{"gene":"RCAN3","run_date":"2026-04-28T19:45:45","timeline":{"discoveries":[{"year":2006,"finding":"RCAN3 (DSCR1L2) protein interacts with human cardiac troponin I (TNNI3), the heart-specific inhibitory subunit of the troponin complex; exon 2 of RCAN3 is sufficient and required for this binding.","method":"Yeast two-hybrid screening of human heart cDNA library, confirmed by yeast cotransformation and GST fusion protein pulldown assay","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal yeast two-hybrid plus GST pulldown in a single lab; two orthogonal methods","pmids":["16516408"],"is_preprint":false},{"year":2007,"finding":"Multiple RCAN3 protein isoforms (including those lacking exon 3 or exon 4) all retain the ability to interact with cardiac troponin I (TNNI3), consistent with exon 2 being the key binding determinant.","method":"Yeast cotransformation and GST fusion protein assay with individual isoforms","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 — two orthogonal binding methods, single lab, replicates finding from prior paper","pmids":["18022329"],"is_preprint":false},{"year":2015,"finding":"RCAN3 inhibits tumor growth and tumor angiogenesis in an orthotopic breast cancer model via the calcineurin (CN)-NFATc pathway; mutation of the conserved CIC (calcipressin inhibitor of calcineurin) motif abolishes this tumor suppressor effect, and a peptide spanning the CIC motif (EGFP-R3(178-210)) recapitulates the full antitumor activity of RCAN3, including inhibition of CN-NFATc signaling and NFATc-dependent COX-2 induction.","method":"Orthotopic breast cancer mouse model with RCAN3 overexpression, CIC-motif point mutant, and peptide constructs; CN-NFATc reporter assays; COX-2 gene expression analysis","journal":"Carcinogenesis","confidence":"High","confidence_rationale":"Tier 2 — in vivo loss-of-function via motif mutation, peptide rescue, and pathway reporter assays; multiple orthogonal methods in single study","pmids":["25916653"],"is_preprint":false},{"year":2022,"finding":"The PxIxIT motif of RCAN3 (native sequence PSVVVH, within peptide EGFP-R3(178-210)) binds calcineurin and inhibits NFAT-mediated cytokine gene expression without affecting calcineurin phosphatase activity, and suppresses tumor growth and angiogenesis in a syngeneic immunocompetent TNBC mouse model.","method":"Orthotopic syngeneic mouse tumor model, CN binding assays, NFAT-dependent gene expression assays","journal":"Carcinogenesis","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo tumor model plus CN binding and pathway assays; single lab but replicates and extends prior finding with immunocompetent model","pmids":["35640493"],"is_preprint":false}],"current_model":"RCAN3 is an endogenous regulator of the calcineurin–NFATc pathway that binds calcineurin through its conserved PxIxIT/CIC motif to inhibit NFATc dephosphorylation and activation (without affecting calcineurin phosphatase activity), thereby suppressing NFATc-dependent gene expression (e.g., COX-2), tumor angiogenesis, and tumor growth; it also interacts with cardiac troponin I (TNNI3) via its exon 2-encoded domain, suggesting an additional role in cardiac contractile regulation."},"narrative":{"teleology":[{"year":2006,"claim":"Identification of TNNI3 as a physical partner of RCAN3 established that this RCAN family member has a role beyond calcineurin regulation, potentially in cardiac contractile function.","evidence":"Yeast two-hybrid screen of human heart cDNA library plus GST pulldown validation","pmids":["16516408"],"confidence":"Medium","gaps":["No in vivo or cellular confirmation of the RCAN3–TNNI3 interaction","Functional consequence of RCAN3 binding on troponin complex activity or cardiac contractility unknown","No structural detail of the exon 2–TNNI3 interface"]},{"year":2007,"claim":"Demonstrating that multiple RCAN3 splice isoforms all bind TNNI3 via exon 2 confirmed this domain as the necessary and sufficient binding determinant, ruling out contributions from alternatively spliced exons 3 and 4.","evidence":"Yeast cotransformation and GST pulldown with individual isoform constructs","pmids":["18022329"],"confidence":"Medium","gaps":["Findings limited to recombinant binding assays; no endogenous co-IP or co-localization data","Whether different isoforms modulate TNNI3 binding affinity quantitatively is untested","Physiological relevance in cardiomyocytes not addressed"]},{"year":2015,"claim":"Establishing that RCAN3 suppresses tumor growth and angiogenesis through its CIC motif defined the calcineurin–NFATc axis as the mechanistically essential target, and showed a minimal peptide spanning the CIC motif is sufficient for full antitumor activity.","evidence":"Orthotopic breast cancer mouse model with wild-type RCAN3, CIC-motif point mutant, and EGFP-R3(178-210) peptide; CN-NFATc reporter and COX-2 expression assays","pmids":["25916653"],"confidence":"High","gaps":["Endogenous RCAN3 loss-of-function (knockout) not tested","Whether RCAN3 competes with NFAT for the same calcineurin docking site not structurally resolved","Contribution of immune cell–intrinsic NFATc inhibition versus tumor cell–intrinsic effects not delineated"]},{"year":2022,"claim":"Replication in an immunocompetent syngeneic TNBC model confirmed that the PxIxIT motif peptide inhibits NFAT-dependent gene expression and tumor growth without blocking calcineurin phosphatase activity, separating RCAN3's mechanism from catalytic-site inhibitors like cyclosporin.","evidence":"Syngeneic orthotopic mouse tumor model, calcineurin binding assays, NFAT-dependent gene expression assays","pmids":["35640493"],"confidence":"Medium","gaps":["Single-lab replication; independent group confirmation still lacking","Effect on immune cell subsets (T cells, macrophages) within the tumor microenvironment not dissected","No structural or biophysical characterization of the RCAN3 PxIxIT–calcineurin complex"]},{"year":null,"claim":"The relationship between RCAN3's two distinct interaction interfaces — calcineurin binding via the CIC/PxIxIT motif and TNNI3 binding via exon 2 — and whether they are coordinately regulated or function independently in different tissues remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No loss-of-function genetic model (knockout mouse or CRISPR cell line) for RCAN3 exists","Structural basis for calcineurin or TNNI3 binding not determined","Tissue-specific expression and isoform usage under physiological conditions poorly characterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,3]}],"localization":[],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,3]}],"complexes":[],"partners":["TNNI3","PPP3CA"],"other_free_text":[]},"mechanistic_narrative":"RCAN3 is an endogenous inhibitor of the calcineurin–NFATc signaling axis that binds calcineurin through its conserved CIC/PxIxIT motif (PSVVVH) to block NFATc dephosphorylation and nuclear translocation without affecting calcineurin phosphatase activity, thereby suppressing NFATc-dependent gene expression including COX-2; mutation of the CIC motif abolishes this inhibitory function, and a minimal peptide spanning the motif recapitulates full antitumor and anti-angiogenic activity in orthotopic breast cancer models [PMID:25916653, PMID:35640493]. RCAN3 also interacts with cardiac troponin I (TNNI3) through its exon 2-encoded domain, with all tested splice isoforms retaining this binding capacity, indicating a second functional interface distinct from the calcineurin-binding region [PMID:16516408, PMID:18022329]."},"prefetch_data":{"uniprot":{"accession":"Q9UKA8","full_name":"Calcipressin-3","aliases":["Down syndrome candidate region 1-like protein 2","Myocyte-enriched calcineurin-interacting protein 3","MCIP3","Regulator of calcineurin 3"],"length_aa":241,"mass_kda":27.5,"function":"Inhibits calcineurin-dependent transcriptional responses by binding to the catalytic domain of calcineurin A. Could play a role during central nervous system development (By similarity)","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q9UKA8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RCAN3","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/RCAN3","total_profiled":1310},"omim":[{"mim_id":"605860","title":"RCAN FAMILY MEMBER 3; RCAN3","url":"https://www.omim.org/entry/605860"},{"mim_id":"602917","title":"REGULATOR OF CALCINEURIN 1; RCAN1","url":"https://www.omim.org/entry/602917"},{"mim_id":"191044","title":"TROPONIN I, CARDIAC; TNNI3","url":"https://www.omim.org/entry/191044"},{"mim_id":"114105","title":"PROTEIN PHOSPHATASE 3, CATALYTIC SUBUNIT, ALPHA ISOFORM; PPP3CA","url":"https://www.omim.org/entry/114105"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nuclear speckles","reliability":"Approved"},{"location":"Nucleoli fibrillar center","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"prostate","ntpm":31.7}],"url":"https://www.proteinatlas.org/search/RCAN3"},"hgnc":{"alias_symbol":[],"prev_symbol":["DSCR1L2"]},"alphafold":{"accession":"Q9UKA8","domains":[{"cath_id":"3.30.70.330","chopping":"47-120","consensus_level":"high","plddt":94.0378,"start":47,"end":120}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UKA8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UKA8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UKA8-F1-predicted_aligned_error_v6.png","plddt_mean":74.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RCAN3","jax_strain_url":"https://www.jax.org/strain/search?query=RCAN3"},"sequence":{"accession":"Q9UKA8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UKA8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UKA8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UKA8"}},"corpus_meta":[{"pmid":"10756093","id":"PMC_10756093","title":"A new gene family including DSCR1 (Down Syndrome Candidate Region 1) and ZAKI-4: characterization from yeast to human and identification of DSCR1-like 2, a novel human member (DSCR1L2).","date":"2000","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/10756093","citation_count":67,"is_preprint":false},{"pmid":"25916653","id":"PMC_25916653","title":"A novel role for an RCAN3-derived peptide as a tumor suppressor in breast cancer.","date":"2015","source":"Carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/25916653","citation_count":17,"is_preprint":false},{"pmid":"16516408","id":"PMC_16516408","title":"Proteins encoded by human Down syndrome critical region gene 1-like 2 (DSCR1L2) mRNA and by a novel DSCR1L2 mRNA isoform interact with cardiac troponin I (TNNI3).","date":"2006","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/16516408","citation_count":15,"is_preprint":false},{"pmid":"21961037","id":"PMC_21961037","title":"Complexity of bidirectional transcription and alternative splicing at human RCAN3 locus.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21961037","citation_count":12,"is_preprint":false},{"pmid":"18022329","id":"PMC_18022329","title":"Identification and analysis of human RCAN3 (DSCR1L2) mRNA and protein isoforms.","date":"2007","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/18022329","citation_count":12,"is_preprint":false},{"pmid":"32345470","id":"PMC_32345470","title":"Functional implications of miR-145/RCAN3 axis in the progression of cervical cancer.","date":"2020","source":"Reproductive biology","url":"https://pubmed.ncbi.nlm.nih.gov/32345470","citation_count":4,"is_preprint":false},{"pmid":"35640493","id":"PMC_35640493","title":"The PxIxIT motif of the RCAN3 inhibits angiogenesis and tumor progression in Triple Negative breast cancer in immunocompetent mice.","date":"2022","source":"Carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/35640493","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.03.15.643421","title":"Spatial single-cell interactome and niche-specific molecular signatures in alcohol-related liver disease","date":"2025-03-17","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.15.643421","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6203,"output_tokens":1074,"usd":0.017359},"stage2":{"model":"claude-opus-4-6","input_tokens":4276,"output_tokens":1492,"usd":0.08802},"total_usd":0.105379,"stage1_batch_id":"msgbatch_01SUR8NDzVrNmyszWyJeCct7","stage2_batch_id":"msgbatch_01G7Yfutko3cDWzejrwH5AMx","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2006,\n      \"finding\": \"RCAN3 (DSCR1L2) protein interacts with human cardiac troponin I (TNNI3), the heart-specific inhibitory subunit of the troponin complex; exon 2 of RCAN3 is sufficient and required for this binding.\",\n      \"method\": \"Yeast two-hybrid screening of human heart cDNA library, confirmed by yeast cotransformation and GST fusion protein pulldown assay\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal yeast two-hybrid plus GST pulldown in a single lab; two orthogonal methods\",\n      \"pmids\": [\"16516408\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Multiple RCAN3 protein isoforms (including those lacking exon 3 or exon 4) all retain the ability to interact with cardiac troponin I (TNNI3), consistent with exon 2 being the key binding determinant.\",\n      \"method\": \"Yeast cotransformation and GST fusion protein assay with individual isoforms\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — two orthogonal binding methods, single lab, replicates finding from prior paper\",\n      \"pmids\": [\"18022329\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"RCAN3 inhibits tumor growth and tumor angiogenesis in an orthotopic breast cancer model via the calcineurin (CN)-NFATc pathway; mutation of the conserved CIC (calcipressin inhibitor of calcineurin) motif abolishes this tumor suppressor effect, and a peptide spanning the CIC motif (EGFP-R3(178-210)) recapitulates the full antitumor activity of RCAN3, including inhibition of CN-NFATc signaling and NFATc-dependent COX-2 induction.\",\n      \"method\": \"Orthotopic breast cancer mouse model with RCAN3 overexpression, CIC-motif point mutant, and peptide constructs; CN-NFATc reporter assays; COX-2 gene expression analysis\",\n      \"journal\": \"Carcinogenesis\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo loss-of-function via motif mutation, peptide rescue, and pathway reporter assays; multiple orthogonal methods in single study\",\n      \"pmids\": [\"25916653\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The PxIxIT motif of RCAN3 (native sequence PSVVVH, within peptide EGFP-R3(178-210)) binds calcineurin and inhibits NFAT-mediated cytokine gene expression without affecting calcineurin phosphatase activity, and suppresses tumor growth and angiogenesis in a syngeneic immunocompetent TNBC mouse model.\",\n      \"method\": \"Orthotopic syngeneic mouse tumor model, CN binding assays, NFAT-dependent gene expression assays\",\n      \"journal\": \"Carcinogenesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo tumor model plus CN binding and pathway assays; single lab but replicates and extends prior finding with immunocompetent model\",\n      \"pmids\": [\"35640493\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RCAN3 is an endogenous regulator of the calcineurin–NFATc pathway that binds calcineurin through its conserved PxIxIT/CIC motif to inhibit NFATc dephosphorylation and activation (without affecting calcineurin phosphatase activity), thereby suppressing NFATc-dependent gene expression (e.g., COX-2), tumor angiogenesis, and tumor growth; it also interacts with cardiac troponin I (TNNI3) via its exon 2-encoded domain, suggesting an additional role in cardiac contractile regulation.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"RCAN3 is an endogenous inhibitor of the calcineurin–NFATc signaling axis that binds calcineurin through its conserved CIC/PxIxIT motif (PSVVVH) to block NFATc dephosphorylation and nuclear translocation without affecting calcineurin phosphatase activity, thereby suppressing NFATc-dependent gene expression including COX-2; mutation of the CIC motif abolishes this inhibitory function, and a minimal peptide spanning the motif recapitulates full antitumor and anti-angiogenic activity in orthotopic breast cancer models [PMID:25916653, PMID:35640493]. RCAN3 also interacts with cardiac troponin I (TNNI3) through its exon 2-encoded domain, with all tested splice isoforms retaining this binding capacity, indicating a second functional interface distinct from the calcineurin-binding region [PMID:16516408, PMID:18022329].\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Identification of TNNI3 as a physical partner of RCAN3 established that this RCAN family member has a role beyond calcineurin regulation, potentially in cardiac contractile function.\",\n      \"evidence\": \"Yeast two-hybrid screen of human heart cDNA library plus GST pulldown validation\",\n      \"pmids\": [\"16516408\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No in vivo or cellular confirmation of the RCAN3–TNNI3 interaction\",\n        \"Functional consequence of RCAN3 binding on troponin complex activity or cardiac contractility unknown\",\n        \"No structural detail of the exon 2–TNNI3 interface\"\n      ]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Demonstrating that multiple RCAN3 splice isoforms all bind TNNI3 via exon 2 confirmed this domain as the necessary and sufficient binding determinant, ruling out contributions from alternatively spliced exons 3 and 4.\",\n      \"evidence\": \"Yeast cotransformation and GST pulldown with individual isoform constructs\",\n      \"pmids\": [\"18022329\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Findings limited to recombinant binding assays; no endogenous co-IP or co-localization data\",\n        \"Whether different isoforms modulate TNNI3 binding affinity quantitatively is untested\",\n        \"Physiological relevance in cardiomyocytes not addressed\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Establishing that RCAN3 suppresses tumor growth and angiogenesis through its CIC motif defined the calcineurin–NFATc axis as the mechanistically essential target, and showed a minimal peptide spanning the CIC motif is sufficient for full antitumor activity.\",\n      \"evidence\": \"Orthotopic breast cancer mouse model with wild-type RCAN3, CIC-motif point mutant, and EGFP-R3(178-210) peptide; CN-NFATc reporter and COX-2 expression assays\",\n      \"pmids\": [\"25916653\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Endogenous RCAN3 loss-of-function (knockout) not tested\",\n        \"Whether RCAN3 competes with NFAT for the same calcineurin docking site not structurally resolved\",\n        \"Contribution of immune cell–intrinsic NFATc inhibition versus tumor cell–intrinsic effects not delineated\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Replication in an immunocompetent syngeneic TNBC model confirmed that the PxIxIT motif peptide inhibits NFAT-dependent gene expression and tumor growth without blocking calcineurin phosphatase activity, separating RCAN3's mechanism from catalytic-site inhibitors like cyclosporin.\",\n      \"evidence\": \"Syngeneic orthotopic mouse tumor model, calcineurin binding assays, NFAT-dependent gene expression assays\",\n      \"pmids\": [\"35640493\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-lab replication; independent group confirmation still lacking\",\n        \"Effect on immune cell subsets (T cells, macrophages) within the tumor microenvironment not dissected\",\n        \"No structural or biophysical characterization of the RCAN3 PxIxIT–calcineurin complex\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The relationship between RCAN3's two distinct interaction interfaces — calcineurin binding via the CIC/PxIxIT motif and TNNI3 binding via exon 2 — and whether they are coordinately regulated or function independently in different tissues remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No loss-of-function genetic model (knockout mouse or CRISPR cell line) for RCAN3 exists\",\n        \"Structural basis for calcineurin or TNNI3 binding not determined\",\n        \"Tissue-specific expression and isoform usage under physiological conditions poorly characterized\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0098772\",\n        \"supporting_discovery_ids\": [2, 3]\n      }\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\n        \"term_id\": \"R-HSA-162582\",\n        \"supporting_discovery_ids\": [2, 3]\n      }\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"TNNI3\",\n      \"PPP3CA\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}