{"gene":"CPNE3","run_date":"2026-06-09T22:57:19","timeline":{"discoveries":[{"year":2013,"finding":"CPNE3 knockdown by siRNA reduced migration and invasion of NSCLC cell lines (SPC-A1sci, H1299), and overexpression of CPNE3 promoted migration and invasion in SPC-A-1 and XL-2 cells in vitro; targeted knockdown inhibited in vivo metastasis in mouse xenograft models.","method":"siRNA-mediated knockdown, overexpression, in vitro migration/invasion assays, mouse metastasis model","journal":"Journal of proteome research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined cellular phenotype in multiple cell lines plus in vivo validation, single lab","pmids":["23713811"],"is_preprint":false},{"year":2018,"finding":"CPNE3 interacts with phosphorylated ErbB2 (pErbB2) and RACK1, and activates the focal adhesion kinase (FAK) signaling pathway in NSCLC cells; knockdown of RACK1 inhibited cell motility in CPNE3-overexpressing NSCLC cells, placing CPNE3 upstream of RACK1/FAK in the metastasis pathway.","method":"Co-immunoprecipitation, overexpression, siRNA knockdown, FAK pathway western blot, migration/invasion assays","journal":"Journal of Cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP and epistasis (RACK1 knockdown rescues CPNE3 OE phenotype), single lab","pmids":["30519322"],"is_preprint":false},{"year":2021,"finding":"CPNE3 silencing in GBM cells impaired migratory, invasive, and proliferative abilities associated with inactivation of the FAK signaling pathway.","method":"siRNA knockdown, western blot for FAK pathway markers, migration/invasion assays","journal":"Journal of molecular histology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single approach (KD + pathway western blot), no direct binding demonstrated","pmids":["33725213"],"is_preprint":false},{"year":2021,"finding":"CPNE3 overexpression promoted cell proliferation and inhibited apoptosis in GBM cells in vitro and in vivo by activating the PI3K/AKT signaling pathway; pharmacological inhibition of PI3K/AKT with LY294002 reversed the proliferative enhancement induced by CPNE3 overexpression.","method":"Overexpression, nude mouse xenograft, GSEA, PI3K/AKT pathway western blot (phospho-markers), pharmacological inhibition (LY294002)","journal":"Journal of Cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pharmacological rescue experiment plus in vivo validation supports pathway placement, single lab","pmids":["35003348"],"is_preprint":false},{"year":2021,"finding":"CPNE3 interacts with RACK1 in cardiomyocytes; CPNE3 overexpression upregulated RACK1 expression, increased cell viability, suppressed LDH release, inhibited inflammatory cytokine release, and decreased apoptosis in hypoxia/reoxygenation-induced H9c2 cells, protecting against myocardial ischemia/reperfusion injury.","method":"Co-immunoprecipitation, overexpression, siRNA-RACK1 knockdown, western blot, TUNEL staining, LDH assay, rat I/R injury model","journal":"Experimental and therapeutic medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus RACK1 epistasis (siRNA-RACK1 reverses CPNE3 OE effects), single lab","pmids":["34970351"],"is_preprint":false},{"year":2021,"finding":"Silencing of Cpne3 in INS-1 (832/13) pancreatic β-cells impaired glucose-stimulated insulin secretion (GSIS), insulin content, and glucose uptake without affecting cell viability, and downregulated key regulators Insulin, GLUT2, NeuroD1, and INSR at mRNA and protein levels.","method":"siRNA knockdown, GSIS assay, glucose uptake assay, western blot, RT-qPCR","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined functional readout and downstream marker validation, single lab, two orthogonal methods","pmids":["34667273"],"is_preprint":false},{"year":2024,"finding":"CPNE3 is a direct transcriptional target of the YAP1/TEAD complex; CPNE3 protein in turn binds YAP1 in the cytoplasm and inhibits its ubiquitination and degradation mediated by the E3 ligase β-TRCP, forming a positive feedback loop that activates YAP1 downstream target gene transcription to promote gastric cancer progression.","method":"ChIP/luciferase reporter for YAP1/TEAD→CPNE3, co-immunoprecipitation (CPNE3–YAP1 interaction), ubiquitination assay, overexpression/knockdown with proliferation and invasion readouts","journal":"Cellular and molecular life sciences : CMLS","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (reporter, co-IP, ubiquitination assay) in a single lab establishing both arms of the feedback loop","pmids":["38493426"],"is_preprint":false},{"year":2025,"finding":"CPNE3 interacts with RACK1 specifically through its VWFA domain, and this interaction activates MET (c-MET) signaling to promote proliferation and migration of NSCLC cells; the MET inhibitor JNJ-38877605 and RACK1 knockdown both suppressed these effects in vitro and in vivo.","method":"Co-immunoprecipitation, immunofluorescence, domain mapping (VWFA), RACK1 siRNA knockdown, MET inhibitor treatment, CCK-8/clonogenic/Transwell assays, xenograft model","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP with domain identification plus pharmacological and genetic epistasis, single lab, multiple orthogonal methods","pmids":["41190648"],"is_preprint":false},{"year":2025,"finding":"CPNE3 knockdown in lung adenocarcinoma A549 cells promoted EMT (upregulated vimentin, downregulated E-cadherin) and migration; quantitative proteomics (SILAC) revealed CPNE3 regulates SQSTM1/p62, and p62 knockdown enhanced migratory ability and EMT progression in CPNE3-silenced cells, placing CPNE3 upstream of p62 in suppression of EMT.","method":"siRNA knockdown, SILAC quantitative proteomics, western blot (EMT markers), SQSTM1/p62 knockdown rescue, migration assay","journal":"Current medicinal chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — quantitative proteomics plus epistasis (p62 KD in CPNE3-KD background), single lab","pmids":["39844538"],"is_preprint":false},{"year":2025,"finding":"CPNE3 promotes vasculogenic mimicry (VM) formation and cell metastasis in NSCLC via the EMT process, demonstrated by 3D culture VM assay and Transwell migration/invasion assays with western blot confirmation of EMT markers.","method":"Transwell assay, 3D culture VM assay, western blot (EMT markers), overexpression/knockdown","journal":"Discover oncology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, descriptive mechanistic link to EMT without direct binding partner or epistasis experiment","pmids":["41313527"],"is_preprint":false},{"year":2026,"finding":"CPNE3 directly interacts with KIF4 in colorectal cancer cells; CPNE3 overexpression increased KIF4 levels, activated PI3K/AKT/mTOR signaling, and suppressed autophagy markers (ATG5, ATG7, p62, LC3-II); KIF4 knockdown reversed the oncogenic effects of CPNE3 overexpression, placing CPNE3 upstream of KIF4 in the PI3K/AKT/mTOR and autophagy pathways.","method":"Co-immunoprecipitation, immunofluorescence, BioGRID analysis, overexpression/knockdown, western blot (PI3K/AKT/mTOR and autophagy markers), KIF4 rescue experiment","journal":"Journal of gastrointestinal oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP for interaction plus KIF4 genetic epistasis reverting CPNE3 OE phenotype, single lab","pmids":["41816564"],"is_preprint":false},{"year":2024,"finding":"miR-612 targets CPNE3 mRNA, and lncRNA BANCR acts as a ceRNA to sequester miR-612, thereby upregulating CPNE3 and promoting proliferation and migration of endometrial stromal cells; miR-612 mimics reversed BANCR-induced CPNE3 upregulation and cellular effects.","method":"miRNA target prediction and functional validation (miR-612 mimics/inhibitor), BANCR overexpression/knockdown, cell proliferation and migration assays, in vivo subcutaneous implantation model","journal":"Reproductive biomedicine online","confidence":"Low","confidence_rationale":"Tier 3 / Weak — functional ceRNA axis established but no direct biochemical binding between miR-612 and CPNE3 3'UTR reported in abstract; single lab","pmids":["39389002"],"is_preprint":false}],"current_model":"CPNE3 is a calcium-dependent phospholipid-binding protein that promotes cell migration, invasion, and proliferation across multiple cancer types primarily by interacting with RACK1 (via its VWFA domain) to activate FAK and MET signaling; it also activates PI3K/AKT/mTOR and suppresses autophagy through a KIF4 interaction, forms a positive feedback loop with YAP1 by protecting it from β-TRCP-mediated ubiquitination, and suppresses EMT in some contexts through SQSTM1/p62; additionally, CPNE3 regulates glucose-stimulated insulin secretion in pancreatic β-cells by maintaining expression of GLUT2, NeuroD1, and INSR."},"narrative":{"mechanistic_narrative":"CPNE3 is a calcium-dependent phospholipid-binding protein that functions as a pro-tumorigenic signaling adaptor, driving cell migration, invasion, and proliferation across multiple cancer types [PMID:23713811, PMID:41190648]. Its central mechanism is an interaction with the scaffold protein RACK1—mapped to the CPNE3 VWFA domain—that engages receptor tyrosine kinase signaling: CPNE3 associates with phosphorylated ErbB2 and RACK1 to activate focal adhesion kinase (FAK) [PMID:30519322], and the same VWFA-mediated RACK1 interaction activates MET (c-MET) signaling to promote NSCLC proliferation and migration [PMID:41190648]. CPNE3 additionally activates PI3K/AKT signaling to promote proliferation and suppress apoptosis [PMID:35003348], and in colorectal cancer binds KIF4 to drive PI3K/AKT/mTOR activation and suppress autophagy [PMID:41816564]. Beyond kinase pathways, CPNE3 participates in a positive feedback loop with the Hippo effector YAP1, being a YAP1/TEAD transcriptional target that in turn binds cytoplasmic YAP1 and blocks its β-TRCP–mediated ubiquitination and degradation [PMID:38493426]. CPNE3 also suppresses EMT through regulation of SQSTM1/p62, with p62 acting downstream of CPNE3 to restrain migration [PMID:39844538]. Outside cancer, CPNE3 maintains glucose-stimulated insulin secretion in pancreatic β-cells by sustaining expression of GLUT2, NeuroD1, INSR, and insulin [PMID:34667273], and protects cardiomyocytes from ischemia/reperfusion injury via RACK1 [PMID:34970351].","teleology":[{"year":2013,"claim":"Established CPNE3 as a functional driver of cancer cell motility rather than a bystander, by showing loss- and gain-of-function effects on migration, invasion, and in vivo metastasis.","evidence":"siRNA knockdown and overexpression in NSCLC cell lines with in vitro migration/invasion assays and a mouse metastasis model","pmids":["23713811"],"confidence":"Medium","gaps":["No molecular partner or signaling pathway identified","Mechanism of how CPNE3 promotes motility unresolved"]},{"year":2018,"claim":"Connected CPNE3's motility phenotype to a defined signaling axis by identifying RACK1 and phospho-ErbB2 as binding partners and placing CPNE3 upstream of RACK1/FAK.","evidence":"Co-immunoprecipitation and RACK1 siRNA epistasis (knockdown rescues CPNE3-overexpression phenotype) with FAK pathway western blots in NSCLC","pmids":["30519322"],"confidence":"Medium","gaps":["Binding interface on CPNE3 not mapped","Direct vs indirect ErbB2 interaction unclear"]},{"year":2021,"claim":"Extended the migration/invasion and FAK-pathway role of CPNE3 beyond lung cancer to glioblastoma, and additionally implicated PI3K/AKT in CPNE3-driven proliferation and apoptosis suppression.","evidence":"siRNA knockdown (FAK markers) plus overexpression with xenograft, GSEA, and pharmacological PI3K/AKT rescue (LY294002) in GBM cells","pmids":["33725213","35003348"],"confidence":"Medium","gaps":["No direct binding partner demonstrated for the FAK arm in GBM","How CPNE3 engages PI3K/AKT mechanistically unresolved"]},{"year":2021,"claim":"Revealed non-cancer physiological roles, showing CPNE3 is required for glucose-stimulated insulin secretion and for cardioprotection, broadening its functional repertoire.","evidence":"Cpne3 silencing in INS-1 β-cells (GSIS, glucose uptake, downstream regulator markers) and RACK1-dependent overexpression in hypoxia/reoxygenation H9c2 cells plus a rat I/R model","pmids":["34667273","34970351"],"confidence":"Medium","gaps":["Direct molecular targets in β-cells beyond expression changes unknown","Whether cardioprotection uses the same RACK1/kinase axis as cancer unclear"]},{"year":2024,"claim":"Embedded CPNE3 in a self-reinforcing transcriptional circuit by showing it is both a YAP1/TEAD target and a stabilizer of YAP1 protein against β-TRCP-mediated degradation.","evidence":"ChIP/luciferase reporter, CPNE3–YAP1 co-IP, and ubiquitination assays with proliferation/invasion readouts in gastric cancer","pmids":["38493426"],"confidence":"Medium","gaps":["Structural basis of CPNE3–YAP1 binding not defined","How cytoplasmic CPNE3 shields YAP1 from β-TRCP mechanistically unresolved"]},{"year":2025,"claim":"Resolved the structural basis of the RACK1 interaction (VWFA domain) and identified MET as an additional effector, while a parallel arm linked CPNE3 to EMT suppression via SQSTM1/p62.","evidence":"Domain-mapping co-IP, MET inhibitor and RACK1 siRNA epistasis, plus SILAC proteomics and p62 knockdown rescue in NSCLC/LUAD cells with xenografts","pmids":["41190648","39844538","41313527"],"confidence":"Medium","gaps":["Context-dependence of EMT-promoting vs EMT-suppressing effects across studies unreconciled","Whether RACK1 bridges CPNE3 to both FAK and MET via the same interface unclear"]},{"year":2026,"claim":"Identified KIF4 as a direct CPNE3 partner linking it to PI3K/AKT/mTOR activation and autophagy suppression in colorectal cancer.","evidence":"Co-immunoprecipitation, immunofluorescence, and KIF4 knockdown rescue of CPNE3-overexpression phenotype with autophagy and PI3K/AKT/mTOR marker western blots","pmids":["41816564"],"confidence":"Medium","gaps":["Direct biochemical KIF4 binding interface not mapped","Mechanistic link between KIF4 and PI3K/AKT/mTOR unresolved"]},{"year":null,"claim":"It remains unknown how CPNE3's calcium/phospholipid-binding biochemistry mechanistically governs its diverse partner engagements (RACK1, YAP1, KIF4) and whether membrane recruitment integrates these arms into a unified function.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of CPNE3 with any partner","Role of calcium/lipid binding in partner selection untested","Reciprocal/context-dependent EMT effects not reconciled"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,6,7,10]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[7]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[1,3,7,10]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[10]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[6]}],"complexes":[],"partners":["RACK1","ERBB2","YAP1","KIF4","MET","SQSTM1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O75131","full_name":"Copine-3","aliases":["Copine III"],"length_aa":537,"mass_kda":60.1,"function":"Calcium-dependent phospholipid-binding protein that plays a role in ERBB2-mediated tumor cell migration in response to growth factor heregulin stimulation (PubMed:20010870)","subcellular_location":"Nucleus; Cytoplasm; Cell membrane; Cell junction; Cell junction, focal adhesion","url":"https://www.uniprot.org/uniprotkb/O75131/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CPNE3","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CSNK2B","stoichiometry":0.2},{"gene":"TOMM70A","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CPNE3","total_profiled":1310},"omim":[{"mim_id":"604207","title":"COPINE III; CPNE3","url":"https://www.omim.org/entry/604207"},{"mim_id":"176807","title":"PROSTATE CANCER","url":"https://www.omim.org/entry/176807"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CPNE3"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"O75131","domains":[{"cath_id":"2.60.40.150","chopping":"8-136","consensus_level":"high","plddt":91.7694,"start":8,"end":136},{"cath_id":"2.60.40.150","chopping":"140-277","consensus_level":"high","plddt":94.3874,"start":140,"end":277},{"cath_id":"3.40.50","chopping":"304-523","consensus_level":"high","plddt":92.5562,"start":304,"end":523}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O75131","model_url":"https://alphafold.ebi.ac.uk/files/AF-O75131-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O75131-F1-predicted_aligned_error_v6.png","plddt_mean":92.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CPNE3","jax_strain_url":"https://www.jax.org/strain/search?query=CPNE3"},"sequence":{"accession":"O75131","fasta_url":"https://rest.uniprot.org/uniprotkb/O75131.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O75131/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O75131"}},"corpus_meta":[{"pmid":"23713811","id":"PMC_23713811","title":"Quantitative proteomic analysis identifies CPNE3 as a novel metastasis-promoting gene in NSCLC.","date":"2013","source":"Journal of proteome research","url":"https://pubmed.ncbi.nlm.nih.gov/23713811","citation_count":52,"is_preprint":false},{"pmid":"34667273","id":"PMC_34667273","title":"Copine 3 \"CPNE3\" is a novel regulator for insulin secretion and glucose uptake in pancreatic β-cells.","date":"2021","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/34667273","citation_count":20,"is_preprint":false},{"pmid":"30519322","id":"PMC_30519322","title":"CPNE3 promotes migration and invasion in non-small cell lung cancer by interacting with RACK1 via FAK signaling activation.","date":"2018","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/30519322","citation_count":19,"is_preprint":false},{"pmid":"29297177","id":"PMC_29297177","title":"Low CPNE3 expression is associated with risk of acute myocardial infarction: A feasible genetic marker of acute myocardial infarction in patients with stable coronary artery disease.","date":"2018","source":"Cardiology journal","url":"https://pubmed.ncbi.nlm.nih.gov/29297177","citation_count":17,"is_preprint":false},{"pmid":"33725213","id":"PMC_33725213","title":"Upregulation of CPNE3 suppresses invasion, migration and proliferation of glioblastoma cells through FAK pathway inactivation.","date":"2021","source":"Journal of molecular histology","url":"https://pubmed.ncbi.nlm.nih.gov/33725213","citation_count":13,"is_preprint":false},{"pmid":"38493426","id":"PMC_38493426","title":"YAP1-CPNE3 positive feedback pathway promotes gastric cancer cell progression.","date":"2024","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/38493426","citation_count":5,"is_preprint":false},{"pmid":"35003348","id":"PMC_35003348","title":"CPNE3 regulates the cell proliferation and apoptosis in human Glioblastoma via the activation of PI3K/AKT signaling pathway.","date":"2021","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/35003348","citation_count":5,"is_preprint":false},{"pmid":"33767297","id":"PMC_33767297","title":"CPNE3 moderates the association between anxiety and working memory.","date":"2021","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/33767297","citation_count":4,"is_preprint":false},{"pmid":"34970351","id":"PMC_34970351","title":"CPNE3 interaction with RACK1 protects against myocardial ischemia/reperfusion injury.","date":"2021","source":"Experimental and therapeutic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34970351","citation_count":3,"is_preprint":false},{"pmid":"39389002","id":"PMC_39389002","title":"New insights into molecular mechanisms underlying malignant transformation of endometriosis: BANCR promotes miR-612/CPNE3 pathway activity.","date":"2024","source":"Reproductive biomedicine online","url":"https://pubmed.ncbi.nlm.nih.gov/39389002","citation_count":1,"is_preprint":false},{"pmid":"41190648","id":"PMC_41190648","title":"Targeting MET Signalling Activated by CPNE3-RACK1 Interaction Through VWFA Domain to Suppress Lung Cancer Progression.","date":"2025","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/41190648","citation_count":1,"is_preprint":false},{"pmid":"39844538","id":"PMC_39844538","title":"SQSTM1/p62 Mediates the Effects of CPNE3 on the Epithelialmesenchymal Transition and Migration Inhibition of Lung Adenocarcinoma Cells.","date":"2025","source":"Current medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/39844538","citation_count":1,"is_preprint":false},{"pmid":"41313527","id":"PMC_41313527","title":"Integrated analysis of the oncogenic value of CPNE3 in non-small cell lung cancer.","date":"2025","source":"Discover oncology","url":"https://pubmed.ncbi.nlm.nih.gov/41313527","citation_count":0,"is_preprint":false},{"pmid":"41816564","id":"PMC_41816564","title":"CPNE3 promotes colorectal cancer progression by regulating KIF4-mediated autophagy.","date":"2026","source":"Journal of gastrointestinal oncology","url":"https://pubmed.ncbi.nlm.nih.gov/41816564","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8861,"output_tokens":3060,"usd":0.036242,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10471,"output_tokens":2970,"usd":0.063302,"stage2_stop_reason":"end_turn"},"total_usd":0.099544,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"CPNE3 knockdown by siRNA reduced migration and invasion of NSCLC cell lines (SPC-A1sci, H1299), and overexpression of CPNE3 promoted migration and invasion in SPC-A-1 and XL-2 cells in vitro; targeted knockdown inhibited in vivo metastasis in mouse xenograft models.\",\n      \"method\": \"siRNA-mediated knockdown, overexpression, in vitro migration/invasion assays, mouse metastasis model\",\n      \"journal\": \"Journal of proteome research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined cellular phenotype in multiple cell lines plus in vivo validation, single lab\",\n      \"pmids\": [\"23713811\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"CPNE3 interacts with phosphorylated ErbB2 (pErbB2) and RACK1, and activates the focal adhesion kinase (FAK) signaling pathway in NSCLC cells; knockdown of RACK1 inhibited cell motility in CPNE3-overexpressing NSCLC cells, placing CPNE3 upstream of RACK1/FAK in the metastasis pathway.\",\n      \"method\": \"Co-immunoprecipitation, overexpression, siRNA knockdown, FAK pathway western blot, migration/invasion assays\",\n      \"journal\": \"Journal of Cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP and epistasis (RACK1 knockdown rescues CPNE3 OE phenotype), single lab\",\n      \"pmids\": [\"30519322\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CPNE3 silencing in GBM cells impaired migratory, invasive, and proliferative abilities associated with inactivation of the FAK signaling pathway.\",\n      \"method\": \"siRNA knockdown, western blot for FAK pathway markers, migration/invasion assays\",\n      \"journal\": \"Journal of molecular histology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single approach (KD + pathway western blot), no direct binding demonstrated\",\n      \"pmids\": [\"33725213\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CPNE3 overexpression promoted cell proliferation and inhibited apoptosis in GBM cells in vitro and in vivo by activating the PI3K/AKT signaling pathway; pharmacological inhibition of PI3K/AKT with LY294002 reversed the proliferative enhancement induced by CPNE3 overexpression.\",\n      \"method\": \"Overexpression, nude mouse xenograft, GSEA, PI3K/AKT pathway western blot (phospho-markers), pharmacological inhibition (LY294002)\",\n      \"journal\": \"Journal of Cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pharmacological rescue experiment plus in vivo validation supports pathway placement, single lab\",\n      \"pmids\": [\"35003348\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CPNE3 interacts with RACK1 in cardiomyocytes; CPNE3 overexpression upregulated RACK1 expression, increased cell viability, suppressed LDH release, inhibited inflammatory cytokine release, and decreased apoptosis in hypoxia/reoxygenation-induced H9c2 cells, protecting against myocardial ischemia/reperfusion injury.\",\n      \"method\": \"Co-immunoprecipitation, overexpression, siRNA-RACK1 knockdown, western blot, TUNEL staining, LDH assay, rat I/R injury model\",\n      \"journal\": \"Experimental and therapeutic medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus RACK1 epistasis (siRNA-RACK1 reverses CPNE3 OE effects), single lab\",\n      \"pmids\": [\"34970351\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Silencing of Cpne3 in INS-1 (832/13) pancreatic β-cells impaired glucose-stimulated insulin secretion (GSIS), insulin content, and glucose uptake without affecting cell viability, and downregulated key regulators Insulin, GLUT2, NeuroD1, and INSR at mRNA and protein levels.\",\n      \"method\": \"siRNA knockdown, GSIS assay, glucose uptake assay, western blot, RT-qPCR\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined functional readout and downstream marker validation, single lab, two orthogonal methods\",\n      \"pmids\": [\"34667273\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CPNE3 is a direct transcriptional target of the YAP1/TEAD complex; CPNE3 protein in turn binds YAP1 in the cytoplasm and inhibits its ubiquitination and degradation mediated by the E3 ligase β-TRCP, forming a positive feedback loop that activates YAP1 downstream target gene transcription to promote gastric cancer progression.\",\n      \"method\": \"ChIP/luciferase reporter for YAP1/TEAD→CPNE3, co-immunoprecipitation (CPNE3–YAP1 interaction), ubiquitination assay, overexpression/knockdown with proliferation and invasion readouts\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (reporter, co-IP, ubiquitination assay) in a single lab establishing both arms of the feedback loop\",\n      \"pmids\": [\"38493426\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CPNE3 interacts with RACK1 specifically through its VWFA domain, and this interaction activates MET (c-MET) signaling to promote proliferation and migration of NSCLC cells; the MET inhibitor JNJ-38877605 and RACK1 knockdown both suppressed these effects in vitro and in vivo.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence, domain mapping (VWFA), RACK1 siRNA knockdown, MET inhibitor treatment, CCK-8/clonogenic/Transwell assays, xenograft model\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP with domain identification plus pharmacological and genetic epistasis, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"41190648\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CPNE3 knockdown in lung adenocarcinoma A549 cells promoted EMT (upregulated vimentin, downregulated E-cadherin) and migration; quantitative proteomics (SILAC) revealed CPNE3 regulates SQSTM1/p62, and p62 knockdown enhanced migratory ability and EMT progression in CPNE3-silenced cells, placing CPNE3 upstream of p62 in suppression of EMT.\",\n      \"method\": \"siRNA knockdown, SILAC quantitative proteomics, western blot (EMT markers), SQSTM1/p62 knockdown rescue, migration assay\",\n      \"journal\": \"Current medicinal chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — quantitative proteomics plus epistasis (p62 KD in CPNE3-KD background), single lab\",\n      \"pmids\": [\"39844538\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CPNE3 promotes vasculogenic mimicry (VM) formation and cell metastasis in NSCLC via the EMT process, demonstrated by 3D culture VM assay and Transwell migration/invasion assays with western blot confirmation of EMT markers.\",\n      \"method\": \"Transwell assay, 3D culture VM assay, western blot (EMT markers), overexpression/knockdown\",\n      \"journal\": \"Discover oncology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, descriptive mechanistic link to EMT without direct binding partner or epistasis experiment\",\n      \"pmids\": [\"41313527\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"CPNE3 directly interacts with KIF4 in colorectal cancer cells; CPNE3 overexpression increased KIF4 levels, activated PI3K/AKT/mTOR signaling, and suppressed autophagy markers (ATG5, ATG7, p62, LC3-II); KIF4 knockdown reversed the oncogenic effects of CPNE3 overexpression, placing CPNE3 upstream of KIF4 in the PI3K/AKT/mTOR and autophagy pathways.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence, BioGRID analysis, overexpression/knockdown, western blot (PI3K/AKT/mTOR and autophagy markers), KIF4 rescue experiment\",\n      \"journal\": \"Journal of gastrointestinal oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP for interaction plus KIF4 genetic epistasis reverting CPNE3 OE phenotype, single lab\",\n      \"pmids\": [\"41816564\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"miR-612 targets CPNE3 mRNA, and lncRNA BANCR acts as a ceRNA to sequester miR-612, thereby upregulating CPNE3 and promoting proliferation and migration of endometrial stromal cells; miR-612 mimics reversed BANCR-induced CPNE3 upregulation and cellular effects.\",\n      \"method\": \"miRNA target prediction and functional validation (miR-612 mimics/inhibitor), BANCR overexpression/knockdown, cell proliferation and migration assays, in vivo subcutaneous implantation model\",\n      \"journal\": \"Reproductive biomedicine online\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — functional ceRNA axis established but no direct biochemical binding between miR-612 and CPNE3 3'UTR reported in abstract; single lab\",\n      \"pmids\": [\"39389002\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CPNE3 is a calcium-dependent phospholipid-binding protein that promotes cell migration, invasion, and proliferation across multiple cancer types primarily by interacting with RACK1 (via its VWFA domain) to activate FAK and MET signaling; it also activates PI3K/AKT/mTOR and suppresses autophagy through a KIF4 interaction, forms a positive feedback loop with YAP1 by protecting it from β-TRCP-mediated ubiquitination, and suppresses EMT in some contexts through SQSTM1/p62; additionally, CPNE3 regulates glucose-stimulated insulin secretion in pancreatic β-cells by maintaining expression of GLUT2, NeuroD1, and INSR.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CPNE3 is a calcium-dependent phospholipid-binding protein that functions as a pro-tumorigenic signaling adaptor, driving cell migration, invasion, and proliferation across multiple cancer types [#0, #7]. Its central mechanism is an interaction with the scaffold protein RACK1—mapped to the CPNE3 VWFA domain—that engages receptor tyrosine kinase signaling: CPNE3 associates with phosphorylated ErbB2 and RACK1 to activate focal adhesion kinase (FAK) [#1], and the same VWFA-mediated RACK1 interaction activates MET (c-MET) signaling to promote NSCLC proliferation and migration [#7]. CPNE3 additionally activates PI3K/AKT signaling to promote proliferation and suppress apoptosis [#3], and in colorectal cancer binds KIF4 to drive PI3K/AKT/mTOR activation and suppress autophagy [#10]. Beyond kinase pathways, CPNE3 participates in a positive feedback loop with the Hippo effector YAP1, being a YAP1/TEAD transcriptional target that in turn binds cytoplasmic YAP1 and blocks its β-TRCP–mediated ubiquitination and degradation [#6]. CPNE3 also suppresses EMT through regulation of SQSTM1/p62, with p62 acting downstream of CPNE3 to restrain migration [#8]. Outside cancer, CPNE3 maintains glucose-stimulated insulin secretion in pancreatic β-cells by sustaining expression of GLUT2, NeuroD1, INSR, and insulin [#5], and protects cardiomyocytes from ischemia/reperfusion injury via RACK1 [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Established CPNE3 as a functional driver of cancer cell motility rather than a bystander, by showing loss- and gain-of-function effects on migration, invasion, and in vivo metastasis.\",\n      \"evidence\": \"siRNA knockdown and overexpression in NSCLC cell lines with in vitro migration/invasion assays and a mouse metastasis model\",\n      \"pmids\": [\"23713811\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No molecular partner or signaling pathway identified\", \"Mechanism of how CPNE3 promotes motility unresolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Connected CPNE3's motility phenotype to a defined signaling axis by identifying RACK1 and phospho-ErbB2 as binding partners and placing CPNE3 upstream of RACK1/FAK.\",\n      \"evidence\": \"Co-immunoprecipitation and RACK1 siRNA epistasis (knockdown rescues CPNE3-overexpression phenotype) with FAK pathway western blots in NSCLC\",\n      \"pmids\": [\"30519322\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Binding interface on CPNE3 not mapped\", \"Direct vs indirect ErbB2 interaction unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extended the migration/invasion and FAK-pathway role of CPNE3 beyond lung cancer to glioblastoma, and additionally implicated PI3K/AKT in CPNE3-driven proliferation and apoptosis suppression.\",\n      \"evidence\": \"siRNA knockdown (FAK markers) plus overexpression with xenograft, GSEA, and pharmacological PI3K/AKT rescue (LY294002) in GBM cells\",\n      \"pmids\": [\"33725213\", \"35003348\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct binding partner demonstrated for the FAK arm in GBM\", \"How CPNE3 engages PI3K/AKT mechanistically unresolved\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Revealed non-cancer physiological roles, showing CPNE3 is required for glucose-stimulated insulin secretion and for cardioprotection, broadening its functional repertoire.\",\n      \"evidence\": \"Cpne3 silencing in INS-1 β-cells (GSIS, glucose uptake, downstream regulator markers) and RACK1-dependent overexpression in hypoxia/reoxygenation H9c2 cells plus a rat I/R model\",\n      \"pmids\": [\"34667273\", \"34970351\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular targets in β-cells beyond expression changes unknown\", \"Whether cardioprotection uses the same RACK1/kinase axis as cancer unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Embedded CPNE3 in a self-reinforcing transcriptional circuit by showing it is both a YAP1/TEAD target and a stabilizer of YAP1 protein against β-TRCP-mediated degradation.\",\n      \"evidence\": \"ChIP/luciferase reporter, CPNE3–YAP1 co-IP, and ubiquitination assays with proliferation/invasion readouts in gastric cancer\",\n      \"pmids\": [\"38493426\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of CPNE3–YAP1 binding not defined\", \"How cytoplasmic CPNE3 shields YAP1 from β-TRCP mechanistically unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Resolved the structural basis of the RACK1 interaction (VWFA domain) and identified MET as an additional effector, while a parallel arm linked CPNE3 to EMT suppression via SQSTM1/p62.\",\n      \"evidence\": \"Domain-mapping co-IP, MET inhibitor and RACK1 siRNA epistasis, plus SILAC proteomics and p62 knockdown rescue in NSCLC/LUAD cells with xenografts\",\n      \"pmids\": [\"41190648\", \"39844538\", \"41313527\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Context-dependence of EMT-promoting vs EMT-suppressing effects across studies unreconciled\", \"Whether RACK1 bridges CPNE3 to both FAK and MET via the same interface unclear\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identified KIF4 as a direct CPNE3 partner linking it to PI3K/AKT/mTOR activation and autophagy suppression in colorectal cancer.\",\n      \"evidence\": \"Co-immunoprecipitation, immunofluorescence, and KIF4 knockdown rescue of CPNE3-overexpression phenotype with autophagy and PI3K/AKT/mTOR marker western blots\",\n      \"pmids\": [\"41816564\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct biochemical KIF4 binding interface not mapped\", \"Mechanistic link between KIF4 and PI3K/AKT/mTOR unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how CPNE3's calcium/phospholipid-binding biochemistry mechanistically governs its diverse partner engagements (RACK1, YAP1, KIF4) and whether membrane recruitment integrates these arms into a unified function.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of CPNE3 with any partner\", \"Role of calcium/lipid binding in partner selection untested\", \"Reciprocal/context-dependent EMT effects not reconciled\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 6, 7, 10]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [1, 3, 7, 10]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [10]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RACK1\", \"ERBB2\", \"YAP1\", \"KIF4\", \"MET\", \"SQSTM1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":5,"faith_total":6,"faith_pct":83.33333333333333}}