{"gene":"CCNY","run_date":"2026-06-09T22:57:17","timeline":{"discoveries":[{"year":2019,"finding":"CDK16/CCNY complex phosphorylates PRC1 (regulator of cytokinesis 1) at Thr481; specific inhibition of CDK16 (using analog-sensitive CDK16 generated by CRISPR-Cas9) induces PRC1 dephosphorylation at Thr481 and delocalization to the nucleus during interphase. Epistasis experiments showed CDK16 inhibition and PRC1 downregulation act through a single pathway for cell viability, identifying PRC1 as the first substrate of the CDK16/CCNY complex.","method":"Analog-sensitive CDK16 (CRISPR-Cas9 mutagenesis), complementary proteomic approaches for substrate identification, epistasis analysis of cell viability","journal":"Experimental & molecular medicine","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — chemical-genetic (analog-sensitive kinase) plus proteomics plus epistasis in one study, multiple orthogonal methods establishing substrate and pathway position","pmids":["30992425"],"is_preprint":false},{"year":2015,"finding":"CCNY (Cyclin Y) interacts with CDK16, and this interaction mutually stabilizes both proteins and increases CDK16 kinase activity. Phosphorylation sites on the N-terminal region of CDK16 (identified by mass spectrometry) are indispensable for CCNYL1 (not CCNY) binding and modulation of CDK16 kinase activity. Notably, Ccny knockout mice displayed normal fertility, indicating CCNY is dispensable for spermatogenesis (in contrast to CCNYL1).","method":"Co-immunoprecipitation, mass spectrometry (phosphorylation site mapping), Ccny knockout mouse model (fertility assay), kinase activity assay","journal":"PLoS genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal protein interaction data and kinase activity assay for CDK16/CCNY complex, confirmed by knockout model, single lab with multiple orthogonal methods","pmids":["26305884"],"is_preprint":false},{"year":2010,"finding":"Lentivirus-mediated RNAi knockdown of CCNY in glioma cells inhibited cell proliferation, colony formation, and cell cycle progression, establishing a role for CCNY in promoting glioma cell cycle progression.","method":"Lentivirus-mediated RNAi knockdown, cell proliferation assay, colony formation assay, cell cycle analysis","journal":"Oncology research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single knockdown approach with phenotypic readout but no pathway placement","pmids":["20441050"],"is_preprint":false},{"year":2018,"finding":"Fisetin decreases TET1 expression and reduces 5-hydroxymethylcytosine (5hmC) modification at CpG islands in the promoters of CCNY and CDK16 in renal cancer stem cells, thereby reducing CCNY and CDK16 transcription and activity, causing cell cycle arrest.","method":"ChIP-PCR (5hmC at CCNY promoter CpG islands), in vivo and in vitro proliferation/invasion assays, TET1 expression analysis","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP-PCR directly shows epigenetic regulation of CCNY promoter, supported by in vivo and in vitro experiments, single lab","pmids":["30411496"],"is_preprint":false},{"year":2020,"finding":"CCNY promotes cell proliferation in laryngeal carcinoma (Hep2) cells via activation of MEK/ERK signaling and upregulation of cyclin E protein. CCNY knockout (CRISPR/Cas9) reduced phospho-MEK, phospho-ERK, and cyclin E levels, while CCNY overexpression increased them, with corresponding changes in G1-phase cell cycle distribution.","method":"CRISPR/Cas9 knockout and overexpression, Western blot (MEK/ERK phosphorylation, cyclin E), flow cytometry (cell cycle), MTS/colony formation assays","journal":"Cancer management and research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR knockout and overexpression with Western blot pathway readout, single lab, multiple cellular assays","pmids":["32606977"],"is_preprint":false},{"year":2020,"finding":"Ccny knockout mice are more susceptible to kainic acid-induced epilepsy than wild-type mice, and CCNY levels regulate expression of numerous epilepsy-associated genes (e.g., Chrna4, Gabrd, Nhlrc1, Reln) in hippocampal neurons. CCNY is highly expressed in terminally differentiated neurons and acts as a postsynaptic protein with an inhibitory role in long-term potentiation.","method":"Ccny knockout mouse model, kainic acid epilepsy model, RNA-sequencing of hippocampal neurons overexpressing or depleting CCNY, mRNA/protein validation of epilepsy-associated genes","journal":"Pharmacological research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — knockout mouse with defined seizure phenotype and transcriptomic mechanism, single lab, RNA-seq plus in vivo model","pmids":["32739426"],"is_preprint":false},{"year":2021,"finding":"Conditional knockout of Ccny in intestinal epithelial cells (IECs) did not affect cell proliferation, Wnt/β-catenin signaling, autophagy, or disease activity in the DSS colitis model. CDK14 (cyclin-Y-associated CDK) expression was found to be exceedingly low specifically in IECs, providing a mechanistic explanation for why CCNY is dispensable in this cell type.","method":"Conditional (epithelial-specific) Ccny knockout mouse, DSS colitis model, in vitro IEC loss-of-function (Wnt signaling, proliferation, autophagy assays), CDK14 expression analysis","journal":"Cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional knockout with multiple functional readouts; NEGATIVE result: CCNY dispensable in IECs due to low CDK14; single lab","pmids":["34571979"],"is_preprint":false},{"year":2025,"finding":"CCNY promotes PRC1 phosphorylation in NSCLC cells; silencing CCNY reduced cell growth, impaired spindle formation, induced G2/M arrest, and increased multi-nucleated cells. Separately, TET2 demethylates and activates PRC1 transcription by interacting with BACH1. These represent two independent regulatory axes (CCNY-mediated phosphorylation and TET2-BACH1-driven transcription) converging on PRC1.","method":"Genetic knockdown and pharmaceutical inhibition (CCNY, TET2, BACH1), subcutaneous xenograft and orthotopic isograft models, cell cycle analysis, spindle formation assay, tissue microarray, Western blot, qPCR","journal":"Journal of experimental & clinical cancer research : CR","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with multiple cellular and in vivo phenotypic readouts, single lab, several orthogonal methods","pmids":["40665337"],"is_preprint":false}],"current_model":"CCNY (Cyclin Y) functions as a regulatory cyclin that forms an active complex with CDK16 to phosphorylate substrates including PRC1 at Thr481 (promoting cell division and cytoskeletal organization), activates MEK/ERK/cyclin E signaling to drive cell cycle progression, is itself transcriptionally regulated by TET1/TET2-mediated epigenetic (5hmC) modifications at its promoter, and acts as a postsynaptic protein in neurons where it inhibits long-term potentiation and protects against epilepsy—with its activity in any given cell type dependent on the co-expression of appropriate CDK partners."},"narrative":{"mechanistic_narrative":"CCNY (Cyclin Y) is a regulatory cyclin that controls cell cycle progression and cytoskeletal organization by activating cyclin-dependent kinase partners, with its functional output dictated by the cell-type-specific availability of those partners [PMID:26305884, PMID:34571979]. CCNY binds CDK16 in a mutually stabilizing interaction that elevates CDK16 kinase activity [PMID:26305884], and the CDK16/CCNY complex phosphorylates PRC1 at Thr481 — the first identified substrate of this complex — to maintain PRC1 at its proper subcellular location during interphase and support cell viability [PMID:30992425]. This phosphoregulatory axis governs mitotic fidelity: in NSCLC cells, loss of CCNY reduces PRC1 phosphorylation, impairs spindle formation, induces G2/M arrest, and produces multinucleated cells [PMID:40665337]. CCNY also promotes G1-phase progression and proliferation in laryngeal carcinoma cells through activation of MEK/ERK signaling and upregulation of cyclin E [PMID:32606977], and its knockdown arrests glioma cell cycle progression [PMID:20441050]. CCNY itself is transcriptionally regulated by TET1-mediated 5-hydroxymethylcytosine modification at its promoter CpG islands, linking epigenetic control to its expression in cancer stem cells [PMID:30411496]. In terminally differentiated neurons, CCNY is a postsynaptic protein that inhibits long-term potentiation and protects against kainic-acid-induced epilepsy by regulating epilepsy-associated gene expression in hippocampal neurons [PMID:32739426]. CCNY is dispensable in tissues lacking its CDK partners — it is not required for spermatogenesis [PMID:26305884] nor for intestinal epithelial proliferation, the latter explained by very low CDK14 expression in those cells [PMID:34571979].","teleology":[{"year":2010,"claim":"Established a cellular requirement for CCNY in driving cancer cell proliferation, before any molecular mechanism was known.","evidence":"Lentiviral RNAi knockdown of CCNY in glioma cells with proliferation, colony formation, and cell cycle readouts","pmids":["20441050"],"confidence":"Low","gaps":["Single knockdown approach with no pathway placement","No CDK partner or substrate identified","Off-target RNAi effects not excluded"]},{"year":2015,"claim":"Defined CCNY's biochemical mode of action by showing it binds and activates CDK16, while genetics revealed it is dispensable in some tissues.","evidence":"Co-IP, mass spectrometry phosphosite mapping, kinase activity assays, and Ccny knockout mouse fertility analysis","pmids":["26305884"],"confidence":"Medium","gaps":["No substrate of the activated CDK16/CCNY complex identified","Functional consequences of CDK16 activation in vivo not established","Distinction from paralog CCNYL1 leaves CCNY-specific roles incompletely mapped"]},{"year":2018,"claim":"Identified an upstream layer controlling CCNY abundance, linking epigenetic 5hmC marks to its transcription in cancer stem cells.","evidence":"ChIP-PCR for 5hmC at CCNY promoter CpG islands plus TET1 modulation and proliferation assays in renal cancer stem cells","pmids":["30411496"],"confidence":"Medium","gaps":["Direct demonstration that TET1 binds the CCNY promoter not shown","Generality beyond cancer stem cells unknown","Effect mediated by a small-molecule (fisetin) rather than genetic TET1 perturbation"]},{"year":2019,"claim":"Named the first substrate of the CDK16/CCNY complex and placed it in a single pathway controlling cell viability.","evidence":"Analog-sensitive CDK16 (CRISPR-Cas9), proteomics for substrate identification, and epistasis analysis of viability","pmids":["30992425"],"confidence":"High","gaps":["Direct requirement of CCNY (vs CDK16 alone) for PRC1 phosphorylation not isolated in this study","Broader substrate repertoire not defined","Structural basis of PRC1 Thr481 recognition unknown"]},{"year":2020,"claim":"Extended CCNY function to a CDK-independent-framed proliferative pathway (MEK/ERK/cyclin E) and revealed a distinct neuronal, postsynaptic role.","evidence":"CRISPR knockout/overexpression with MEK/ERK/cyclin E Western blots in laryngeal carcinoma; Ccny knockout mice with kainic acid epilepsy model and hippocampal RNA-seq","pmids":["32606977","32739426"],"confidence":"Medium","gaps":["Mechanistic link between CCNY and MEK/ERK activation not resolved","Whether neuronal CCNY acts via a CDK partner not established","Direct targets among epilepsy-associated genes not distinguished from secondary effects"]},{"year":2021,"claim":"Demonstrated that CCNY function is gated by co-expression of its CDK partner, explaining tissue-specific dispensability.","evidence":"Epithelial-specific conditional Ccny knockout, DSS colitis model, Wnt/proliferation/autophagy assays, and CDK14 expression analysis in IECs","pmids":["34571979"],"confidence":"Medium","gaps":["Negative result; does not exclude CCNY function in other intestinal contexts","CDK14-CCNY complex activity in cells with normal CDK14 not directly tested here","Compensation by paralogs not formally excluded"]},{"year":2025,"claim":"Consolidated CCNY's role in mitotic fidelity via PRC1 phosphorylation and showed PRC1 is also independently controlled transcriptionally.","evidence":"CCNY knockdown/inhibition with spindle, cell-cycle, and multinucleation readouts plus xenograft/isograft models in NSCLC; TET2-BACH1 transcriptional axis on PRC1","pmids":["40665337"],"confidence":"Medium","gaps":["Whether the CCNY-PRC1 axis here is CDK16-dependent not directly shown","Relative contributions of phosphorylation vs transcription to PRC1 output not quantified","Single-lab in vivo models"]},{"year":null,"claim":"How a single cyclin is partitioned among distinct CDK partners (CDK16, CDK14) and CDK-independent signaling outputs across proliferating, epithelial, and neuronal cell types remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of CCNY-CDK complexes in the corpus","Mechanism linking CCNY to MEK/ERK activation unknown","Full substrate repertoire beyond PRC1 uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[5]}],"pathway":[{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0,4,7]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[4]}],"complexes":["CDK16/CCNY complex"],"partners":["CDK16","CDK14"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8ND76","full_name":"Cyclin-Y","aliases":["Cyclin box protein 1","Cyclin fold protein 1","cyclin-X"],"length_aa":341,"mass_kda":39.3,"function":"Positive regulatory subunit of the cyclin-dependent kinases CDK14/PFTK1 and CDK16. Acts as a cell-cycle regulator of Wnt signaling pathway during G2/M phase by recruiting CDK14/PFTK1 to the plasma membrane and promoting phosphorylation of LRP6, leading to the activation of the Wnt signaling pathway. Recruits CDK16 to the plasma membrane. Isoform 3 might play a role in the activation of MYC-mediated transcription","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q8ND76/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CCNY","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/CCNY","total_profiled":1310},"omim":[{"mim_id":"620559","title":"CYCLIN Y-LIKE 1; CCNYL1","url":"https://www.omim.org/entry/620559"},{"mim_id":"620059","title":"LONG INTERGENIC NONCODING RNA 472; LINC00472","url":"https://www.omim.org/entry/620059"},{"mim_id":"612786","title":"CYCLIN Y; CCNY","url":"https://www.omim.org/entry/612786"},{"mim_id":"266600","title":"INFLAMMATORY BOWEL DISEASE (CROHN DISEASE) 1; IBD1","url":"https://www.omim.org/entry/266600"},{"mim_id":"222100","title":"TYPE 1 DIABETES MELLITUS; T1D","url":"https://www.omim.org/entry/222100"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nucleoli","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CCNY"},"hgnc":{"alias_symbol":["CFP1","CBCP1"],"prev_symbol":["C10orf9"]},"alphafold":{"accession":"Q8ND76","domains":[{"cath_id":"1.10.472.10","chopping":"114-284","consensus_level":"high","plddt":93.3675,"start":114,"end":284}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8ND76","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8ND76-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8ND76-F1-predicted_aligned_error_v6.png","plddt_mean":78.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CCNY","jax_strain_url":"https://www.jax.org/strain/search?query=CCNY"},"sequence":{"accession":"Q8ND76","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8ND76.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8ND76/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8ND76"}},"corpus_meta":[{"pmid":"30411496","id":"PMC_30411496","title":"Fisetin decreases TET1 activity and CCNY/CDK16 promoter 5hmC levels to inhibit the proliferation and invasion of renal cancer stem cell.","date":"2018","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/30411496","citation_count":47,"is_preprint":false},{"pmid":"26305884","id":"PMC_26305884","title":"CCNYL1, but Not CCNY, Cooperates with CDK16 to Regulate Spermatogenesis in Mouse.","date":"2015","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/26305884","citation_count":46,"is_preprint":false},{"pmid":"20441050","id":"PMC_20441050","title":"Lentivirus-mediated knockdown of cyclin Y (CCNY) inhibits glioma cell proliferation.","date":"2010","source":"Oncology research","url":"https://pubmed.ncbi.nlm.nih.gov/20441050","citation_count":35,"is_preprint":false},{"pmid":"30992425","id":"PMC_30992425","title":"Phosphoregulation of the oncogenic protein regulator of cytokinesis 1 (PRC1) by the atypical CDK16/CCNY complex.","date":"2019","source":"Experimental & molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/30992425","citation_count":26,"is_preprint":false},{"pmid":"33489809","id":"PMC_33489809","title":"Coexistence of a novel CCNY-ALK and ATIC-ALK double-fusion in one patient with ALK-positive NSCLC and response to crizotinib: a case report.","date":"2020","source":"Translational lung cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/33489809","citation_count":13,"is_preprint":false},{"pmid":"32401167","id":"PMC_32401167","title":"New tricks of an old autophagy regulator: AMPK-dependent regulation of autophagy through CCNY (cyclin Y)-CDK16.","date":"2020","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/32401167","citation_count":8,"is_preprint":false},{"pmid":"32739426","id":"PMC_32739426","title":"Ccny knockout mice display an enhanced susceptibility to kainic acid-induced epilepsy.","date":"2020","source":"Pharmacological research","url":"https://pubmed.ncbi.nlm.nih.gov/32739426","citation_count":6,"is_preprint":false},{"pmid":"30774378","id":"PMC_30774378","title":"Establishing a detection method for CCNY: a potentially significant clinical investigative marker in NSCLC patients.","date":"2019","source":"OncoTargets and therapy","url":"https://pubmed.ncbi.nlm.nih.gov/30774378","citation_count":4,"is_preprint":false},{"pmid":"40665337","id":"PMC_40665337","title":"CCNY-mediated phosphorylation and TET2-BACH1-driven DNA demethylation activate PRC1 to augment NSCLC progression.","date":"2025","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/40665337","citation_count":2,"is_preprint":false},{"pmid":"34571979","id":"PMC_34571979","title":"The Candidate IBD Risk Gene CCNY Is Dispensable for Intestinal Epithelial Homeostasis.","date":"2021","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/34571979","citation_count":2,"is_preprint":false},{"pmid":"32606977","id":"PMC_32606977","title":"CCNY Accelerates Cylcin E Expression to Regulate the Proliferation of Laryngeal Carcinoma Cells via MEK/ERK Signaling Pathway.","date":"2020","source":"Cancer management and research","url":"https://pubmed.ncbi.nlm.nih.gov/32606977","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7299,"output_tokens":2258,"usd":0.027883,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9382,"output_tokens":2875,"usd":0.059393,"stage2_stop_reason":"end_turn"},"total_usd":0.087276,"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\": 2019,\n      \"finding\": \"CDK16/CCNY complex phosphorylates PRC1 (regulator of cytokinesis 1) at Thr481; specific inhibition of CDK16 (using analog-sensitive CDK16 generated by CRISPR-Cas9) induces PRC1 dephosphorylation at Thr481 and delocalization to the nucleus during interphase. Epistasis experiments showed CDK16 inhibition and PRC1 downregulation act through a single pathway for cell viability, identifying PRC1 as the first substrate of the CDK16/CCNY complex.\",\n      \"method\": \"Analog-sensitive CDK16 (CRISPR-Cas9 mutagenesis), complementary proteomic approaches for substrate identification, epistasis analysis of cell viability\",\n      \"journal\": \"Experimental & molecular medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — chemical-genetic (analog-sensitive kinase) plus proteomics plus epistasis in one study, multiple orthogonal methods establishing substrate and pathway position\",\n      \"pmids\": [\"30992425\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CCNY (Cyclin Y) interacts with CDK16, and this interaction mutually stabilizes both proteins and increases CDK16 kinase activity. Phosphorylation sites on the N-terminal region of CDK16 (identified by mass spectrometry) are indispensable for CCNYL1 (not CCNY) binding and modulation of CDK16 kinase activity. Notably, Ccny knockout mice displayed normal fertility, indicating CCNY is dispensable for spermatogenesis (in contrast to CCNYL1).\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry (phosphorylation site mapping), Ccny knockout mouse model (fertility assay), kinase activity assay\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal protein interaction data and kinase activity assay for CDK16/CCNY complex, confirmed by knockout model, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"26305884\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Lentivirus-mediated RNAi knockdown of CCNY in glioma cells inhibited cell proliferation, colony formation, and cell cycle progression, establishing a role for CCNY in promoting glioma cell cycle progression.\",\n      \"method\": \"Lentivirus-mediated RNAi knockdown, cell proliferation assay, colony formation assay, cell cycle analysis\",\n      \"journal\": \"Oncology research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single knockdown approach with phenotypic readout but no pathway placement\",\n      \"pmids\": [\"20441050\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Fisetin decreases TET1 expression and reduces 5-hydroxymethylcytosine (5hmC) modification at CpG islands in the promoters of CCNY and CDK16 in renal cancer stem cells, thereby reducing CCNY and CDK16 transcription and activity, causing cell cycle arrest.\",\n      \"method\": \"ChIP-PCR (5hmC at CCNY promoter CpG islands), in vivo and in vitro proliferation/invasion assays, TET1 expression analysis\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP-PCR directly shows epigenetic regulation of CCNY promoter, supported by in vivo and in vitro experiments, single lab\",\n      \"pmids\": [\"30411496\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CCNY promotes cell proliferation in laryngeal carcinoma (Hep2) cells via activation of MEK/ERK signaling and upregulation of cyclin E protein. CCNY knockout (CRISPR/Cas9) reduced phospho-MEK, phospho-ERK, and cyclin E levels, while CCNY overexpression increased them, with corresponding changes in G1-phase cell cycle distribution.\",\n      \"method\": \"CRISPR/Cas9 knockout and overexpression, Western blot (MEK/ERK phosphorylation, cyclin E), flow cytometry (cell cycle), MTS/colony formation assays\",\n      \"journal\": \"Cancer management and research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR knockout and overexpression with Western blot pathway readout, single lab, multiple cellular assays\",\n      \"pmids\": [\"32606977\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Ccny knockout mice are more susceptible to kainic acid-induced epilepsy than wild-type mice, and CCNY levels regulate expression of numerous epilepsy-associated genes (e.g., Chrna4, Gabrd, Nhlrc1, Reln) in hippocampal neurons. CCNY is highly expressed in terminally differentiated neurons and acts as a postsynaptic protein with an inhibitory role in long-term potentiation.\",\n      \"method\": \"Ccny knockout mouse model, kainic acid epilepsy model, RNA-sequencing of hippocampal neurons overexpressing or depleting CCNY, mRNA/protein validation of epilepsy-associated genes\",\n      \"journal\": \"Pharmacological research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — knockout mouse with defined seizure phenotype and transcriptomic mechanism, single lab, RNA-seq plus in vivo model\",\n      \"pmids\": [\"32739426\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Conditional knockout of Ccny in intestinal epithelial cells (IECs) did not affect cell proliferation, Wnt/β-catenin signaling, autophagy, or disease activity in the DSS colitis model. CDK14 (cyclin-Y-associated CDK) expression was found to be exceedingly low specifically in IECs, providing a mechanistic explanation for why CCNY is dispensable in this cell type.\",\n      \"method\": \"Conditional (epithelial-specific) Ccny knockout mouse, DSS colitis model, in vitro IEC loss-of-function (Wnt signaling, proliferation, autophagy assays), CDK14 expression analysis\",\n      \"journal\": \"Cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional knockout with multiple functional readouts; NEGATIVE result: CCNY dispensable in IECs due to low CDK14; single lab\",\n      \"pmids\": [\"34571979\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CCNY promotes PRC1 phosphorylation in NSCLC cells; silencing CCNY reduced cell growth, impaired spindle formation, induced G2/M arrest, and increased multi-nucleated cells. Separately, TET2 demethylates and activates PRC1 transcription by interacting with BACH1. These represent two independent regulatory axes (CCNY-mediated phosphorylation and TET2-BACH1-driven transcription) converging on PRC1.\",\n      \"method\": \"Genetic knockdown and pharmaceutical inhibition (CCNY, TET2, BACH1), subcutaneous xenograft and orthotopic isograft models, cell cycle analysis, spindle formation assay, tissue microarray, Western blot, qPCR\",\n      \"journal\": \"Journal of experimental & clinical cancer research : CR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with multiple cellular and in vivo phenotypic readouts, single lab, several orthogonal methods\",\n      \"pmids\": [\"40665337\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CCNY (Cyclin Y) functions as a regulatory cyclin that forms an active complex with CDK16 to phosphorylate substrates including PRC1 at Thr481 (promoting cell division and cytoskeletal organization), activates MEK/ERK/cyclin E signaling to drive cell cycle progression, is itself transcriptionally regulated by TET1/TET2-mediated epigenetic (5hmC) modifications at its promoter, and acts as a postsynaptic protein in neurons where it inhibits long-term potentiation and protects against epilepsy—with its activity in any given cell type dependent on the co-expression of appropriate CDK partners.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CCNY (Cyclin Y) is a regulatory cyclin that controls cell cycle progression and cytoskeletal organization by activating cyclin-dependent kinase partners, with its functional output dictated by the cell-type-specific availability of those partners [#1, #6]. CCNY binds CDK16 in a mutually stabilizing interaction that elevates CDK16 kinase activity [#1], and the CDK16/CCNY complex phosphorylates PRC1 at Thr481 — the first identified substrate of this complex — to maintain PRC1 at its proper subcellular location during interphase and support cell viability [#0]. This phosphoregulatory axis governs mitotic fidelity: in NSCLC cells, loss of CCNY reduces PRC1 phosphorylation, impairs spindle formation, induces G2/M arrest, and produces multinucleated cells [#7]. CCNY also promotes G1-phase progression and proliferation in laryngeal carcinoma cells through activation of MEK/ERK signaling and upregulation of cyclin E [#4], and its knockdown arrests glioma cell cycle progression [#2]. CCNY itself is transcriptionally regulated by TET1-mediated 5-hydroxymethylcytosine modification at its promoter CpG islands, linking epigenetic control to its expression in cancer stem cells [#3]. In terminally differentiated neurons, CCNY is a postsynaptic protein that inhibits long-term potentiation and protects against kainic-acid-induced epilepsy by regulating epilepsy-associated gene expression in hippocampal neurons [#5]. CCNY is dispensable in tissues lacking its CDK partners — it is not required for spermatogenesis [#1] nor for intestinal epithelial proliferation, the latter explained by very low CDK14 expression in those cells [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Established a cellular requirement for CCNY in driving cancer cell proliferation, before any molecular mechanism was known.\",\n      \"evidence\": \"Lentiviral RNAi knockdown of CCNY in glioma cells with proliferation, colony formation, and cell cycle readouts\",\n      \"pmids\": [\"20441050\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single knockdown approach with no pathway placement\", \"No CDK partner or substrate identified\", \"Off-target RNAi effects not excluded\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined CCNY's biochemical mode of action by showing it binds and activates CDK16, while genetics revealed it is dispensable in some tissues.\",\n      \"evidence\": \"Co-IP, mass spectrometry phosphosite mapping, kinase activity assays, and Ccny knockout mouse fertility analysis\",\n      \"pmids\": [\"26305884\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No substrate of the activated CDK16/CCNY complex identified\", \"Functional consequences of CDK16 activation in vivo not established\", \"Distinction from paralog CCNYL1 leaves CCNY-specific roles incompletely mapped\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identified an upstream layer controlling CCNY abundance, linking epigenetic 5hmC marks to its transcription in cancer stem cells.\",\n      \"evidence\": \"ChIP-PCR for 5hmC at CCNY promoter CpG islands plus TET1 modulation and proliferation assays in renal cancer stem cells\",\n      \"pmids\": [\"30411496\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct demonstration that TET1 binds the CCNY promoter not shown\", \"Generality beyond cancer stem cells unknown\", \"Effect mediated by a small-molecule (fisetin) rather than genetic TET1 perturbation\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Named the first substrate of the CDK16/CCNY complex and placed it in a single pathway controlling cell viability.\",\n      \"evidence\": \"Analog-sensitive CDK16 (CRISPR-Cas9), proteomics for substrate identification, and epistasis analysis of viability\",\n      \"pmids\": [\"30992425\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct requirement of CCNY (vs CDK16 alone) for PRC1 phosphorylation not isolated in this study\", \"Broader substrate repertoire not defined\", \"Structural basis of PRC1 Thr481 recognition unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Extended CCNY function to a CDK-independent-framed proliferative pathway (MEK/ERK/cyclin E) and revealed a distinct neuronal, postsynaptic role.\",\n      \"evidence\": \"CRISPR knockout/overexpression with MEK/ERK/cyclin E Western blots in laryngeal carcinoma; Ccny knockout mice with kainic acid epilepsy model and hippocampal RNA-seq\",\n      \"pmids\": [\"32606977\", \"32739426\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic link between CCNY and MEK/ERK activation not resolved\", \"Whether neuronal CCNY acts via a CDK partner not established\", \"Direct targets among epilepsy-associated genes not distinguished from secondary effects\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Demonstrated that CCNY function is gated by co-expression of its CDK partner, explaining tissue-specific dispensability.\",\n      \"evidence\": \"Epithelial-specific conditional Ccny knockout, DSS colitis model, Wnt/proliferation/autophagy assays, and CDK14 expression analysis in IECs\",\n      \"pmids\": [\"34571979\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Negative result; does not exclude CCNY function in other intestinal contexts\", \"CDK14-CCNY complex activity in cells with normal CDK14 not directly tested here\", \"Compensation by paralogs not formally excluded\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Consolidated CCNY's role in mitotic fidelity via PRC1 phosphorylation and showed PRC1 is also independently controlled transcriptionally.\",\n      \"evidence\": \"CCNY knockdown/inhibition with spindle, cell-cycle, and multinucleation readouts plus xenograft/isograft models in NSCLC; TET2-BACH1 transcriptional axis on PRC1\",\n      \"pmids\": [\"40665337\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the CCNY-PRC1 axis here is CDK16-dependent not directly shown\", \"Relative contributions of phosphorylation vs transcription to PRC1 output not quantified\", \"Single-lab in vivo models\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single cyclin is partitioned among distinct CDK partners (CDK16, CDK14) and CDK-independent signaling outputs across proliferating, epithelial, and neuronal cell types remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of CCNY-CDK complexes in the corpus\", \"Mechanism linking CCNY to MEK/ERK activation unknown\", \"Full substrate repertoire beyond PRC1 uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0, 4, 7]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"complexes\": [\n      \"CDK16/CCNY complex\"\n    ],\n    \"partners\": [\n      \"CDK16\",\n      \"CDK14\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":7,"faith_total":7,"faith_pct":100.0}}