35706812]. EFNA3 expression is controlled at multiple regulatory layers: hypoxia drives HIF-dependent accumulation of EFNA3-locus lncRNAs and Ephrin-A3 protein to enhance breast cancer extravasation and metastasis [PMID:25023702]; transcriptionally it is activated by hMAGEA2 promoter binding upstream of the Ras/Braf/MEK/ERK1/2 cascade [PMID:38925815] and by HOTTIP-recruited CTCF [PMID:36628218]; post-transcriptionally it is stabilized by NSUN5-mediated m5C modification of its mRNA to support glycolysis [PMID:40730949]; and it is repressed by multiple miRNAs including miR-210-3p, miR-423-5p, miR-365, and miR-326, the latter relieved by the ceRNA LINC01270 [PMID:32695810, PMID:36967852, PMID:38009813, PMID:35345980]. In normal epithelial physiology, basal-cell-derived EFNA3 acts on luminal cells to enhance OXPHOS-driven collective migration and branching morphogenesis [PMID:bio_10.1101_2024.10.18.619009], and recombinant EFNA3 regulates desmosomal cadherin (DSG1) expression to maintain vaginal epithelial barrier function [PMID:bio_10.1101_2024.10.29.620915].","teleology":[{"year":1996,"claim":"Established the molecular identity of EFNA3 as a GPI-anchored ephrin ligand, defining the biochemical class through which it would later be understood to signal.","evidence":"Southern hybridization, FISH, genomic mapping and sequence analysis classifying LERK-3/EPLG3 as a GPI-anchored Eph receptor ligand","pmids":["8660976"],"confidence":"High","gaps":["No receptor-specific binding kinetics or downstream signaling defined","Cellular and tissue functions not addressed"]},{"year":2013,"claim":"First placed EFNA3 downstream of a miRNA and gave it a pro-tumor function, showing miR-210 directly represses EFNA3 to limit proliferation and invasion.","evidence":"Luciferase reporter validation, qRT-PCR, Western blot and functional assays in MPNST cells","pmids":["24512729"],"confidence":"Medium","gaps":["Signaling pathway downstream of EFNA3 not defined","Single tumor type"]},{"year":2014,"claim":"Connected EFNA3 to hypoxic signaling, showing HIF-driven EFNA3-locus lncRNAs raise Ephrin-A3 protein to promote breast cancer extravasation, decoupling protein accumulation from coding mRNA levels.","evidence":"HIF pathway manipulation, lncRNA characterization, protein measurement and extravasation assays in breast cancer cells","pmids":["25023702"],"confidence":"Medium","gaps":["Molecular link between lncRNAs and protein accumulation not resolved","Receptor engagement during extravasation not characterized"]},{"year":2020,"claim":"Linked EFNA3 to PI3K/AKT signaling control in endothelial cells, showing ephrinA3 levels inversely regulate AKT phosphorylation and angiogenic behavior.","evidence":"Luciferase validation of miR-210-3p targeting, mimic/inhibitor transfection and phospho-AKT Western blot in HUVECs","pmids":["32695810"],"confidence":"Medium","gaps":["Mechanism connecting EFNA3 to AKT not defined","Single cell system"]},{"year":2022,"claim":"Extended EFNA3 regulation to extracellular-vesicle miRNA delivery and additional transcriptional/loss-of-function contexts, establishing EFNA3 as a convergent node for angiogenesis, inflammation, and apoptosis control.","evidence":"miR-210-3p in hypoxic MSC-EVs (sequencing, in vivo bone model); HOTTIP/CTCF promoter recruitment by ChIP in asthma model; lentiviral knockdown with Bax/caspase-3 readout in LUAD; LINC01270 ceRNA sponging miR-326 in gastric cancer","pmids":["35850484","36628218","35706812","35345980"],"confidence":"Medium","gaps":["Receptor-level signaling underlying these phenotypes not directly tested","Findings distributed across distinct disease models without unifying mechanism"]},{"year":2023,"claim":"Reinforced miRNA control of EFNA3 in non-cancer tissue, identifying miR-423-5p and miR-365 as repressors whose loss drives angiogenic and disc-degenerative phenotypes via EFNA3.","evidence":"Luciferase validation, EFNA3 overexpression rescue, and in vivo MI and IDD models","pmids":["36967852","38009813"],"confidence":"Medium","gaps":["Downstream effectors of EFNA3 in these tissues not defined"]},{"year":2024,"claim":"Identified upstream transcriptional and post-transcriptional regulators (hMAGEA2 promoter binding; NSUN5 m5C mRNA modification) and revealed normal epithelial roles in OXPHOS-driven migration and desmosomal barrier maintenance, broadening EFNA3 beyond a tumor effector.","evidence":"Luciferase promoter assay and pathway knockdown (prostate cancer); MeRIP and glycolysis rescue (HCC); live imaging/OXPHOS measurement (mammary); recombinant EFNA3 dose-response in vivo (vaginal epithelium, preprint)","pmids":["38925815","40730949","bio_10.1101_2024.10.18.619009","bio_10.1101_2024.10.29.620915"],"confidence":"Medium","gaps":["Two normal-physiology findings are preprints","Whether OXPHOS and barrier effects require Eph receptor engagement is untested"]},{"year":2025,"claim":"Provided direct receptor-level mechanism, confirming EphA3 binds EFNA3 and that reverse signaling activates ERK1/2 to drive EMT and metastasis.","evidence":"Co-immunoprecipitation, knockdown/overexpression, migration assays and mouse tumor models in colorectal cancer","pmids":["40928719"],"confidence":"Medium","gaps":["Structural basis of binding not resolved","Single tumor type for reverse-signaling claim"]},{"year":2026,"claim":"Defined the autophagy-suppressing arm of EFNA3 signaling, showing knockdown activates autophagy and attenuates tumor growth via reduced PI3K/AKT/mTOR signaling.","evidence":"Knockdown with LC3 staining, TEM, pathway Western blot and xenograft model in breast cancer","pmids":["41763291"],"confidence":"Medium","gaps":["Direct biochemical link from EFNA3 to PI3K/AKT/mTOR not established","Receptor dependence not tested"]},{"year":null,"claim":"Whether EFNA3's forward (Eph receptor activation) versus reverse (ligand-side) signaling distinctly drive the ERK1/2, PI3K/AKT/mTOR, and OXPHOS outputs, and how its GPI-anchored ectodomain transmits these signals, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of EFNA3-receptor complexes in the corpus","Mechanism converting receptor binding to intracellular ERK/AKT activation not defined","Receptor partners beyond EphA3 not identified"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0048018","term_label":"receptor ligand activity","supporting_discovery_ids":[1,6]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[6,15]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[15]}],"complexes":[],"partners":["EPHA3"],"other_free_text":[]}},"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":"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":83,"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":79,"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":20,"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":15,"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":"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":12,"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":"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":8,"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":"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":"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":1,"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":"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":"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":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":14428,"output_tokens":4506,"usd":0.055437,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12459,"output_tokens":3371,"usd":0.073285,"stage2_stop_reason":"end_turn"},"total_usd":0.128722,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"Hypoxia induces HIF-mediated expression of long noncoding RNAs from the EFNA3 locus; these lncRNAs cause Ephrin-A3 protein accumulation (coding EFNA3 mRNA levels remain relatively stable), and sustained expression of both Ephrin-A3 and the EFNA3 lncRNAs increases metastatic potential of breast cancer cells, at least partly by increasing extravasation ability.\",\n      \"method\": \"HIF pathway manipulation, lncRNA characterization, breast cancer cell functional assays (extravasation), Western blot for protein levels\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — single lab, multiple orthogonal methods (lncRNA characterization, protein level measurement, functional extravasation assays), but mechanistic detail on lncRNA-to-protein link is not fully resolved\",\n      \"pmids\": [\"25023702\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"EFNA3 (LERK-3/EPLG3) encodes a GPI-anchored membrane-bound ligand for Eph-related receptor tyrosine kinases (hek and elk), placing it in the GPI-anchored subgroup of ephrin ligands distinct from type-1 transmembrane ephrin members.\",\n      \"method\": \"Southern hybridization, FISH, genomic mapping, sequence analysis\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct biochemical classification (GPI-anchored vs transmembrane) established by sequence and hybridization analysis, consistent with the broader corpus\",\n      \"pmids\": [\"8660976\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"EFNA3 is a direct target of miR-210-3p; ephrinA3 protein levels negatively regulate HUVEC migration and proliferation, and downregulation of ephrinA3 increases phosphorylated AKT, activating the PI3K/AKT pathway, while upregulation of ephrinA3 suppresses PI3K/AKT signaling.\",\n      \"method\": \"Luciferase reporter assay (miR-210-3p targeting EFNA3 3'UTR), miR-210-3p mimic/inhibitor transfection, Western blot for phospho-AKT, HUVEC migration/tube formation assays\",\n      \"journal\": \"BioMed research international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — luciferase validation of direct targeting plus functional rescue assays in HUVECs, single lab\",\n      \"pmids\": [\"32695810\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"miR-210 directly targets EFNA3 (validated by luciferase reporter assay) and regulates its mRNA and protein expression in MPNST cells; EFNA3 upregulation (when miR-210 is low) promotes proliferation and invasion of peripheral nerve sheath tumor cells.\",\n      \"method\": \"Luciferase reporter assay, qRT-PCR, Western blot, colony formation, cell cycle analysis, invasion assay\",\n      \"journal\": \"Oncology research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct target validation by luciferase plus multiple functional readouts, single lab\",\n      \"pmids\": [\"24512729\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"miR-210-3p carried in hypoxic MSC-derived small extracellular vesicles suppresses EFNA3 expression and consequently activates the PI3K/AKT pathway to promote angiogenesis; HIF-1α drives miR-210-3p upregulation under hypoxia.\",\n      \"method\": \"miRNA sequencing, miR-210-3p mimic/inhibitor transfection, Western blot for EFNA3 and phospho-PI3K/AKT, HUVEC functional assays, calvarial bone defect in vivo model\",\n      \"journal\": \"Acta biomaterialia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (sequencing, transfection, Western blot, in vivo model), single lab\",\n      \"pmids\": [\"35850484\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"miR-423-5p delivered by hucMSC-derived extracellular vesicles inhibits EFNA3 expression; EFNA3 overexpression reverses the pro-angiogenic effects of these EVs on HUVEC migration and tube formation, establishing EFNA3 as a negative regulator of angiogenesis downstream of miR-423-5p.\",\n      \"method\": \"EV isolation/co-culture, miR-423-5p mimic transfection, EFNA3 overexpression rescue, HUVEC migration/tube formation assays, rat MI in vivo model\",\n      \"journal\": \"Postepy w kardiologii interwencyjnej\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — rescue experiment with EFNA3 overexpression, multiple assays, in vivo validation, single lab\",\n      \"pmids\": [\"36967852\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"EphA3 receptor binds to EFNA3 (confirmed by co-immunoprecipitation); EphA3/EFNA3 reverse signaling activates ERK1/2 signaling and promotes epithelial-to-mesenchymal transition (EMT) to facilitate colorectal cancer metastasis.\",\n      \"method\": \"Co-immunoprecipitation, EFNA3 knockdown and overexpression, transwell/wound healing assays, subcutaneous and spleen injection tumor models in nude mice, Western blot for EMT markers and phospho-ERK1/2\",\n      \"journal\": \"Digestive diseases and sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal binding confirmed by Co-IP, functional rescue with overexpression, in vivo validation, single lab\",\n      \"pmids\": [\"40928719\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"hMAGEA2 binds to the EFNA3 promoter region and transcriptionally regulates EFNA3 expression (confirmed by luciferase assay); EFNA3 downregulation upon hMAGEA2 knockdown reduces Ras/Braf/MEK/Erk1/2 phosphorylation, placing EFNA3 upstream of the Erk1/2 signaling cascade in prostate cancer.\",\n      \"method\": \"Luciferase reporter assay (EFNA3 promoter), hMAGEA2 knockdown stable cell lines, Western blot for Erk1/2 pathway components, proliferation/invasion/colony formation assays\",\n      \"journal\": \"Anticancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — luciferase validates direct promoter binding, pathway knockdown connects EFNA3 to Erk1/2, single lab\",\n      \"pmids\": [\"38925815\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The lncRNA HOTTIP promotes EFNA3 transcription by recruiting CTCF (CCCTC-binding factor) to the EFNA3 promoter; EFNA3 knockdown in vivo reduces OVA-induced airway inflammation in asthmatic mice, demonstrating EFNA3 as a downstream effector of HOTTIP-mediated inflammation.\",\n      \"method\": \"RNA pull-down, RNA immunoprecipitation, luciferase reporter assay, chromatin immunoprecipitation (ChIP), EFNA3 knockdown in OVA-mouse model, ELISA for inflammatory cytokines\",\n      \"journal\": \"American journal of translational research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP confirms CTCF recruitment to EFNA3 promoter, multiple orthogonal methods, in vivo validation, single lab\",\n      \"pmids\": [\"36628218\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NSUN5 (an RNA m5C methyltransferase) promotes m5C modification of EFNA3 mRNA, stabilizing EFNA3 expression; EFNA3 overexpression rescues glycolysis inhibition caused by NSUN5 knockdown in liver hepatocellular carcinoma cells, placing EFNA3 downstream of NSUN5-mediated m5C modification in glycolysis regulation.\",\n      \"method\": \"Methylated RNA immunoprecipitation (MeRIP), dual-luciferase reporter assay, NSUN5 knockdown, EFNA3 overexpression rescue, glycolysis measurement, xenograft tumor model\",\n      \"journal\": \"BMC cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MeRIP directly detects m5C on EFNA3 mRNA, rescue experiment links EFNA3 to glycolysis, in vivo validation, single lab\",\n      \"pmids\": [\"40730949\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"EFNA3 knockdown in lung adenocarcinoma cells (A549 and PC9) reduces cell viability and proliferation, increases apoptosis, and upregulates apoptosis-related proteins Bax and caspase-3, demonstrating that EFNA3 promotes LUAD progression by inhibiting apoptosis.\",\n      \"method\": \"Lentiviral EFNA3 knockdown, MTT assay, ELISA for proliferation/apoptosis, RT-PCR and Western blot for Bax and caspase-3\",\n      \"journal\": \"Translational cancer research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — loss-of-function with defined phenotype but no upstream/downstream pathway mechanism beyond apoptosis marker measurement, single lab, single method set\",\n      \"pmids\": [\"35706812\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Topical administration of recombinant EFNA3 promotes vaginal DSG1 (desmoglein-1) expression in a biphasic dose-dependent manner and partially reverses loss of vaginal epithelial barrier function induced by progestin (DMPA) treatment in mice, identifying EFNA3 as a regulator of desmosomal cadherin gene expression in vaginal epithelium.\",\n      \"method\": \"Recombinant EFNA3 topical administration in mice, DSG1/DSC1 expression measurement, epithelial barrier function assay, HSV-2 infection model\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct in vivo functional rescue with recombinant protein, dose-response validation, multiple readouts; preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2024.10.29.620915\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Basal mammary epithelial cells produce EFNA3, which acts on luminal cells to enhance oxidative phosphorylation (OXPHOS) and energy production, thereby promoting collective epithelial migration and branching morphogenesis in vivo; inhibition of EFNA3 slows breast cancer metastasis.\",\n      \"method\": \"Live imaging of collective migration, EFNA3 inhibition/knockdown, OXPHOS measurement, in vivo mammary gland branching morphogenesis assay, breast cancer metastasis model\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo functional validation with EFNA3 inhibition and OXPHOS measurement, multiple assays; preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2024.10.18.619009\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"miR-365 directly targets EFNA3 (validated by luciferase reporter assay); EFNA3 upregulation in nucleus pulposus cells increases apoptosis and catabolic marker (MMP-13) expression while reducing collagen II and aggrecan, demonstrating EFNA3 as a pro-degenerative effector in intervertebral disc degeneration.\",\n      \"method\": \"Luciferase reporter assay, miR-365 mimic/inhibitor transfection, EFNA3 overexpression, apoptosis assay, immunofluorescence for ECM markers, rat IDD in vivo model\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct target validation by luciferase, EFNA3 overexpression phenotype, in vivo validation, single lab\",\n      \"pmids\": [\"38009813\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"EFNA3 promotes choroidal melanoma cell growth and migration through activation of the Stat3/Akt signaling pathway; artesunate inhibits this tumor-promoting effect by downregulating EFNA3.\",\n      \"method\": \"EFNA3 knockdown, Western blot for Stat3/Akt pathway, clonogenic assay, CCK-8, transwell migration, xenograft tumor model\",\n      \"journal\": \"Journal of cancer research and clinical oncology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — pathway association by Western blot after knockdown, no direct mechanistic link between EFNA3 and Stat3/Akt established, single lab\",\n      \"pmids\": [\"38630320\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"EFNA3 knockdown in breast cancer cells inhibits proliferation, migration, invasion and activates autophagy; mechanistically, EFNA3 activates the PI3K/AKT/mTOR pathway and suppresses autophagy, as confirmed in a xenograft model where EFNA3 knockdown reduces tumor growth, enhances autophagy markers, and reduces PI3K/AKT/mTOR signaling.\",\n      \"method\": \"EFNA3 knockdown, LC3 staining, TEM for autophagy, Western blot for PI3K/AKT/mTOR pathway, xenograft model, proliferation/apoptosis/invasion assays\",\n      \"journal\": \"The international journal of biochemistry & cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods including TEM for autophagy and in vivo rescue, single lab\",\n      \"pmids\": [\"41763291\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"lncRNA LINC01270 acts as a competing endogenous RNA (ceRNA) by sponging miR-326, thereby positively regulating EFNA3 expression; EFNA3 overexpression rescues the anti-proliferative and anti-invasive effects of LINC01270 knockdown in gastric cancer cells.\",\n      \"method\": \"Luciferase reporter assay, RNA pull-down assay, LINC01270 knockdown, miR-326 inhibitor, EFNA3 overexpression rescue, CCK-8, colony formation, transwell assay\",\n      \"journal\": \"Bioengineered\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNA pull-down and luciferase validate ceRNA interaction, rescue experiment confirms EFNA3 as effector, single lab\",\n      \"pmids\": [\"35345980\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"EFNA3 encodes a GPI-anchored ephrin-A ligand that engages Eph receptor tyrosine kinases (notably EphA3) to trigger bidirectional (including reverse) signaling; in tumor contexts, EphA3/EFNA3 reverse signaling activates ERK1/2 to promote EMT and metastasis, EFNA3 activates PI3K/AKT/mTOR signaling to suppress autophagy and promote proliferation, and EFNA3 is subject to transcriptional regulation by HIF-lncRNAs, HOTTIP-recruited CTCF, and hMAGEA2, as well as post-transcriptional suppression by multiple miRNAs (miR-210-3p, miR-423-5p, miR-365, miR-326); additionally, in normal epithelial physiology, basal-cell-derived EFNA3 targets luminal cells to enhance OXPHOS-driven collective migration, and recombinant EFNA3 regulates desmosomal cadherin gene expression to maintain vaginal epithelial barrier function.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"EFNA3 (LERK-3/EPLG3) encodes a GPI-anchored, membrane-bound ephrin-A ligand for Eph-related receptor tyrosine kinases, distinguishing it biochemically from the type-1 transmembrane ephrins [#1]. In tumor contexts it functions as a pro-progression effector: EphA3 binds EFNA3 and the resulting reverse signaling activates ERK1/2 to drive epithelial-to-mesenchymal transition and metastasis [#6], while EFNA3 also engages PI3K/AKT/mTOR signaling to suppress autophagy and sustain proliferation, migration, and invasion [#15]. Consistent with a growth-promoting role, EFNA3 inhibits apoptosis in lung adenocarcinoma cells, with knockdown upregulating Bax and caspase-3 [#10]. EFNA3 expression is controlled at multiple regulatory layers: hypoxia drives HIF-dependent accumulation of EFNA3-locus lncRNAs and Ephrin-A3 protein to enhance breast cancer extravasation and metastasis [#0]; transcriptionally it is activated by hMAGEA2 promoter binding upstream of the Ras/Braf/MEK/ERK1/2 cascade [#7] and by HOTTIP-recruited CTCF [#8]; post-transcriptionally it is stabilized by NSUN5-mediated m5C modification of its mRNA to support glycolysis [#9]; and it is repressed by multiple miRNAs including miR-210-3p, miR-423-5p, miR-365, and miR-326, the latter relieved by the ceRNA LINC01270 [#2, #5, #13, #16]. In normal epithelial physiology, basal-cell-derived EFNA3 acts on luminal cells to enhance OXPHOS-driven collective migration and branching morphogenesis [#12], and recombinant EFNA3 regulates desmosomal cadherin (DSG1) expression to maintain vaginal epithelial barrier function [#11].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Established the molecular identity of EFNA3 as a GPI-anchored ephrin ligand, defining the biochemical class through which it would later be understood to signal.\",\n      \"evidence\": \"Southern hybridization, FISH, genomic mapping and sequence analysis classifying LERK-3/EPLG3 as a GPI-anchored Eph receptor ligand\",\n      \"pmids\": [\"8660976\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No receptor-specific binding kinetics or downstream signaling defined\", \"Cellular and tissue functions not addressed\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"First placed EFNA3 downstream of a miRNA and gave it a pro-tumor function, showing miR-210 directly represses EFNA3 to limit proliferation and invasion.\",\n      \"evidence\": \"Luciferase reporter validation, qRT-PCR, Western blot and functional assays in MPNST cells\",\n      \"pmids\": [\"24512729\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Signaling pathway downstream of EFNA3 not defined\", \"Single tumor type\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Connected EFNA3 to hypoxic signaling, showing HIF-driven EFNA3-locus lncRNAs raise Ephrin-A3 protein to promote breast cancer extravasation, decoupling protein accumulation from coding mRNA levels.\",\n      \"evidence\": \"HIF pathway manipulation, lncRNA characterization, protein measurement and extravasation assays in breast cancer cells\",\n      \"pmids\": [\"25023702\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular link between lncRNAs and protein accumulation not resolved\", \"Receptor engagement during extravasation not characterized\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Linked EFNA3 to PI3K/AKT signaling control in endothelial cells, showing ephrinA3 levels inversely regulate AKT phosphorylation and angiogenic behavior.\",\n      \"evidence\": \"Luciferase validation of miR-210-3p targeting, mimic/inhibitor transfection and phospho-AKT Western blot in HUVECs\",\n      \"pmids\": [\"32695810\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting EFNA3 to AKT not defined\", \"Single cell system\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Extended EFNA3 regulation to extracellular-vesicle miRNA delivery and additional transcriptional/loss-of-function contexts, establishing EFNA3 as a convergent node for angiogenesis, inflammation, and apoptosis control.\",\n      \"evidence\": \"miR-210-3p in hypoxic MSC-EVs (sequencing, in vivo bone model); HOTTIP/CTCF promoter recruitment by ChIP in asthma model; lentiviral knockdown with Bax/caspase-3 readout in LUAD; LINC01270 ceRNA sponging miR-326 in gastric cancer\",\n      \"pmids\": [\"35850484\", \"36628218\", \"35706812\", \"35345980\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Receptor-level signaling underlying these phenotypes not directly tested\", \"Findings distributed across distinct disease models without unifying mechanism\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Reinforced miRNA control of EFNA3 in non-cancer tissue, identifying miR-423-5p and miR-365 as repressors whose loss drives angiogenic and disc-degenerative phenotypes via EFNA3.\",\n      \"evidence\": \"Luciferase validation, EFNA3 overexpression rescue, and in vivo MI and IDD models\",\n      \"pmids\": [\"36967852\", \"38009813\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Downstream effectors of EFNA3 in these tissues not defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified upstream transcriptional and post-transcriptional regulators (hMAGEA2 promoter binding; NSUN5 m5C mRNA modification) and revealed normal epithelial roles in OXPHOS-driven migration and desmosomal barrier maintenance, broadening EFNA3 beyond a tumor effector.\",\n      \"evidence\": \"Luciferase promoter assay and pathway knockdown (prostate cancer); MeRIP and glycolysis rescue (HCC); live imaging/OXPHOS measurement (mammary); recombinant EFNA3 dose-response in vivo (vaginal epithelium, preprint)\",\n      \"pmids\": [\"38925815\", \"40730949\", \"bio_10.1101_2024.10.18.619009\", \"bio_10.1101_2024.10.29.620915\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Two normal-physiology findings are preprints\", \"Whether OXPHOS and barrier effects require Eph receptor engagement is untested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Provided direct receptor-level mechanism, confirming EphA3 binds EFNA3 and that reverse signaling activates ERK1/2 to drive EMT and metastasis.\",\n      \"evidence\": \"Co-immunoprecipitation, knockdown/overexpression, migration assays and mouse tumor models in colorectal cancer\",\n      \"pmids\": [\"40928719\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of binding not resolved\", \"Single tumor type for reverse-signaling claim\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined the autophagy-suppressing arm of EFNA3 signaling, showing knockdown activates autophagy and attenuates tumor growth via reduced PI3K/AKT/mTOR signaling.\",\n      \"evidence\": \"Knockdown with LC3 staining, TEM, pathway Western blot and xenograft model in breast cancer\",\n      \"pmids\": [\"41763291\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct biochemical link from EFNA3 to PI3K/AKT/mTOR not established\", \"Receptor dependence not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether EFNA3's forward (Eph receptor activation) versus reverse (ligand-side) signaling distinctly drive the ERK1/2, PI3K/AKT/mTOR, and OXPHOS outputs, and how its GPI-anchored ectodomain transmits these signals, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of EFNA3-receptor complexes in the corpus\", \"Mechanism converting receptor binding to intracellular ERK/AKT activation not defined\", \"Receptor partners beyond EphA3 not identified\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0048018\", \"supporting_discovery_ids\": [1, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [6, 15]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [15]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"EPHA3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}