Affinage

CLCA2

Calcium-activated chloride channel regulator 2 · UniProt Q9UQC9

Length
943 aa
Mass
103.9 kDa
Annotated
2026-06-09
25 papers in source corpus 14 papers cited in narrative 14 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 4/6 claims corpus-supported (67%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

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).

Mechanistic history

Synthesis pass · year-by-year structured walk · 13 steps
  1. 1999 High

    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

    PMID:10554024

    Open questions at the time
    • Molecular mechanism of invasion suppression not defined
    • Restricted to breast cancer models
  2. 2001 High

    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

    PMID:11320086

    Open questions at the time
    • Whether endothelial-surface CLCA2 reflects its epithelial tumor-suppressive role unclear
    • Stoichiometry and binding interface with β4 integrin not mapped
  3. 2004 High

    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

    PMID:14973555

    Open questions at the time
    • Trigger initiating de novo methylation unknown
    • Does not address non-methylation modes of loss
  4. 2012 High

    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

    PMID:22431922 PMID:22990203

    Open questions at the time
    • How CLCA2 represses FAK transcription not mechanistically resolved
    • Senescence pathway downstream of CLCA2 incompletely mapped
  5. 2016 High

    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

    PMID:26930581

    Open questions at the time
    • How the EVA1/ZO-1 and β-catenin complexes are physically coordinated unclear
    • Mechanism linking junctional CLCA2 to β-catenin downregulation not resolved
  6. 2018 High

    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

    PMID:29758025

    Open questions at the time
    • Structural basis of ORAI-1/STIM-1 interaction unknown
    • Link between calcium/chloride function and tumor suppression not established
  7. 2018 Medium

    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

    PMID:29743348

    Open questions at the time
    • Direct ATF2 binding to the CLCA2 promoter not demonstrated
    • Adhesion molecules mediating protection not identified
  8. 2018 High

    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

    PMID:29536528

    Open questions at the time
    • Relative contribution of each repressive mechanism in vivo unclear
    • Generalizability beyond prostate cancer untested
  9. 2022 Medium

    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

    PMID:36280802

    Open questions at the time
    • Mechanism limited to pathway marker correlation
    • Direct CLCA2 effector upstream of MAPK not identified
  10. 2022 Medium

    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

    PMID:36389428

    Open questions at the time
    • Functional conservation of signaling roles not tested
    • Cleavage site and protease not defined here
  11. 2024 High

    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

    PMID:38602325

    Open questions at the time
    • How a membrane protein enters EVs and the nucleus mechanistically unclear
    • Apparent contradiction with junctional CLCA2 downregulating β-catenin unresolved
  12. 2024 Medium

    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

    PMID:38528613

    Open questions at the time
    • How CLCA2 activates ATM signaling not defined
    • Single-lab ovarian context
  13. 2026 Medium

    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

    PMID:41616882

    Open questions at the time
    • Functional consequence of CLCA2 stabilization for tumor phenotype not dissected
    • m6A site mapping on CLCA2 not resolved at nucleotide level

Open questions

Synthesis pass · forward-looking unresolved questions
  • 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.
  • No unified model integrating membrane, junctional, and nuclear CLCA2 pools
  • Context-dependence across tissues not mechanistically explained

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 3 GO:0060089 molecular transducer activity 1 GO:0098631 cell adhesion mediator activity 1
Localization
GO:0005886 plasma membrane 3 GO:0005634 nucleus 1 GO:0031410 cytoplasmic vesicle 1
Pathway
R-HSA-162582 Signal Transduction 3 R-HSA-1643685 Disease 3 R-HSA-5357801 Programmed Cell Death 2
Partners
CTNNB1EVA1ITGB4ORAI1RBM3STIM1TJP1TMEM16A
Complex memberships
CLCA2-EVA1-ZO-1 junctional complexCTBP1/ZEB1/EP300/HDAC repressor complex (acts on CLCA2 promoter)

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2001 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. In vitro cell adhesion assay, antibody-blocking experiments, matrilysin cleavage, in vivo lung colonization model The Journal of biological chemistry High 11320086
1999 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. Stable transfection, Matrigel invasion assay, nude mouse xenograft model Cancer research High 10554024
2004 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. Bisulfite sequencing, demethylating agent treatment, RT-PCR expression analysis Oncogene High 14973555
2012 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. Promoter reporter assay, ChIP, siRNA knockdown, ectopic expression, FAK inhibitor rescue, migration/invasion assays Cancer biology & therapy High 22990203
2012 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. Genome-wide expression screening, siRNA knockdown, ectopic expression, senescence markers assay (SA-β-gal and others) Neoplasia (New York, N.Y.) Medium 22431922
2016 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. Membrane dihybrid screening, co-immunoprecipitation, deletion analysis, co-localization by immunofluorescence, siRNA knockdown, gene expression analysis PloS one High 26930581
2018 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. Calcium imaging, co-immunoprecipitation, whole-cell patch-clamp electrophysiology in HEK293 cells stably expressing TMEM16A PloS one High 29758025
2018 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. siRNA knockdown, signaling inhibitor experiments, organotypic skin culture, apoptosis assay Science translational medicine Medium 29743348
2018 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. ChIP, promoter reporter assay, luciferase 3′UTR reporter assay, siRNA knockdown, miRNA microarray International journal of cancer High 29536528
2024 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. Live-cell imaging, nuclear fractionation, extracellular vesicle isolation, NLS-mutant analysis, mass-spectrometry interaction screen, co-immunoprecipitation, functional rescue experiments, Wnt reporter assay Journal of extracellular vesicles High 38602325
2022 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. Ectopic overexpression, MAPK pathway inhibitor/activation assays, in vitro migration/invasion/proliferation/apoptosis assays, xenograft model BMC molecular and cell biology Medium 36280802
2024 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. Dual luciferase reporter assay, western blot, immunofluorescence, siRNA knockdown, ATM inhibitor rescue, cell apoptosis assay Journal of ovarian research Medium 38528613
2022 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. Immunoblotting, immunofluorescence, immunohistochemistry, heterologous expression PeerJ Medium 36389428
2026 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. RIP-qPCR, MeRIP-qPCR, MeRIP-seq, molecular docking Journal of ethnopharmacology Medium 41616882

Source papers

Stage 0 corpus · 25 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2001 The breast cancer beta 4 integrin and endothelial human CLCA2 mediate lung metastasis. The Journal of biological chemistry 110 11320086
1999 Tumorigenicity of human breast cancer is associated with loss of the Ca2+-activated chloride channel CLCA2. Cancer research 80 10554024
2001 Expression of the Ca2+-activated chloride channel genes CLCA1 and CLCA2 is downregulated in human colorectal cancer. DNA and cell biology 79 11445004
1985 Cl-/Ca2+-dependent L-glutamate binding sites do not correspond to 2-amino-4-phosphonobutanoate-sensitive excitatory amino acid receptors. British journal of pharmacology 55 2998527
2012 CLCA2, a target of the p53 family, negatively regulates cancer cell migration and invasion. Cancer biology & therapy 53 22990203
2004 CLCA2 tumour suppressor gene in 1p31 is epigenetically regulated in breast cancer. Oncogene 46 14973555
2012 CLCA2 as a p53-inducible senescence mediator. Neoplasia (New York, N.Y.) 36 22431922
2016 CLCA2 Interactor EVA1 Is Required for Mammary Epithelial Cell Differentiation. PloS one 33 26930581
2018 CLCA2 is a positive regulator of store-operated calcium entry and TMEM16A. PloS one 31 29758025
2018 CLCA2 epigenetic regulation by CTBP1, HDACs, ZEB1, EP300 and miR-196b-5p impacts prostate cancer cell adhesion and EMT in metabolic syndrome disease. International journal of cancer 29 29536528
2018 Humidity-regulated CLCA2 protects the epidermis from hyperosmotic stress. Science translational medicine 29 29743348
1986 Identification of a Cl-/Ca2+-dependent glutamate (quisqualate) binding site in bovine pineal organ. Journal of pineal research 28 3534213
2014 CLCA2 as a novel immunohistochemical marker for differential diagnosis of squamous cell carcinoma from adenocarcinoma of the lung. Disease markers 21 25548429
1983 Regional distribution and ionic requirement of Cl-/Ca2+-activated and Cl-/Ca2+-independent glutamate receptors in rat brain. Brain research 20 6315142
2020 CLCA2 expression is associated with survival among African American women with triple negative breast cancer. PloS one 11 32298355
2010 CLCA2, a novel RUNX1 partner gene in a therapy-related leukemia with t(1;21)(p22;q22). Cancer genetics and cytogenetics 9 20875871
2022 CLCA2 overexpression suppresses epithelial-to-mesenchymal transition in cervical cancer cells through inactivation of ERK/JNK/p38-MAPK signaling pathways. BMC molecular and cell biology 8 36280802
2024 Transport of CLCA2 to the nucleus by extracellular vesicles controls keratinocyte survival and migration. Journal of extracellular vesicles 6 38602325
2019 A newly identified missense mutation in CLCA2 is associated with autosomal dominant cardiac conduction block. Gene 6 31326550
2024 TP63 truncating mutation causes increased cell apoptosis and premature ovarian insufficiency by enhanced transcriptional activation of CLCA2. Journal of ovarian research 5 38528613
2021 CLCA2 suppresses the proliferation, migration and invasion of cervical cancer. Experimental and therapeutic medicine 5 34055075
2024 CLCA2: A Potential Guardian against Premature Senescence and Skin Aging. Biomedicines 3 38540205
2022 Genomic, biochemical and expressional properties reveal strong conservation of the CLCA2 gene in birds and mammals. PeerJ 1 36389428
2026 Fuzheng Shengbai decoction enhances antitumor immunity via YTHDC2-dependent stabilization of CLCA2 mRNA in colorectal cancer. Journal of ethnopharmacology 0 41616882
2024 Expression of Survivin, CK7, ASH1, HMGB3, L587S, and CLCA2 in Peripheral Blood of Lung Cancer Patients by Real-Time Polymerase Chain Reaction. Cureus 0 39130876

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