{"gene":"CLCA2","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":2001,"finding":"CLCA2 expressed on the luminal endothelial surface of pulmonary arteries/arterioles/venules mediates adhesion of breast cancer cells via direct binding to β4 integrin, establishing a cell-cell adhesion function for this integrin–CLCA2 pair; adhesion was abolished by matrilysin-mediated cleavage of β4 integrin and by adhesion-blocking antibodies against either partner.","method":"In vitro cell adhesion assay, antibody-blocking experiments, matrilysin cleavage, in vivo lung colonization model","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal blocking antibodies against both partners, in vitro adhesion assay, and in vivo lung colonization rescue; multiple orthogonal methods in a single rigorous study","pmids":["11320086"],"is_preprint":false},{"year":1999,"finding":"Stable reintroduction of CLCA2 into CLCA2-negative tumorigenic breast cancer cell lines (MDA-MB-231, MDA-MB-435) reduced Matrigel invasion in vitro and suppressed subcutaneous and metastatic tumor formation in nude mice, defining a tumor-suppressive loss-of-function role for CLCA2.","method":"Stable transfection, Matrigel invasion assay, nude mouse xenograft model","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 2 / Strong — stable rescue in multiple cell lines plus in vivo validation with two orthogonal readouts","pmids":["10554024"],"is_preprint":false},{"year":2004,"finding":"CLCA2 is silenced in breast cancer primarily through promoter CpG island hypermethylation; treatment with demethylating agents restored CLCA2 expression in CLCA2-negative breast cancer cell lines, and bisulfite sequencing confirmed hypermethylation in tumors lacking expression.","method":"Bisulfite sequencing, demethylating agent treatment, RT-PCR expression analysis","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 / Strong — bisulfite sequencing plus pharmacological demethylation rescue across multiple cell lines and tumor specimens","pmids":["14973555"],"is_preprint":false},{"year":2012,"finding":"CLCA2 is a direct transcriptional target of the p53 family (p53, p73, p63); p53 family proteins bind a conserved consensus p53-binding site in the CLCA2 promoter, CLCA2 is induced by DNA damage in a p53-dependent manner, and ectopic CLCA2 expression inhibits cancer cell migration while CLCA2 knockdown enhances migration/invasion through upregulation of FAK and its promoter activity; FAK inhibition rescues the pro-migratory effect of CLCA2 siRNA.","method":"Promoter reporter assay, ChIP, siRNA knockdown, ectopic expression, FAK inhibitor rescue, migration/invasion assays","journal":"Cancer biology & therapy","confidence":"High","confidence_rationale":"Tier 2 / Strong — ChIP demonstrating direct promoter binding, promoter reporter assay, bidirectional loss- and gain-of-function experiments, and pharmacological rescue with multiple orthogonal methods","pmids":["22990203"],"is_preprint":false},{"year":2012,"finding":"CLCA2 is induced by p53 during replicative senescence and oxidative stress; ectopic CLCA2 expression induces cellular senescence, and siRNA-mediated CLCA2 knockdown inhibits oxidative stress-induced senescence, placing CLCA2 downstream of p53 in a senescence pathway.","method":"Genome-wide expression screening, siRNA knockdown, ectopic expression, senescence markers assay (SA-β-gal and others)","journal":"Neoplasia (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — bidirectional functional experiments (OE and KD) with defined senescence readouts in a single lab","pmids":["22431922"],"is_preprint":false},{"year":2016,"finding":"CLCA2 interacts physically with the junctional protein EVA1 via their transmembrane segments; both co-localize with E-cadherin at cell-cell junctions. CLCA2 is also found in two distinct complexes: one with EVA1 and ZO-1, and another with β-catenin. Overexpression of CLCA2 causes downregulation of β-catenin and β-catenin-activated genes. Knockdown of CLCA2 causes EMT in immortalized human mammary epithelial cells.","method":"Membrane dihybrid screening, co-immunoprecipitation, deletion analysis, co-localization by immunofluorescence, siRNA knockdown, gene expression analysis","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Strong — interaction confirmed by co-IP, domain mapping by deletion analysis, co-localization, and functional knockdown with defined EMT readout; multiple orthogonal methods in one study","pmids":["26930581"],"is_preprint":false},{"year":2018,"finding":"CLCA2 enhances store-operated calcium entry (SOCE) and moderately augments intracellular store release; CLCA2 co-immunoprecipitates with ORAI-1 (plasma membrane store-operated calcium channel) and STIM-1 (ER calcium sensor). Co-expression of CLCA2 with TMEM16A nearly doubles Ca2+-activated chloride current (ICaCC) in response to a calcium ionophore, establishing a mechanism by which CLCA2 activates chloride conductance via boosting calcium entry.","method":"Calcium imaging, co-immunoprecipitation, whole-cell patch-clamp electrophysiology in HEK293 cells stably expressing TMEM16A","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — direct electrophysiology combined with calcium imaging and co-IP; multiple orthogonal methods in a single rigorous study","pmids":["29758025"],"is_preprint":false},{"year":2018,"finding":"Hyperosmolarity upregulates CLCA2 in keratinocytes via p38/JNK–ATF2 signaling; CLCA2 knockdown promotes keratinocyte apoptosis induced by hyperosmotic stress through impairment of cell-cell adhesion.","method":"siRNA knockdown, signaling inhibitor experiments, organotypic skin culture, apoptosis assay","journal":"Science translational medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — knockdown with defined apoptosis and adhesion readouts plus pathway inhibitor identification in a single lab","pmids":["29743348"],"is_preprint":false},{"year":2018,"finding":"CTBP1 represses CLCA2 transcription by binding to the CLCA2 promoter as part of a repressor complex containing ZEB1, EP300, and HDACs; in addition, miR-196b-5p directly targets the CLCA2 3′UTR (confirmed by luciferase reporter assay) to suppress CLCA2 expression in prostate cancer.","method":"ChIP, promoter reporter assay, luciferase 3′UTR reporter assay, siRNA knockdown, miRNA microarray","journal":"International journal of cancer","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct promoter ChIP, luciferase reporter for miRNA targeting, and functional rescue in xenograft model; multiple orthogonal methods","pmids":["29536528"],"is_preprint":false},{"year":2024,"finding":"CLCA2 is transported to the nucleus of keratinocytes via extracellular vesicles; a nuclear localization signal in CLCA2 is required for its nuclear function. In the nucleus, CLCA2 binds and activates β-catenin, enhancing Wnt target gene expression; RNA-binding protein 3 (RBM3) was identified as a key nuclear effector of CLCA2 by mass-spectrometry interaction screening and functional rescue studies. Nuclear CLCA2 suppresses keratinocyte migration and protects against hyperosmotic stress-induced cell death.","method":"Live-cell imaging, nuclear fractionation, extracellular vesicle isolation, NLS-mutant analysis, mass-spectrometry interaction screen, co-immunoprecipitation, functional rescue experiments, Wnt reporter assay","journal":"Journal of extracellular vesicles","confidence":"High","confidence_rationale":"Tier 2 / Strong — NLS mutant loss-of-function combined with MS-based interaction screen, co-IP, functional rescue, and reporter assay; multiple orthogonal methods in a single rigorous study","pmids":["38602325"],"is_preprint":false},{"year":2022,"finding":"Overexpression of CLCA2 in cervical cancer cells suppresses EMT through inactivation of ERK/JNK/p38-MAPK signaling pathways, and inhibits proliferation, migration, invasion while promoting apoptosis both in vitro and in vivo.","method":"Ectopic overexpression, MAPK pathway inhibitor/activation assays, in vitro migration/invasion/proliferation/apoptosis assays, xenograft model","journal":"BMC molecular and cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — in vitro and in vivo gain-of-function with pathway readouts but mechanistic depth limited to MAPK signaling markers; single lab","pmids":["36280802"],"is_preprint":false},{"year":2024,"finding":"A truncated TP63 protein (TP63-mut) binds the CLCA2 promoter and activates CLCA2 transcription more strongly than wild-type TP63; elevated CLCA2 then promotes apoptosis via the ATM pathway. siRNA silencing of CLCA2 or ATM inhibition (KU55933) attenuated apoptosis caused by TP63-mut overexpression, placing CLCA2 downstream of TP63 in an apoptosis pathway.","method":"Dual luciferase reporter assay, western blot, immunofluorescence, siRNA knockdown, ATM inhibitor rescue, cell apoptosis assay","journal":"Journal of ovarian research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reporter assay for direct promoter activation, bidirectional rescue by siRNA and pharmacological inhibition; single lab","pmids":["38528613"],"is_preprint":false},{"year":2022,"finding":"Biochemical analysis of heterologously expressed avian (chicken) CLCA2 revealed that, like mammalian CLCA2, it undergoes protein cleavage, glycosylation, and plasma membrane anchoring, and is expressed in epidermal keratinocytes across birds and mammals, establishing these as conserved canonical properties of the CLCA2 protein.","method":"Immunoblotting, immunofluorescence, immunohistochemistry, heterologous expression","journal":"PeerJ","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — biochemical characterization with multiple methods (immunoblot + immunofluorescence) across multiple species in a single study","pmids":["36389428"],"is_preprint":false},{"year":2026,"finding":"YTHDC2 stabilizes CLCA2 mRNA through m6A-dependent mechanisms; RIP-qPCR and MeRIP-qPCR/seq demonstrated that YTHDC2 binds m6A-modified CLCA2 mRNA and promotes its stability, thereby increasing CLCA2 protein expression in colorectal cancer.","method":"RIP-qPCR, MeRIP-qPCR, MeRIP-seq, molecular docking","journal":"Journal of ethnopharmacology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct RNA-protein interaction by RIP-qPCR and m6A mapping by MeRIP-seq; single lab, limited functional dissection of CLCA2 specifically","pmids":["41616882"],"is_preprint":false}],"current_model":"CLCA2 is a p53/p63-inducible transmembrane protein expressed in epithelial cells (especially keratinocytes) that functions as a tumor suppressor by inhibiting EMT, migration, invasion, and promoting cellular senescence; it directly binds β4 integrin (mediating cancer cell–endothelium adhesion), interacts with EVA1/ZO-1 and β-catenin at cell junctions, activates store-operated calcium entry through physical interaction with ORAI-1 and STIM-1 thereby potentiating TMEM16A-dependent chloride currents, and is transported via extracellular vesicles to the nucleus where it activates β-catenin/Wnt signaling and RBM3; its expression is regulated transcriptionally by p53 family members and repressed by promoter hypermethylation, a CTBP1/ZEB1/HDAC complex, and miR-196b-5p."},"narrative":{"mechanistic_narrative":"CLCA2 is a cleaved, glycosylated, plasma-membrane-anchored transmembrane protein of epithelial cells and keratinocytes that acts as a tumor suppressor restraining migration, invasion, and epithelial-mesenchymal transition while promoting cellular senescence and stress-induced apoptosis [PMID:10554024, PMID:22431922, PMID:36389428]. Its expression is controlled by the p53 family: p53, p73, and p63 bind a consensus site in the CLCA2 promoter and induce CLCA2 upon DNA damage, downstream of which CLCA2 restrains cell migration by limiting FAK, and a truncated TP63 variant superactivates CLCA2 to drive apoptosis through the ATM pathway [PMID:22990203, PMID:38528613]. CLCA2 is silenced in cancer through CpG island promoter hypermethylation, a CTBP1/ZEB1/EP300/HDAC repressor complex, and miR-196b-5p targeting of its 3'UTR, while m6A-dependent stabilization by YTHDC2 raises its expression [PMID:14973555, PMID:29536528, PMID:41616882]. At cell-cell junctions CLCA2 partners with EVA1 and ZO-1 and forms a separate complex with β-catenin, downregulating β-catenin-activated genes and suppressing EMT, with knockdown driving EMT in mammary epithelial cells [PMID:26930581]. CLCA2 also directly binds β4 integrin to mediate breast cancer cell adhesion to pulmonary endothelium [PMID:11320086], and it potentiates calcium signaling by physically associating with ORAI-1 and STIM-1 to enhance store-operated calcium entry and thereby boost TMEM16A-dependent calcium-activated chloride currents [PMID:29758025]. A nuclear pool of CLCA2, delivered via extracellular vesicles and dependent on an internal nuclear localization signal, binds and activates β-catenin/Wnt signaling through the effector RBM3 to suppress keratinocyte migration and protect against hyperosmotic stress [PMID:38602325].","teleology":[{"year":1999,"claim":"Establishing whether CLCA2 loss is functionally consequential in cancer, reintroduction defined it as a tumor suppressor.","evidence":"Stable transfection into CLCA2-negative breast cancer lines with Matrigel invasion and nude mouse xenograft readouts","pmids":["10554024"],"confidence":"High","gaps":["Molecular mechanism of invasion suppression not defined","Restricted to breast cancer models"]},{"year":2001,"claim":"To explain CLCA2's role in metastatic colonization, it was shown to mediate cancer cell adhesion to endothelium via a defined receptor.","evidence":"In vitro adhesion assays with reciprocal blocking antibodies, matrilysin cleavage, and in vivo lung colonization","pmids":["11320086"],"confidence":"High","gaps":["Whether endothelial-surface CLCA2 reflects its epithelial tumor-suppressive role unclear","Stoichiometry and binding interface with β4 integrin not mapped"]},{"year":2004,"claim":"To explain how CLCA2 is lost in tumors, promoter hypermethylation was identified as the silencing mechanism.","evidence":"Bisulfite sequencing and demethylating-agent rescue across breast cancer cell lines and tumors","pmids":["14973555"],"confidence":"High","gaps":["Trigger initiating de novo methylation unknown","Does not address non-methylation modes of loss"]},{"year":2012,"claim":"Connecting CLCA2 to a master tumor-suppressor network, it was defined as a direct p53-family transcriptional target acting through FAK and senescence.","evidence":"ChIP, promoter reporter, bidirectional knockdown/overexpression, FAK inhibitor rescue, and senescence marker assays","pmids":["22990203","22431922"],"confidence":"High","gaps":["How CLCA2 represses FAK transcription not mechanistically resolved","Senescence pathway downstream of CLCA2 incompletely mapped"]},{"year":2016,"claim":"To define CLCA2's molecular role at junctions, it was placed in junctional complexes restraining β-catenin and EMT.","evidence":"Membrane dihybrid screen, co-IP, deletion mapping, immunofluorescence co-localization, and siRNA-induced EMT in mammary epithelial cells","pmids":["26930581"],"confidence":"High","gaps":["How the EVA1/ZO-1 and β-catenin complexes are physically coordinated unclear","Mechanism linking junctional CLCA2 to β-catenin downregulation not resolved"]},{"year":2018,"claim":"Resolving a long-standing question about CLCA proteins and chloride conductance, CLCA2 was shown to act through calcium entry rather than as a channel itself.","evidence":"Calcium imaging, co-IP with ORAI-1/STIM-1, and patch-clamp of TMEM16A-expressing HEK293 cells","pmids":["29758025"],"confidence":"High","gaps":["Structural basis of ORAI-1/STIM-1 interaction unknown","Link between calcium/chloride function and tumor suppression not established"]},{"year":2018,"claim":"In skin physiology, CLCA2 was placed downstream of osmotic stress signaling and shown to maintain keratinocyte survival via adhesion.","evidence":"siRNA knockdown, signaling inhibitors, organotypic culture, and apoptosis assays","pmids":["29743348"],"confidence":"Medium","gaps":["Direct ATF2 binding to the CLCA2 promoter not demonstrated","Adhesion molecules mediating protection not identified"]},{"year":2018,"claim":"Expanding the silencing repertoire, transcriptional repression by a CTBP1/ZEB1/HDAC complex and post-transcriptional repression by miR-196b-5p were defined.","evidence":"ChIP, promoter and 3'UTR luciferase reporters, siRNA, and prostate cancer xenograft","pmids":["29536528"],"confidence":"High","gaps":["Relative contribution of each repressive mechanism in vivo unclear","Generalizability beyond prostate cancer untested"]},{"year":2022,"claim":"Extending tumor suppression to other tissues, CLCA2 overexpression was shown to suppress EMT via MAPK inactivation in cervical cancer.","evidence":"Ectopic overexpression, MAPK pathway modulation, and in vitro/in vivo proliferation/migration/apoptosis assays","pmids":["36280802"],"confidence":"Medium","gaps":["Mechanism limited to pathway marker correlation","Direct CLCA2 effector upstream of MAPK not identified"]},{"year":2022,"claim":"To define conserved biochemical features of the protein, avian CLCA2 was shown to share cleavage, glycosylation, membrane anchoring, and keratinocyte expression with mammals.","evidence":"Heterologous expression, immunoblotting, immunofluorescence, and immunohistochemistry across species","pmids":["36389428"],"confidence":"Medium","gaps":["Functional conservation of signaling roles not tested","Cleavage site and protease not defined here"]},{"year":2024,"claim":"Revealing an unexpected mode of action, CLCA2 was shown to traffic via extracellular vesicles to the nucleus where it activates Wnt/β-catenin through RBM3.","evidence":"Live imaging, nuclear fractionation, EV isolation, NLS-mutant analysis, MS interaction screen, co-IP, and Wnt reporter","pmids":["38602325"],"confidence":"High","gaps":["How a membrane protein enters EVs and the nucleus mechanistically unclear","Apparent contradiction with junctional CLCA2 downregulating β-catenin unresolved"]},{"year":2024,"claim":"A gain-of-function TP63 variant was shown to superactivate CLCA2 to trigger ATM-dependent apoptosis, refining the p63-CLCA2 axis.","evidence":"Dual luciferase reporter, western blot, siRNA, and ATM inhibitor (KU55933) rescue in apoptosis assays","pmids":["38528613"],"confidence":"Medium","gaps":["How CLCA2 activates ATM signaling not defined","Single-lab ovarian context"]},{"year":2026,"claim":"Adding an RNA-level control, YTHDC2 was shown to stabilize CLCA2 mRNA through m6A in colorectal cancer.","evidence":"RIP-qPCR, MeRIP-qPCR/seq, and molecular docking","pmids":["41616882"],"confidence":"Medium","gaps":["Functional consequence of CLCA2 stabilization for tumor phenotype not dissected","m6A site mapping on CLCA2 not resolved at nucleotide level"]},{"year":null,"claim":"It remains unresolved how CLCA2's opposing activities — junctional β-catenin downregulation versus nuclear β-catenin/Wnt activation, and tumor suppression versus pro-adhesive metastatic roles — are reconciled within a single protein.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unified model integrating membrane, junctional, and nuclear CLCA2 pools","Context-dependence across tissues not mechanistically explained"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098631","term_label":"cell adhesion mediator activity","supporting_discovery_ids":[0]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[6]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[5,6,9]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,6,12]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[9]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[9]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[6,9,10]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[1,2,3]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[7,11]}],"complexes":["CLCA2-EVA1-ZO-1 junctional complex","CTBP1/ZEB1/EP300/HDAC repressor complex (acts on CLCA2 promoter)"],"partners":["ITGB4","EVA1","TJP1","CTNNB1","ORAI1","STIM1","TMEM16A","RBM3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UQC9","full_name":"Calcium-activated chloride channel regulator 2","aliases":["Calcium-activated chloride channel family member 2","hCLCA2","Calcium-activated chloride channel protein 3","CaCC-3","hCaCC-3"],"length_aa":943,"mass_kda":103.9,"function":"Plays a role in modulating chloride current across the plasma membrane in a calcium-dependent manner, and cell adhesion. Involved in basal cell adhesion and/or stratification of squamous epithelia. May act as a tumor suppressor in breast and colorectal cancer. Plays a key role for cell adhesion in the beginning stages of lung metastasis via the binding to ITGB4","subcellular_location":"Secreted","url":"https://www.uniprot.org/uniprotkb/Q9UQC9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CLCA2","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CLCA2","total_profiled":1310},"omim":[{"mim_id":"616857","title":"CHLORIDE CHANNEL ACCESSORY 4; CLCA4","url":"https://www.omim.org/entry/616857"},{"mim_id":"604337","title":"CHLORIDE CHANNEL ACCESSORY 3, PSEUDOGENE; CLCA3P","url":"https://www.omim.org/entry/604337"},{"mim_id":"604003","title":"CHLORIDE CHANNEL ACCESSORY 2; CLCA2","url":"https://www.omim.org/entry/604003"},{"mim_id":"603906","title":"CHLORIDE CHANNEL ACCESSORY 1; CLCA1","url":"https://www.omim.org/entry/603906"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Plasma membrane","reliability":"Supported"},{"location":"Cell Junctions","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"cervix","ntpm":43.0},{"tissue":"esophagus","ntpm":110.4},{"tissue":"skin 1","ntpm":83.8},{"tissue":"vagina","ntpm":53.4}],"url":"https://www.proteinatlas.org/search/CLCA2"},"hgnc":{"alias_symbol":["CLCRG2"],"prev_symbol":[]},"alphafold":{"accession":"Q9UQC9","domains":[{"cath_id":"3.40.50.410","chopping":"310-471","consensus_level":"medium","plddt":92.0027,"start":310,"end":471},{"cath_id":"2.60.120.380","chopping":"489-603","consensus_level":"medium","plddt":94.8311,"start":489,"end":603},{"cath_id":"2.60.40.1930","chopping":"604-699_738-759","consensus_level":"medium","plddt":91.247,"start":604,"end":759},{"cath_id":"2.60.40.10","chopping":"774-844_858-886","consensus_level":"high","plddt":90.0433,"start":774,"end":886},{"cath_id":"3.40.390","chopping":"29-176_284-307","consensus_level":"medium","plddt":91.5699,"start":29,"end":307}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UQC9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UQC9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UQC9-F1-predicted_aligned_error_v6.png","plddt_mean":86.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CLCA2","jax_strain_url":"https://www.jax.org/strain/search?query=CLCA2"},"sequence":{"accession":"Q9UQC9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UQC9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UQC9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UQC9"}},"corpus_meta":[{"pmid":"11320086","id":"PMC_11320086","title":"The breast cancer beta 4 integrin and endothelial human CLCA2 mediate lung metastasis.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11320086","citation_count":110,"is_preprint":false},{"pmid":"10554024","id":"PMC_10554024","title":"Tumorigenicity of human breast cancer is associated with loss of the Ca2+-activated chloride channel CLCA2.","date":"1999","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/10554024","citation_count":80,"is_preprint":false},{"pmid":"11445004","id":"PMC_11445004","title":"Expression of the Ca2+-activated chloride channel genes CLCA1 and CLCA2 is downregulated in human colorectal cancer.","date":"2001","source":"DNA and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/11445004","citation_count":79,"is_preprint":false},{"pmid":"2998527","id":"PMC_2998527","title":"Cl-/Ca2+-dependent L-glutamate binding sites do not correspond to 2-amino-4-phosphonobutanoate-sensitive excitatory amino acid receptors.","date":"1985","source":"British journal of pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/2998527","citation_count":55,"is_preprint":false},{"pmid":"22990203","id":"PMC_22990203","title":"CLCA2, a target of the p53 family, negatively regulates cancer cell migration and invasion.","date":"2012","source":"Cancer biology & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/22990203","citation_count":53,"is_preprint":false},{"pmid":"14973555","id":"PMC_14973555","title":"CLCA2 tumour suppressor gene in 1p31 is epigenetically regulated in breast cancer.","date":"2004","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/14973555","citation_count":46,"is_preprint":false},{"pmid":"22431922","id":"PMC_22431922","title":"CLCA2 as a p53-inducible senescence mediator.","date":"2012","source":"Neoplasia (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/22431922","citation_count":36,"is_preprint":false},{"pmid":"26930581","id":"PMC_26930581","title":"CLCA2 Interactor EVA1 Is Required for Mammary Epithelial Cell Differentiation.","date":"2016","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/26930581","citation_count":33,"is_preprint":false},{"pmid":"29758025","id":"PMC_29758025","title":"CLCA2 is a positive regulator of store-operated calcium entry and TMEM16A.","date":"2018","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/29758025","citation_count":31,"is_preprint":false},{"pmid":"29536528","id":"PMC_29536528","title":"CLCA2 epigenetic regulation by CTBP1, HDACs, ZEB1, EP300 and miR-196b-5p impacts prostate cancer cell adhesion and EMT in metabolic syndrome disease.","date":"2018","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/29536528","citation_count":29,"is_preprint":false},{"pmid":"29743348","id":"PMC_29743348","title":"Humidity-regulated CLCA2 protects the epidermis from hyperosmotic stress.","date":"2018","source":"Science translational 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biology","url":"https://pubmed.ncbi.nlm.nih.gov/36280802","citation_count":8,"is_preprint":false},{"pmid":"38602325","id":"PMC_38602325","title":"Transport of CLCA2 to the nucleus by extracellular vesicles controls keratinocyte survival and migration.","date":"2024","source":"Journal of extracellular vesicles","url":"https://pubmed.ncbi.nlm.nih.gov/38602325","citation_count":6,"is_preprint":false},{"pmid":"31326550","id":"PMC_31326550","title":"A newly identified missense mutation in CLCA2 is associated with autosomal dominant cardiac conduction block.","date":"2019","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/31326550","citation_count":6,"is_preprint":false},{"pmid":"38528613","id":"PMC_38528613","title":"TP63 truncating mutation causes increased cell apoptosis and premature ovarian insufficiency by enhanced transcriptional activation of CLCA2.","date":"2024","source":"Journal of ovarian research","url":"https://pubmed.ncbi.nlm.nih.gov/38528613","citation_count":5,"is_preprint":false},{"pmid":"34055075","id":"PMC_34055075","title":"CLCA2 suppresses the proliferation, migration and invasion of cervical cancer.","date":"2021","source":"Experimental and therapeutic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34055075","citation_count":5,"is_preprint":false},{"pmid":"38540205","id":"PMC_38540205","title":"CLCA2: A Potential Guardian against Premature Senescence and Skin Aging.","date":"2024","source":"Biomedicines","url":"https://pubmed.ncbi.nlm.nih.gov/38540205","citation_count":3,"is_preprint":false},{"pmid":"36389428","id":"PMC_36389428","title":"Genomic, biochemical and expressional properties reveal strong conservation of the CLCA2 gene in birds and mammals.","date":"2022","source":"PeerJ","url":"https://pubmed.ncbi.nlm.nih.gov/36389428","citation_count":1,"is_preprint":false},{"pmid":"39130876","id":"PMC_39130876","title":"Expression of Survivin, CK7, ASH1, HMGB3, L587S, and CLCA2 in Peripheral Blood of Lung Cancer Patients by Real-Time Polymerase Chain Reaction.","date":"2024","source":"Cureus","url":"https://pubmed.ncbi.nlm.nih.gov/39130876","citation_count":0,"is_preprint":false},{"pmid":"41616882","id":"PMC_41616882","title":"Fuzheng Shengbai decoction enhances antitumor immunity via YTHDC2-dependent stabilization of CLCA2 mRNA in colorectal cancer.","date":"2026","source":"Journal of ethnopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/41616882","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13918,"output_tokens":3691,"usd":0.048559,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11447,"output_tokens":4156,"usd":0.080568,"stage2_stop_reason":"end_turn"},"total_usd":0.129127,"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\": 2001,\n      \"finding\": \"CLCA2 expressed on the luminal endothelial surface of pulmonary arteries/arterioles/venules mediates adhesion of breast cancer cells via direct binding to β4 integrin, establishing a cell-cell adhesion function for this integrin–CLCA2 pair; adhesion was abolished by matrilysin-mediated cleavage of β4 integrin and by adhesion-blocking antibodies against either partner.\",\n      \"method\": \"In vitro cell adhesion assay, antibody-blocking experiments, matrilysin cleavage, in vivo lung colonization model\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal blocking antibodies against both partners, in vitro adhesion assay, and in vivo lung colonization rescue; multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"11320086\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Stable reintroduction of CLCA2 into CLCA2-negative tumorigenic breast cancer cell lines (MDA-MB-231, MDA-MB-435) reduced Matrigel invasion in vitro and suppressed subcutaneous and metastatic tumor formation in nude mice, defining a tumor-suppressive loss-of-function role for CLCA2.\",\n      \"method\": \"Stable transfection, Matrigel invasion assay, nude mouse xenograft model\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — stable rescue in multiple cell lines plus in vivo validation with two orthogonal readouts\",\n      \"pmids\": [\"10554024\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"CLCA2 is silenced in breast cancer primarily through promoter CpG island hypermethylation; treatment with demethylating agents restored CLCA2 expression in CLCA2-negative breast cancer cell lines, and bisulfite sequencing confirmed hypermethylation in tumors lacking expression.\",\n      \"method\": \"Bisulfite sequencing, demethylating agent treatment, RT-PCR expression analysis\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — bisulfite sequencing plus pharmacological demethylation rescue across multiple cell lines and tumor specimens\",\n      \"pmids\": [\"14973555\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"CLCA2 is a direct transcriptional target of the p53 family (p53, p73, p63); p53 family proteins bind a conserved consensus p53-binding site in the CLCA2 promoter, CLCA2 is induced by DNA damage in a p53-dependent manner, and ectopic CLCA2 expression inhibits cancer cell migration while CLCA2 knockdown enhances migration/invasion through upregulation of FAK and its promoter activity; FAK inhibition rescues the pro-migratory effect of CLCA2 siRNA.\",\n      \"method\": \"Promoter reporter assay, ChIP, siRNA knockdown, ectopic expression, FAK inhibitor rescue, migration/invasion assays\",\n      \"journal\": \"Cancer biology & therapy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — ChIP demonstrating direct promoter binding, promoter reporter assay, bidirectional loss- and gain-of-function experiments, and pharmacological rescue with multiple orthogonal methods\",\n      \"pmids\": [\"22990203\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"CLCA2 is induced by p53 during replicative senescence and oxidative stress; ectopic CLCA2 expression induces cellular senescence, and siRNA-mediated CLCA2 knockdown inhibits oxidative stress-induced senescence, placing CLCA2 downstream of p53 in a senescence pathway.\",\n      \"method\": \"Genome-wide expression screening, siRNA knockdown, ectopic expression, senescence markers assay (SA-β-gal and others)\",\n      \"journal\": \"Neoplasia (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — bidirectional functional experiments (OE and KD) with defined senescence readouts in a single lab\",\n      \"pmids\": [\"22431922\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"CLCA2 interacts physically with the junctional protein EVA1 via their transmembrane segments; both co-localize with E-cadherin at cell-cell junctions. CLCA2 is also found in two distinct complexes: one with EVA1 and ZO-1, and another with β-catenin. Overexpression of CLCA2 causes downregulation of β-catenin and β-catenin-activated genes. Knockdown of CLCA2 causes EMT in immortalized human mammary epithelial cells.\",\n      \"method\": \"Membrane dihybrid screening, co-immunoprecipitation, deletion analysis, co-localization by immunofluorescence, siRNA knockdown, gene expression analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — interaction confirmed by co-IP, domain mapping by deletion analysis, co-localization, and functional knockdown with defined EMT readout; multiple orthogonal methods in one study\",\n      \"pmids\": [\"26930581\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"CLCA2 enhances store-operated calcium entry (SOCE) and moderately augments intracellular store release; CLCA2 co-immunoprecipitates with ORAI-1 (plasma membrane store-operated calcium channel) and STIM-1 (ER calcium sensor). Co-expression of CLCA2 with TMEM16A nearly doubles Ca2+-activated chloride current (ICaCC) in response to a calcium ionophore, establishing a mechanism by which CLCA2 activates chloride conductance via boosting calcium entry.\",\n      \"method\": \"Calcium imaging, co-immunoprecipitation, whole-cell patch-clamp electrophysiology in HEK293 cells stably expressing TMEM16A\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — direct electrophysiology combined with calcium imaging and co-IP; multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"29758025\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Hyperosmolarity upregulates CLCA2 in keratinocytes via p38/JNK–ATF2 signaling; CLCA2 knockdown promotes keratinocyte apoptosis induced by hyperosmotic stress through impairment of cell-cell adhesion.\",\n      \"method\": \"siRNA knockdown, signaling inhibitor experiments, organotypic skin culture, apoptosis assay\",\n      \"journal\": \"Science translational medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — knockdown with defined apoptosis and adhesion readouts plus pathway inhibitor identification in a single lab\",\n      \"pmids\": [\"29743348\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"CTBP1 represses CLCA2 transcription by binding to the CLCA2 promoter as part of a repressor complex containing ZEB1, EP300, and HDACs; in addition, miR-196b-5p directly targets the CLCA2 3′UTR (confirmed by luciferase reporter assay) to suppress CLCA2 expression in prostate cancer.\",\n      \"method\": \"ChIP, promoter reporter assay, luciferase 3′UTR reporter assay, siRNA knockdown, miRNA microarray\",\n      \"journal\": \"International journal of cancer\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct promoter ChIP, luciferase reporter for miRNA targeting, and functional rescue in xenograft model; multiple orthogonal methods\",\n      \"pmids\": [\"29536528\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CLCA2 is transported to the nucleus of keratinocytes via extracellular vesicles; a nuclear localization signal in CLCA2 is required for its nuclear function. In the nucleus, CLCA2 binds and activates β-catenin, enhancing Wnt target gene expression; RNA-binding protein 3 (RBM3) was identified as a key nuclear effector of CLCA2 by mass-spectrometry interaction screening and functional rescue studies. Nuclear CLCA2 suppresses keratinocyte migration and protects against hyperosmotic stress-induced cell death.\",\n      \"method\": \"Live-cell imaging, nuclear fractionation, extracellular vesicle isolation, NLS-mutant analysis, mass-spectrometry interaction screen, co-immunoprecipitation, functional rescue experiments, Wnt reporter assay\",\n      \"journal\": \"Journal of extracellular vesicles\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — NLS mutant loss-of-function combined with MS-based interaction screen, co-IP, functional rescue, and reporter assay; multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"38602325\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Overexpression of CLCA2 in cervical cancer cells suppresses EMT through inactivation of ERK/JNK/p38-MAPK signaling pathways, and inhibits proliferation, migration, invasion while promoting apoptosis both in vitro and in vivo.\",\n      \"method\": \"Ectopic overexpression, MAPK pathway inhibitor/activation assays, in vitro migration/invasion/proliferation/apoptosis assays, xenograft model\",\n      \"journal\": \"BMC molecular and cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — in vitro and in vivo gain-of-function with pathway readouts but mechanistic depth limited to MAPK signaling markers; single lab\",\n      \"pmids\": [\"36280802\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"A truncated TP63 protein (TP63-mut) binds the CLCA2 promoter and activates CLCA2 transcription more strongly than wild-type TP63; elevated CLCA2 then promotes apoptosis via the ATM pathway. siRNA silencing of CLCA2 or ATM inhibition (KU55933) attenuated apoptosis caused by TP63-mut overexpression, placing CLCA2 downstream of TP63 in an apoptosis pathway.\",\n      \"method\": \"Dual luciferase reporter assay, western blot, immunofluorescence, siRNA knockdown, ATM inhibitor rescue, cell apoptosis assay\",\n      \"journal\": \"Journal of ovarian research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reporter assay for direct promoter activation, bidirectional rescue by siRNA and pharmacological inhibition; single lab\",\n      \"pmids\": [\"38528613\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Biochemical analysis of heterologously expressed avian (chicken) CLCA2 revealed that, like mammalian CLCA2, it undergoes protein cleavage, glycosylation, and plasma membrane anchoring, and is expressed in epidermal keratinocytes across birds and mammals, establishing these as conserved canonical properties of the CLCA2 protein.\",\n      \"method\": \"Immunoblotting, immunofluorescence, immunohistochemistry, heterologous expression\",\n      \"journal\": \"PeerJ\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical characterization with multiple methods (immunoblot + immunofluorescence) across multiple species in a single study\",\n      \"pmids\": [\"36389428\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"YTHDC2 stabilizes CLCA2 mRNA through m6A-dependent mechanisms; RIP-qPCR and MeRIP-qPCR/seq demonstrated that YTHDC2 binds m6A-modified CLCA2 mRNA and promotes its stability, thereby increasing CLCA2 protein expression in colorectal cancer.\",\n      \"method\": \"RIP-qPCR, MeRIP-qPCR, MeRIP-seq, molecular docking\",\n      \"journal\": \"Journal of ethnopharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct RNA-protein interaction by RIP-qPCR and m6A mapping by MeRIP-seq; single lab, limited functional dissection of CLCA2 specifically\",\n      \"pmids\": [\"41616882\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CLCA2 is a p53/p63-inducible transmembrane protein expressed in epithelial cells (especially keratinocytes) that functions as a tumor suppressor by inhibiting EMT, migration, invasion, and promoting cellular senescence; it directly binds β4 integrin (mediating cancer cell–endothelium adhesion), interacts with EVA1/ZO-1 and β-catenin at cell junctions, activates store-operated calcium entry through physical interaction with ORAI-1 and STIM-1 thereby potentiating TMEM16A-dependent chloride currents, and is transported via extracellular vesicles to the nucleus where it activates β-catenin/Wnt signaling and RBM3; its expression is regulated transcriptionally by p53 family members and repressed by promoter hypermethylation, a CTBP1/ZEB1/HDAC complex, and miR-196b-5p.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CLCA2 is a cleaved, glycosylated, plasma-membrane-anchored transmembrane protein of epithelial cells and keratinocytes that acts as a tumor suppressor restraining migration, invasion, and epithelial-mesenchymal transition while promoting cellular senescence and stress-induced apoptosis [#1, #4, #12]. Its expression is controlled by the p53 family: p53, p73, and p63 bind a consensus site in the CLCA2 promoter and induce CLCA2 upon DNA damage, downstream of which CLCA2 restrains cell migration by limiting FAK, and a truncated TP63 variant superactivates CLCA2 to drive apoptosis through the ATM pathway [#3, #11]. CLCA2 is silenced in cancer through CpG island promoter hypermethylation, a CTBP1/ZEB1/EP300/HDAC repressor complex, and miR-196b-5p targeting of its 3'UTR, while m6A-dependent stabilization by YTHDC2 raises its expression [#2, #8, #13]. At cell-cell junctions CLCA2 partners with EVA1 and ZO-1 and forms a separate complex with β-catenin, downregulating β-catenin-activated genes and suppressing EMT, with knockdown driving EMT in mammary epithelial cells [#5]. CLCA2 also directly binds β4 integrin to mediate breast cancer cell adhesion to pulmonary endothelium [#0], and it potentiates calcium signaling by physically associating with ORAI-1 and STIM-1 to enhance store-operated calcium entry and thereby boost TMEM16A-dependent calcium-activated chloride currents [#6]. A nuclear pool of CLCA2, delivered via extracellular vesicles and dependent on an internal nuclear localization signal, binds and activates β-catenin/Wnt signaling through the effector RBM3 to suppress keratinocyte migration and protect against hyperosmotic stress [#9].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Establishing whether CLCA2 loss is functionally consequential in cancer, reintroduction defined it as a tumor suppressor.\",\n      \"evidence\": \"Stable transfection into CLCA2-negative breast cancer lines with Matrigel invasion and nude mouse xenograft readouts\",\n      \"pmids\": [\"10554024\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism of invasion suppression not defined\", \"Restricted to breast cancer models\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"To explain CLCA2's role in metastatic colonization, it was shown to mediate cancer cell adhesion to endothelium via a defined receptor.\",\n      \"evidence\": \"In vitro adhesion assays with reciprocal blocking antibodies, matrilysin cleavage, and in vivo lung colonization\",\n      \"pmids\": [\"11320086\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether endothelial-surface CLCA2 reflects its epithelial tumor-suppressive role unclear\", \"Stoichiometry and binding interface with β4 integrin not mapped\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"To explain how CLCA2 is lost in tumors, promoter hypermethylation was identified as the silencing mechanism.\",\n      \"evidence\": \"Bisulfite sequencing and demethylating-agent rescue across breast cancer cell lines and tumors\",\n      \"pmids\": [\"14973555\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Trigger initiating de novo methylation unknown\", \"Does not address non-methylation modes of loss\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Connecting CLCA2 to a master tumor-suppressor network, it was defined as a direct p53-family transcriptional target acting through FAK and senescence.\",\n      \"evidence\": \"ChIP, promoter reporter, bidirectional knockdown/overexpression, FAK inhibitor rescue, and senescence marker assays\",\n      \"pmids\": [\"22990203\", \"22431922\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How CLCA2 represses FAK transcription not mechanistically resolved\", \"Senescence pathway downstream of CLCA2 incompletely mapped\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"To define CLCA2's molecular role at junctions, it was placed in junctional complexes restraining β-catenin and EMT.\",\n      \"evidence\": \"Membrane dihybrid screen, co-IP, deletion mapping, immunofluorescence co-localization, and siRNA-induced EMT in mammary epithelial cells\",\n      \"pmids\": [\"26930581\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How the EVA1/ZO-1 and β-catenin complexes are physically coordinated unclear\", \"Mechanism linking junctional CLCA2 to β-catenin downregulation not resolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Resolving a long-standing question about CLCA proteins and chloride conductance, CLCA2 was shown to act through calcium entry rather than as a channel itself.\",\n      \"evidence\": \"Calcium imaging, co-IP with ORAI-1/STIM-1, and patch-clamp of TMEM16A-expressing HEK293 cells\",\n      \"pmids\": [\"29758025\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of ORAI-1/STIM-1 interaction unknown\", \"Link between calcium/chloride function and tumor suppression not established\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"In skin physiology, CLCA2 was placed downstream of osmotic stress signaling and shown to maintain keratinocyte survival via adhesion.\",\n      \"evidence\": \"siRNA knockdown, signaling inhibitors, organotypic culture, and apoptosis assays\",\n      \"pmids\": [\"29743348\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct ATF2 binding to the CLCA2 promoter not demonstrated\", \"Adhesion molecules mediating protection not identified\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Expanding the silencing repertoire, transcriptional repression by a CTBP1/ZEB1/HDAC complex and post-transcriptional repression by miR-196b-5p were defined.\",\n      \"evidence\": \"ChIP, promoter and 3'UTR luciferase reporters, siRNA, and prostate cancer xenograft\",\n      \"pmids\": [\"29536528\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contribution of each repressive mechanism in vivo unclear\", \"Generalizability beyond prostate cancer untested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Extending tumor suppression to other tissues, CLCA2 overexpression was shown to suppress EMT via MAPK inactivation in cervical cancer.\",\n      \"evidence\": \"Ectopic overexpression, MAPK pathway modulation, and in vitro/in vivo proliferation/migration/apoptosis assays\",\n      \"pmids\": [\"36280802\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism limited to pathway marker correlation\", \"Direct CLCA2 effector upstream of MAPK not identified\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"To define conserved biochemical features of the protein, avian CLCA2 was shown to share cleavage, glycosylation, membrane anchoring, and keratinocyte expression with mammals.\",\n      \"evidence\": \"Heterologous expression, immunoblotting, immunofluorescence, and immunohistochemistry across species\",\n      \"pmids\": [\"36389428\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional conservation of signaling roles not tested\", \"Cleavage site and protease not defined here\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Revealing an unexpected mode of action, CLCA2 was shown to traffic via extracellular vesicles to the nucleus where it activates Wnt/β-catenin through RBM3.\",\n      \"evidence\": \"Live imaging, nuclear fractionation, EV isolation, NLS-mutant analysis, MS interaction screen, co-IP, and Wnt reporter\",\n      \"pmids\": [\"38602325\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How a membrane protein enters EVs and the nucleus mechanistically unclear\", \"Apparent contradiction with junctional CLCA2 downregulating β-catenin unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"A gain-of-function TP63 variant was shown to superactivate CLCA2 to trigger ATM-dependent apoptosis, refining the p63-CLCA2 axis.\",\n      \"evidence\": \"Dual luciferase reporter, western blot, siRNA, and ATM inhibitor (KU55933) rescue in apoptosis assays\",\n      \"pmids\": [\"38528613\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How CLCA2 activates ATM signaling not defined\", \"Single-lab ovarian context\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Adding an RNA-level control, YTHDC2 was shown to stabilize CLCA2 mRNA through m6A in colorectal cancer.\",\n      \"evidence\": \"RIP-qPCR, MeRIP-qPCR/seq, and molecular docking\",\n      \"pmids\": [\"41616882\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of CLCA2 stabilization for tumor phenotype not dissected\", \"m6A site mapping on CLCA2 not resolved at nucleotide level\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how CLCA2's opposing activities — junctional β-catenin downregulation versus nuclear β-catenin/Wnt activation, and tumor suppression versus pro-adhesive metastatic roles — are reconciled within a single protein.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unified model integrating membrane, junctional, and nuclear CLCA2 pools\", \"Context-dependence across tissues not mechanistically explained\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098631\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [5, 6, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 6, 12]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [6, 9, 10]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [1, 2, 3]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [7, 11]}\n    ],\n    \"complexes\": [\n      \"CLCA2-EVA1-ZO-1 junctional complex\",\n      \"CTBP1/ZEB1/EP300/HDAC repressor complex (acts on CLCA2 promoter)\"\n    ],\n    \"partners\": [\n      \"ITGB4\",\n      \"EVA1\",\n      \"TJP1\",\n      \"CTNNB1\",\n      \"ORAI1\",\n      \"STIM1\",\n      \"TMEM16A\",\n      \"RBM3\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":6,"faith_pct":66.66666666666667}}