{"gene":"CDKN3","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":1993,"finding":"CDI1/CDKN3 is a dual-specificity phosphatase that forms stable complexes with CDK2 (and interacts with Cdc2 and Cdk3 but not Cdk4) in HeLa cells; in vitro it removes phosphate from tyrosine residues in model substrates; a C→S active-site mutant abolishes phosphatase activity and also abolishes cell-cycle delay upon overexpression, establishing that phosphatase activity is required for its cell-cycle function.","method":"Yeast two-hybrid (interaction trap) for binding partners; in vitro phosphatase assay; active-site mutagenesis (C→S); overexpression in yeast and HeLa cells with cell-cycle readout; Co-immunoprecipitation of Cdi1-Cdk2 complex","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro enzymatic assay with active-site mutagenesis confirming catalytic requirement, reciprocal binding studies, overexpression with functional phenotype; foundational study replicated by multiple subsequent papers","pmids":["8242750"],"is_preprint":false},{"year":2013,"finding":"CDKN3 dephosphorylates Thr-161 of CDC2 (CDK1) during mitotic exit; CDKN3 subcellular localization changes throughout the cell cycle; CDC2(pThr-161) is visualized at kinetochores and centrosomes in early mitosis; phosphokinome-wide MS screen identified CKβ phosphorylated at Ser-209 as a downstream phosphotarget that localizes to mitotic centrosomes and controls the spindle checkpoint.","method":"Genome-wide siRNA phosphatase screen; immunofluorescence for subcellular localization across cell cycle stages; phospho-specific antibody detection of CDC2(pThr-161); phosphokinome-wide mass spectrometry screen for downstream targets","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (siRNA screen, MS phosphoproteomics, immunofluorescence, functional spindle checkpoint assay) in a single rigorous study identifying direct substrate and downstream effector","pmids":["23775190"],"is_preprint":false},{"year":2015,"finding":"CDKN3 (Cdkn3) directly binds Mps1 kinase and is recruited to centrosomes via this interaction; centrosomal Cdkn3 controls centrosomal levels of Mps1 through proteasome-mediated degradation, forming a self-regulated feedback loop; knockdown of Cdkn3 stabilizes Mps1 at centrosomes and promotes centrosome overduplication.","method":"Co-immunoprecipitation (direct binding partner identification); siRNA knockdown with centrosome number readout; localization studies by immunofluorescence; proteasome inhibitor experiments","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP identifying direct binding partner, functional siRNA KD with quantitative centrosome phenotype, mechanistic follow-up with proteasome pathway, multiple orthogonal methods in one study","pmids":["26586430"],"is_preprint":false},{"year":2014,"finding":"CDKN3 phosphatase activity is required for its tumor suppressor function in Bcr-Abl-mediated leukemogenesis: a phosphatase-dead mutant (C140S) fails to affect K562 leukemic cell survival or xenograft tumor growth; wild-type CDKN3 overexpression reduces leukemic cell survival by dephosphorylating CDK2, thereby inhibiting CDK2-dependent XIAP expression and delaying G1/S transition.","method":"Active-site mutagenesis (C140S phosphatase-dead mutant); overexpression and knockdown in K562 cells; xenograft mouse model; Western blot for CDK2 phosphorylation and XIAP expression; apoptosis assay; cell cycle analysis","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — active-site mutagenesis establishing catalytic requirement, substrate (CDK2) and downstream effector (XIAP) identified, in vivo validation; single lab","pmids":["25360622"],"is_preprint":false},{"year":2022,"finding":"CDKN3 knockdown decreases cisplatin resistance in bladder cancer cells by inhibiting LDHA expression, thereby suppressing aerobic glycolysis; LDHA overexpression reverses glycolysis inhibition and chemosensitivity caused by CDKN3 knockdown, establishing LDHA as a downstream mediator of CDKN3-regulated chemoresistance.","method":"siRNA knockdown; LDHA overexpression rescue experiment; glycolysis measurement (glucose uptake, lactate production); cell viability assay; Western blot","journal":"OncoTargets and therapy","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — functional rescue experiment identifying LDHA as downstream mediator; single lab, limited mechanistic depth on direct enzymatic connection","pmids":["35388272"],"is_preprint":false},{"year":2019,"finding":"CDKN3 promotes cisplatin resistance in esophageal cancer via RAD51: CDKN3 inhibition reduces RAD51 expression, and RAD51 overexpression reverses cisplatin-induced DNA damage and chemosensitivity in CDKN3-knockdown esophageal cancer cells, placing RAD51 downstream of CDKN3 in the DNA damage repair pathway.","method":"siRNA knockdown; RAD51 overexpression rescue; in vitro and in vivo (xenograft) functional assays; Western blot; DNA damage assay (γH2AX)","journal":"Cancer management and research","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — rescue experiment identifying RAD51 as downstream mediator, in vivo validation; single lab, no direct biochemical interaction shown","pmids":["31114363"],"is_preprint":false},{"year":2023,"finding":"PSMD12 (a 26S proteasome non-ATPase subunit) physically interacts with CDKN3 and reduces its ubiquitination level, thereby stabilizing CDKN3 protein; CDKN3 knockdown reverses PSMD12 overexpression-induced cell proliferation, indicating CDKN3 is a functional downstream effector of PSMD12.","method":"Co-immunoprecipitation; Western blot for ubiquitination; rescue (CDKN3 knockdown reversing PSMD12 overexpression phenotype); in vivo xenograft","journal":"Cancer gene therapy","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP identifying physical interaction, ubiquitination assay, functional rescue; single lab","pmids":["37037907"],"is_preprint":false},{"year":2023,"finding":"GID2 (an E3 ubiquitin ligase subunit) physically interacts with CDKN3 and inhibits its ubiquitination, stabilizing CDKN3 protein; CDKN3 knockdown reverses GID2 overexpression-driven pancreatic cancer cell proliferation.","method":"Co-immunoprecipitation; ubiquitination assay; functional rescue by CDKN3 knockdown; in vivo xenograft","journal":"Laboratory investigation","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP and ubiquitination assay in single lab, functional rescue experiment","pmids":["36828188"],"is_preprint":false},{"year":2026,"finding":"Estrogen receptors mediate sex-specific downregulation of E2F1 and its target gene CDKN3 in female epidermis following UV exposure; CDKN3 depletion impairs SCC cell progression into S-phase and reduces tumor growth in xenograft models, establishing an ER/E2F1/CDKN3 axis that protects females from UV-induced squamous cell carcinoma.","method":"UV-induced SCC mouse model (sex comparison); global transcriptional profiling; estrogen receptor perturbation; siRNA-mediated CDKN3 depletion; S-phase entry assay; xenograft tumor growth assay","journal":"EMBO reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (transcriptomics, ER perturbation, functional KD with S-phase and xenograft readouts) in single study establishing pathway position; single lab","pmids":["41876816"],"is_preprint":false},{"year":2024,"finding":"BACH1 transcription factor directly activates CDKN3 transcription in cardiomyocytes (confirmed by ChIP and luciferase assay); BACH1 disruption attenuates hypoxia/reoxygenation-induced apoptosis, ferroptosis, and inflammation partially by downregulating CDKN3, which in turn activates AMPK signaling.","method":"Chromatin immunoprecipitation (ChIP); luciferase reporter assay; CDKN3 knockdown/overexpression rescue; cell viability, apoptosis, and ferroptosis assays; Western blot for AMPK pathway","journal":"Cardiovascular toxicology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — ChIP and luciferase assay establishing direct transcriptional regulation, functional rescue; single lab","pmids":["39060883"],"is_preprint":false},{"year":2024,"finding":"N-Myc directly binds the CDKN3 promoter and promotes CDKN3 transcription in neuroblastoma cells; CDKN3 knockdown induces neurite outgrowth and upregulates differentiation markers (NSE, βIII-tubulin, GAP43), while reducing proliferation markers (Ki67, PCNA); CDKN3, CDC6, and CDK4 form an interactive network that promotes expression of each other.","method":"ChIP (N-Myc binding to CDKN3 promoter); siRNA knockdown; high-content siRNA screen; Western blot for differentiation and proliferation markers; colony formation assay","journal":"Journal of Cancer","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — ChIP establishing direct transcriptional regulation, functional phenotype by KD; single lab, network interaction not biochemically reconstituted","pmids":["38356706"],"is_preprint":false},{"year":2025,"finding":"CDKN3 knockdown arrests TNBC cells in G2M phase by downregulating CCNB2 (cyclin B2), establishing CDKN3 as a positive regulator of G2M progression through CCNB2.","method":"siRNA knockdown; cell cycle analysis by flow cytometry; Western blot for CCNB2; proliferation and migration assays","journal":"IUBMB life","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single method for CCNB2 connection; no direct biochemical interaction demonstrated","pmids":["39865508"],"is_preprint":false},{"year":2025,"finding":"CDKN3 overexpression increases HSP90 expression in TNBC cells; knockdown of CDKN3 decreases HSP90 expression; an HSP90 inhibitor reverses the pro-tumorigenic effects of CDKN3 overexpression, placing HSP90 downstream of CDKN3 in a ferroptosis-inhibiting pathway.","method":"Lentiviral overexpression and knockdown; HSP90 inhibitor rescue; ferroptosis markers (Fe2+, GSH, ROS, MDA); in vivo 4T1 mammary fat pad model; Western blot","journal":"Toxicology and applied pharmacology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, no direct biochemical interaction between CDKN3 and HSP90 demonstrated; functional rescue only","pmids":["41207514"],"is_preprint":false},{"year":2007,"finding":"NOTE: Paper [4] (PMID 29168185) describing a CDKN3/MDM2/P53/P21 complex was formally RETRACTED (PMID 38059668) due to image duplications; its conclusions are considered unreliable and are excluded.","method":"RETRACTED — excluded","journal":"International journal of cancer","confidence":"Low","confidence_rationale":"Retracted paper — not included as a discovery","pmids":["29168185","38059668"],"is_preprint":false}],"current_model":"CDKN3 (CDI1/KAP) is a dual-specificity protein phosphatase that directly binds and dephosphorylates cyclin-dependent kinases (CDK2, CDC2/CDK1) — removing inhibitory/activating phosphorylations including Thr-161 of CDC2 during mitotic exit — and thereby controls G1/S transition and mitotic exit; it also interacts with Mps1 kinase at centrosomes to regulate Mps1 stability via proteasome-mediated degradation and prevent centrosome overduplication, while its expression is transcriptionally controlled by N-Myc and BACH1 and post-translationally stabilized by PSMD12 and GID2 through reduction of ubiquitination; downstream consequences of CDKN3 activity include modulation of XIAP (via CDK2), RAD51 (DNA repair/cisplatin resistance), LDHA (glycolysis/chemoresistance), and CCNB2 (G2M progression), and its catalytic activity is absolutely required for all observed cell-cycle and tumor-suppressive functions."},"narrative":{"mechanistic_narrative":"CDKN3 (CDI1/KAP) is a dual-specificity protein phosphatase that regulates cell-cycle progression by directly binding and dephosphorylating cyclin-dependent kinases [PMID:8242750]. It forms stable complexes with CDK2 and interacts with CDC2/CDK1 and CDK3 but not CDK4, and its phosphatase activity is strictly required for its cell-cycle function, since an active-site C→S mutant both abolishes catalysis and abolishes the cell-cycle delay caused by overexpression [PMID:8242750]. During mitotic exit CDKN3 dephosphorylates Thr-161 of CDC2/CDK1, with its substrate concentrated at kinetochores and centrosomes in early mitosis, and it acts through downstream phosphotargets that control the spindle checkpoint [PMID:23775190]. At centrosomes CDKN3 directly binds Mps1 kinase, by which it is recruited to the centrosome, and limits centrosomal Mps1 levels through proteasome-mediated degradation in a self-regulated feedback loop that restrains centrosome overduplication [PMID:26586430]. In cancer contexts CDKN3 catalytic activity underlies a tumor-suppressive role in Bcr-Abl leukemogenesis, where wild-type but not phosphatase-dead CDKN3 dephosphorylates CDK2 to lower CDK2-dependent XIAP expression and delay G1/S transition [PMID:25360622]; in other tumor settings CDKN3 supports proliferation and chemoresistance through downstream effectors including RAD51 in DNA-damage repair [PMID:31114363], LDHA-dependent aerobic glycolysis [PMID:35388272], and CCNB2-driven G2/M progression [PMID:39865508]. CDKN3 expression is transcriptionally driven by N-Myc in neuroblastoma [PMID:38356706] and by BACH1 in cardiomyocytes [PMID:39060883], placed under an ER/E2F1 axis in UV-exposed epidermis [PMID:41876816], and its protein level is stabilized by PSMD12 and GID2 through reduced ubiquitination [PMID:37037907, PMID:36828188].","teleology":[{"year":1993,"claim":"Established the founding biochemical identity of CDKN3 as a CDK-binding dual-specificity phosphatase whose catalytic activity is essential for cell-cycle control, answering what kind of molecule it is and how it acts.","evidence":"Yeast two-hybrid, in vitro phosphatase assay, active-site C→S mutagenesis, and overexpression with cell-cycle readout in HeLa cells","pmids":["8242750"],"confidence":"High","gaps":["Did not define the physiological CDK phospho-site dephosphorylated in vivo","Did not resolve which CDK partner is the dominant cellular substrate"]},{"year":2013,"claim":"Identified the in vivo substrate and timing of CDKN3 action, showing it removes the Thr-161 phosphate from CDC2/CDK1 at mitotic exit and feeds into spindle-checkpoint control.","evidence":"Genome-wide siRNA phosphatase screen, phospho-specific immunofluorescence across the cell cycle, and phosphokinome-wide mass spectrometry","pmids":["23775190"],"confidence":"High","gaps":["Mechanism coupling CDKN3 relocalization to substrate access not fully resolved","Direct enzyme-substrate kinetics for Thr-161 not reconstituted"]},{"year":2015,"claim":"Defined a centrosomal function distinct from CDK dephosphorylation, showing CDKN3 binds Mps1 to control its proteasomal turnover and prevent centrosome overduplication.","evidence":"Reciprocal co-immunoprecipitation, siRNA knockdown with centrosome-number readout, immunofluorescence localization, and proteasome inhibitor experiments","pmids":["26586430"],"confidence":"High","gaps":["Whether phosphatase activity is required for Mps1 regulation not established","E3 ligase mediating Mps1 degradation not identified"]},{"year":2014,"claim":"Connected catalytic activity to tumor suppression, showing CDKN3 dephosphorylates CDK2 to suppress XIAP and delay G1/S in leukemic cells.","evidence":"C140S phosphatase-dead mutant, overexpression/knockdown in K562 cells, xenograft model, and Western blot for CDK2 phosphorylation and XIAP","pmids":["25360622"],"confidence":"Medium","gaps":["Single lab","Mechanism linking CDK2 activity to XIAP expression not detailed"]},{"year":2019,"claim":"Placed CDKN3 upstream of DNA-damage repair, identifying RAD51 as a downstream mediator of CDKN3-driven cisplatin resistance.","evidence":"siRNA knockdown, RAD51 overexpression rescue, xenograft assays, and γH2AX DNA-damage readout in esophageal cancer cells","pmids":["31114363"],"confidence":"Medium","gaps":["No direct biochemical interaction between CDKN3 and RAD51 shown","Mechanism by which CDKN3 controls RAD51 expression unknown"]},{"year":2022,"claim":"Linked CDKN3 to tumor metabolism, showing it supports aerobic glycolysis and chemoresistance through LDHA.","evidence":"siRNA knockdown, LDHA overexpression rescue, glucose-uptake/lactate measurements, and viability assays in bladder cancer cells","pmids":["35388272"],"confidence":"Medium","gaps":["Direct enzymatic connection to LDHA not established","Single lab"]},{"year":2023,"claim":"Revealed post-translational control of CDKN3 abundance, identifying PSMD12 and GID2 as physical partners that stabilize CDKN3 by reducing its ubiquitination.","evidence":"Co-immunoprecipitation, ubiquitination assays, and CDKN3-knockdown rescue of overexpression phenotypes with xenograft validation","pmids":["37037907","36828188"],"confidence":"Medium","gaps":["Ubiquitin ligase/deubiquitinase mechanism for CDKN3 not fully defined","Single lab per partner"]},{"year":2024,"claim":"Defined transcriptional regulators of CDKN3, showing N-Myc and BACH1 directly drive its expression in neuroblastoma and cardiomyocytes respectively, with phenotypic consequences for differentiation and stress responses.","evidence":"ChIP and luciferase reporter assays, siRNA knockdown, and differentiation/proliferation or apoptosis/ferroptosis readouts","pmids":["38356706","39060883"],"confidence":"Medium","gaps":["Downstream AMPK link in cardiomyocytes not biochemically traced to CDKN3 activity","CDKN3/CDC6/CDK4 network not reconstituted in vitro"]},{"year":2026,"claim":"Positioned CDKN3 within a sex-specific tumor-protective circuit, showing estrogen receptors downregulate E2F1 and its target CDKN3 to limit UV-induced squamous cell carcinoma.","evidence":"UV-induced SCC mouse model with sex comparison, transcriptional profiling, ER perturbation, and CDKN3 siRNA depletion with S-phase and xenograft readouts","pmids":["41876816"],"confidence":"Medium","gaps":["Direct ER occupancy at the CDKN3 locus not shown","Single lab"]},{"year":null,"claim":"How CDKN3's defined phosphatase activity mechanistically connects to the diverse downstream effectors (RAD51, LDHA, CCNB2, HSP90) reported in tumor models remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No direct enzyme-substrate link between CDKN3 and these effectors established","Whether catalytic activity is required for the metabolic and chemoresistance phenotypes untested in most contexts"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[1,2]}],"pathway":[{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0,1,3]}],"complexes":[],"partners":["CDK2","CDK1","MPS1","PSMD12","GID2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q00526","full_name":"Cyclin-dependent kinase 3","aliases":["Cell division protein kinase 3"],"length_aa":305,"mass_kda":35.0,"function":"Serine/threonine-protein kinase that plays a critical role in the control of the eukaryotic cell cycle; involved in G0-G1 and G1-S cell cycle transitions. Interacts with CCNC/cyclin-C during interphase. Phosphorylates histone H1, ATF1, RB1 and CABLES1. ATF1 phosphorylation triggers ATF1 transactivation and transcriptional activities, and promotes cell proliferation and transformation. CDK3/cyclin-C mediated RB1 phosphorylation is required for G0-G1 transition. Promotes G1-S transition probably by contributing to the activation of E2F1, E2F2 and E2F3 in a RB1-independent manner","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q00526/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CDKN3","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CDKN3","total_profiled":1310},"omim":[{"mim_id":"123838","title":"CYCLIN C; CCNC","url":"https://www.omim.org/entry/123838"},{"mim_id":"123837","title":"CYCLIN E1; CCNE1","url":"https://www.omim.org/entry/123837"},{"mim_id":"123832","title":"CYCLIN-DEPENDENT KINASE INHIBITOR 3; CDKN3","url":"https://www.omim.org/entry/123832"},{"mim_id":"116899","title":"CYCLIN-DEPENDENT KINASE INHIBITOR 1A; CDKN1A","url":"https://www.omim.org/entry/116899"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Cytosol","reliability":"Enhanced"}],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"testis","ntpm":192.4}],"url":"https://www.proteinatlas.org/search/CDKN3"},"hgnc":{"alias_symbol":["KAP","CDI1"],"prev_symbol":[]},"alphafold":{"accession":"Q00526","domains":[{"cath_id":"3.30.200.20","chopping":"5-82","consensus_level":"high","plddt":86.0728,"start":5,"end":82},{"cath_id":"1.10.510.10","chopping":"86-303","consensus_level":"high","plddt":87.0154,"start":86,"end":303}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q00526","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q00526-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q00526-F1-predicted_aligned_error_v6.png","plddt_mean":86.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CDKN3","jax_strain_url":"https://www.jax.org/strain/search?query=CDKN3"},"sequence":{"accession":"Q00526","fasta_url":"https://rest.uniprot.org/uniprotkb/Q00526.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q00526/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q00526"}},"corpus_meta":[{"pmid":"8242750","id":"PMC_8242750","title":"Cdi1, a human G1 and S phase protein phosphatase that associates with Cdk2.","date":"1993","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/8242750","citation_count":1367,"is_preprint":false},{"pmid":"33468140","id":"PMC_33468140","title":"Circular RNA circSDHC serves as a sponge for miR-127-3p to promote the proliferation and metastasis of renal cell carcinoma via the CDKN3/E2F1 axis.","date":"2021","source":"Molecular cancer","url":"https://pubmed.ncbi.nlm.nih.gov/33468140","citation_count":89,"is_preprint":false},{"pmid":"23775190","id":"PMC_23775190","title":"The tumor suppressor CDKN3 controls mitosis.","date":"2013","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/23775190","citation_count":80,"is_preprint":false},{"pmid":"29168185","id":"PMC_29168185","title":"YY1 suppresses proliferation and migration of pancreatic ductal adenocarcinoma by regulating the CDKN3/MdM2/P53/P21 signaling pathway.","date":"2017","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/29168185","citation_count":55,"is_preprint":false},{"pmid":"7698009","id":"PMC_7698009","title":"Chromosomal mapping of the genes for the human cell cycle proteins cyclin C (CCNC), cyclin E (CCNE), p21 (CDKN1) and KAP (CDKN3).","date":"1995","source":"Cytogenetics and cell genetics","url":"https://pubmed.ncbi.nlm.nih.gov/7698009","citation_count":54,"is_preprint":false},{"pmid":"29196103","id":"PMC_29196103","title":"Cyclin-dependent kinase inhibitor 3 (CDKN3) plays a critical role in prostate cancer via regulating cell cycle and DNA replication signaling.","date":"2017","source":"Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie","url":"https://pubmed.ncbi.nlm.nih.gov/29196103","citation_count":52,"is_preprint":false},{"pmid":"35678231","id":"PMC_35678231","title":"ZNF677 suppresses renal cell carcinoma progression through N6-methyladenosine and transcriptional repression of CDKN3.","date":"2022","source":"Clinical and translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35678231","citation_count":42,"is_preprint":false},{"pmid":"21535270","id":"PMC_21535270","title":"Cyclin-dependent kinase inhibitor 3 (CDKN3) novel cell cycle computational network between human non-malignancy associated hepatitis/cirrhosis and hepatocellular carcinoma (HCC) transformation.","date":"2011","source":"Cell proliferation","url":"https://pubmed.ncbi.nlm.nih.gov/21535270","citation_count":40,"is_preprint":false},{"pmid":"31352814","id":"PMC_31352814","title":"Long non-coding RNA NEAT1 inhibits oxidative stress-induced vascular endothelial cell injury by activating the miR-181d-5p/CDKN3 axis.","date":"2019","source":"Artificial cells, nanomedicine, and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/31352814","citation_count":40,"is_preprint":false},{"pmid":"26372210","id":"PMC_26372210","title":"CDKN3 mRNA as a Biomarker for Survival and Therapeutic Target in Cervical Cancer.","date":"2015","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/26372210","citation_count":33,"is_preprint":false},{"pmid":"30628487","id":"PMC_30628487","title":"Tumor-suppressive effects of microRNA-181d-5p on non-small-cell lung cancer through the CDKN3-mediated Akt signaling pathway in vivo and in vitro.","date":"2019","source":"American journal of physiology. 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analysis.","date":"2024","source":"Heliyon","url":"https://pubmed.ncbi.nlm.nih.gov/38380029","citation_count":9,"is_preprint":false},{"pmid":"38106976","id":"PMC_38106976","title":"Comprehensive Analysis Reveals the Potential Roles of CDKN3 in Pancancer and Verification in Endometrial Cancer.","date":"2023","source":"International journal of general medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38106976","citation_count":7,"is_preprint":false},{"pmid":"38356706","id":"PMC_38356706","title":"Identification of CDKN3 as a Key Gene that Regulates Neuroblastoma Cell Differentiation.","date":"2024","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/38356706","citation_count":6,"is_preprint":false},{"pmid":"12927088","id":"PMC_12927088","title":"Characterization of the porcine CDKN3 gene as a potential candidate for congenital splay leg in piglets.","date":"2003","source":"Genetics, selection, evolution : GSE","url":"https://pubmed.ncbi.nlm.nih.gov/12927088","citation_count":6,"is_preprint":false},{"pmid":"38814199","id":"PMC_38814199","title":"N6-Methyladenosine modified circ-NAB1 modulates cell cycle and epithelial-mesenchymal transition via CDKN3 in endometrial cancer.","date":"2024","source":"Cellular and molecular biology (Noisy-le-Grand, France)","url":"https://pubmed.ncbi.nlm.nih.gov/38814199","citation_count":5,"is_preprint":false},{"pmid":"38030294","id":"PMC_38030294","title":"MicroRNA-127-3p Inhibits Cardiomyocyte Inflammation and Apoptosis after Acute Myocardial Infarction via Targeting CDKN3.","date":"2023","source":"International heart journal","url":"https://pubmed.ncbi.nlm.nih.gov/38030294","citation_count":5,"is_preprint":false},{"pmid":"39060883","id":"PMC_39060883","title":"Disruption of BACH1 Protects AC16 Cardiomyocytes Against Hypoxia/Reoxygenation-Evoked Injury by Diminishing CDKN3 Transcription.","date":"2024","source":"Cardiovascular toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/39060883","citation_count":3,"is_preprint":false},{"pmid":"39865508","id":"PMC_39865508","title":"CDKN3 as a key regulator of G2M phase in triple-negative breast cancer: Insights from multi-transcriptomic analysis.","date":"2025","source":"IUBMB life","url":"https://pubmed.ncbi.nlm.nih.gov/39865508","citation_count":2,"is_preprint":false},{"pmid":"39806313","id":"PMC_39806313","title":"The systematic analysis of genes related to butyrate metabolism suggests that CDKN3 could serve as a promising therapeutic target for lung adenocarcinoma treatment.","date":"2025","source":"BMC cancer","url":"https://pubmed.ncbi.nlm.nih.gov/39806313","citation_count":2,"is_preprint":false},{"pmid":"41876816","id":"PMC_41876816","title":"An estrogen receptor/E2F1/CDKN3 axis protects from UV-induced skin cancers in females.","date":"2026","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/41876816","citation_count":0,"is_preprint":false},{"pmid":"40294936","id":"PMC_40294936","title":"[High expression of CDKN3 promotes migration and invasion of gastric cancer cells by regulating the p53/NF-κB signaling pathway and inhibiting cell apoptosis].","date":"2025","source":"Nan fang yi ke da xue xue bao = Journal of Southern Medical University","url":"https://pubmed.ncbi.nlm.nih.gov/40294936","citation_count":0,"is_preprint":false},{"pmid":"38059668","id":"PMC_38059668","title":"Retraction: YY1 suppresses proliferation and migration of pancreatic ductal adenocarcinoma by regulating the CDKN3/MdM2/P53/P21 signaling pathway.","date":"2023","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/38059668","citation_count":0,"is_preprint":false},{"pmid":"41207514","id":"PMC_41207514","title":"CDKN3 promoted triple-negative breast cancer by inhibiting ferroptosis through the upregulation of HSP90.","date":"2025","source":"Toxicology and applied pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/41207514","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.10.14.682348","title":"Association of miR-181a-5p with  <i>Lantana camara</i>  leaf extract-mediated inhibition of proliferation, survival, and migration in luminal A-type MCF-7 cells and triple-negative type MDA-MB-231 cells","date":"2025-10-15","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.14.682348","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.02.12.637819","title":"Estrogen Receptors/E2F1/CDKN3 Axis Protects from UV-induced Skin Cancers in Females","date":"2025-02-16","source":"bioRxiv","url":"https://doi.org/10.1101/2025.02.12.637819","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":23071,"output_tokens":3854,"usd":0.063511,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11615,"output_tokens":3299,"usd":0.070275,"stage2_stop_reason":"end_turn"},"total_usd":0.133786,"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\": 1993,\n      \"finding\": \"CDI1/CDKN3 is a dual-specificity phosphatase that forms stable complexes with CDK2 (and interacts with Cdc2 and Cdk3 but not Cdk4) in HeLa cells; in vitro it removes phosphate from tyrosine residues in model substrates; a C→S active-site mutant abolishes phosphatase activity and also abolishes cell-cycle delay upon overexpression, establishing that phosphatase activity is required for its cell-cycle function.\",\n      \"method\": \"Yeast two-hybrid (interaction trap) for binding partners; in vitro phosphatase assay; active-site mutagenesis (C→S); overexpression in yeast and HeLa cells with cell-cycle readout; Co-immunoprecipitation of Cdi1-Cdk2 complex\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro enzymatic assay with active-site mutagenesis confirming catalytic requirement, reciprocal binding studies, overexpression with functional phenotype; foundational study replicated by multiple subsequent papers\",\n      \"pmids\": [\"8242750\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"CDKN3 dephosphorylates Thr-161 of CDC2 (CDK1) during mitotic exit; CDKN3 subcellular localization changes throughout the cell cycle; CDC2(pThr-161) is visualized at kinetochores and centrosomes in early mitosis; phosphokinome-wide MS screen identified CKβ phosphorylated at Ser-209 as a downstream phosphotarget that localizes to mitotic centrosomes and controls the spindle checkpoint.\",\n      \"method\": \"Genome-wide siRNA phosphatase screen; immunofluorescence for subcellular localization across cell cycle stages; phospho-specific antibody detection of CDC2(pThr-161); phosphokinome-wide mass spectrometry screen for downstream targets\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (siRNA screen, MS phosphoproteomics, immunofluorescence, functional spindle checkpoint assay) in a single rigorous study identifying direct substrate and downstream effector\",\n      \"pmids\": [\"23775190\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CDKN3 (Cdkn3) directly binds Mps1 kinase and is recruited to centrosomes via this interaction; centrosomal Cdkn3 controls centrosomal levels of Mps1 through proteasome-mediated degradation, forming a self-regulated feedback loop; knockdown of Cdkn3 stabilizes Mps1 at centrosomes and promotes centrosome overduplication.\",\n      \"method\": \"Co-immunoprecipitation (direct binding partner identification); siRNA knockdown with centrosome number readout; localization studies by immunofluorescence; proteasome inhibitor experiments\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP identifying direct binding partner, functional siRNA KD with quantitative centrosome phenotype, mechanistic follow-up with proteasome pathway, multiple orthogonal methods in one study\",\n      \"pmids\": [\"26586430\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CDKN3 phosphatase activity is required for its tumor suppressor function in Bcr-Abl-mediated leukemogenesis: a phosphatase-dead mutant (C140S) fails to affect K562 leukemic cell survival or xenograft tumor growth; wild-type CDKN3 overexpression reduces leukemic cell survival by dephosphorylating CDK2, thereby inhibiting CDK2-dependent XIAP expression and delaying G1/S transition.\",\n      \"method\": \"Active-site mutagenesis (C140S phosphatase-dead mutant); overexpression and knockdown in K562 cells; xenograft mouse model; Western blot for CDK2 phosphorylation and XIAP expression; apoptosis assay; cell cycle analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — active-site mutagenesis establishing catalytic requirement, substrate (CDK2) and downstream effector (XIAP) identified, in vivo validation; single lab\",\n      \"pmids\": [\"25360622\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CDKN3 knockdown decreases cisplatin resistance in bladder cancer cells by inhibiting LDHA expression, thereby suppressing aerobic glycolysis; LDHA overexpression reverses glycolysis inhibition and chemosensitivity caused by CDKN3 knockdown, establishing LDHA as a downstream mediator of CDKN3-regulated chemoresistance.\",\n      \"method\": \"siRNA knockdown; LDHA overexpression rescue experiment; glycolysis measurement (glucose uptake, lactate production); cell viability assay; Western blot\",\n      \"journal\": \"OncoTargets and therapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — functional rescue experiment identifying LDHA as downstream mediator; single lab, limited mechanistic depth on direct enzymatic connection\",\n      \"pmids\": [\"35388272\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CDKN3 promotes cisplatin resistance in esophageal cancer via RAD51: CDKN3 inhibition reduces RAD51 expression, and RAD51 overexpression reverses cisplatin-induced DNA damage and chemosensitivity in CDKN3-knockdown esophageal cancer cells, placing RAD51 downstream of CDKN3 in the DNA damage repair pathway.\",\n      \"method\": \"siRNA knockdown; RAD51 overexpression rescue; in vitro and in vivo (xenograft) functional assays; Western blot; DNA damage assay (γH2AX)\",\n      \"journal\": \"Cancer management and research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — rescue experiment identifying RAD51 as downstream mediator, in vivo validation; single lab, no direct biochemical interaction shown\",\n      \"pmids\": [\"31114363\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PSMD12 (a 26S proteasome non-ATPase subunit) physically interacts with CDKN3 and reduces its ubiquitination level, thereby stabilizing CDKN3 protein; CDKN3 knockdown reverses PSMD12 overexpression-induced cell proliferation, indicating CDKN3 is a functional downstream effector of PSMD12.\",\n      \"method\": \"Co-immunoprecipitation; Western blot for ubiquitination; rescue (CDKN3 knockdown reversing PSMD12 overexpression phenotype); in vivo xenograft\",\n      \"journal\": \"Cancer gene therapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP identifying physical interaction, ubiquitination assay, functional rescue; single lab\",\n      \"pmids\": [\"37037907\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"GID2 (an E3 ubiquitin ligase subunit) physically interacts with CDKN3 and inhibits its ubiquitination, stabilizing CDKN3 protein; CDKN3 knockdown reverses GID2 overexpression-driven pancreatic cancer cell proliferation.\",\n      \"method\": \"Co-immunoprecipitation; ubiquitination assay; functional rescue by CDKN3 knockdown; in vivo xenograft\",\n      \"journal\": \"Laboratory investigation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP and ubiquitination assay in single lab, functional rescue experiment\",\n      \"pmids\": [\"36828188\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Estrogen receptors mediate sex-specific downregulation of E2F1 and its target gene CDKN3 in female epidermis following UV exposure; CDKN3 depletion impairs SCC cell progression into S-phase and reduces tumor growth in xenograft models, establishing an ER/E2F1/CDKN3 axis that protects females from UV-induced squamous cell carcinoma.\",\n      \"method\": \"UV-induced SCC mouse model (sex comparison); global transcriptional profiling; estrogen receptor perturbation; siRNA-mediated CDKN3 depletion; S-phase entry assay; xenograft tumor growth assay\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (transcriptomics, ER perturbation, functional KD with S-phase and xenograft readouts) in single study establishing pathway position; single lab\",\n      \"pmids\": [\"41876816\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"BACH1 transcription factor directly activates CDKN3 transcription in cardiomyocytes (confirmed by ChIP and luciferase assay); BACH1 disruption attenuates hypoxia/reoxygenation-induced apoptosis, ferroptosis, and inflammation partially by downregulating CDKN3, which in turn activates AMPK signaling.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP); luciferase reporter assay; CDKN3 knockdown/overexpression rescue; cell viability, apoptosis, and ferroptosis assays; Western blot for AMPK pathway\",\n      \"journal\": \"Cardiovascular toxicology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — ChIP and luciferase assay establishing direct transcriptional regulation, functional rescue; single lab\",\n      \"pmids\": [\"39060883\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"N-Myc directly binds the CDKN3 promoter and promotes CDKN3 transcription in neuroblastoma cells; CDKN3 knockdown induces neurite outgrowth and upregulates differentiation markers (NSE, βIII-tubulin, GAP43), while reducing proliferation markers (Ki67, PCNA); CDKN3, CDC6, and CDK4 form an interactive network that promotes expression of each other.\",\n      \"method\": \"ChIP (N-Myc binding to CDKN3 promoter); siRNA knockdown; high-content siRNA screen; Western blot for differentiation and proliferation markers; colony formation assay\",\n      \"journal\": \"Journal of Cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — ChIP establishing direct transcriptional regulation, functional phenotype by KD; single lab, network interaction not biochemically reconstituted\",\n      \"pmids\": [\"38356706\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CDKN3 knockdown arrests TNBC cells in G2M phase by downregulating CCNB2 (cyclin B2), establishing CDKN3 as a positive regulator of G2M progression through CCNB2.\",\n      \"method\": \"siRNA knockdown; cell cycle analysis by flow cytometry; Western blot for CCNB2; proliferation and migration assays\",\n      \"journal\": \"IUBMB life\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single method for CCNB2 connection; no direct biochemical interaction demonstrated\",\n      \"pmids\": [\"39865508\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CDKN3 overexpression increases HSP90 expression in TNBC cells; knockdown of CDKN3 decreases HSP90 expression; an HSP90 inhibitor reverses the pro-tumorigenic effects of CDKN3 overexpression, placing HSP90 downstream of CDKN3 in a ferroptosis-inhibiting pathway.\",\n      \"method\": \"Lentiviral overexpression and knockdown; HSP90 inhibitor rescue; ferroptosis markers (Fe2+, GSH, ROS, MDA); in vivo 4T1 mammary fat pad model; Western blot\",\n      \"journal\": \"Toxicology and applied pharmacology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, no direct biochemical interaction between CDKN3 and HSP90 demonstrated; functional rescue only\",\n      \"pmids\": [\"41207514\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"NOTE: Paper [4] (PMID 29168185) describing a CDKN3/MDM2/P53/P21 complex was formally RETRACTED (PMID 38059668) due to image duplications; its conclusions are considered unreliable and are excluded.\",\n      \"method\": \"RETRACTED — excluded\",\n      \"journal\": \"International journal of cancer\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Retracted paper — not included as a discovery\",\n      \"pmids\": [\"29168185\", \"38059668\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CDKN3 (CDI1/KAP) is a dual-specificity protein phosphatase that directly binds and dephosphorylates cyclin-dependent kinases (CDK2, CDC2/CDK1) — removing inhibitory/activating phosphorylations including Thr-161 of CDC2 during mitotic exit — and thereby controls G1/S transition and mitotic exit; it also interacts with Mps1 kinase at centrosomes to regulate Mps1 stability via proteasome-mediated degradation and prevent centrosome overduplication, while its expression is transcriptionally controlled by N-Myc and BACH1 and post-translationally stabilized by PSMD12 and GID2 through reduction of ubiquitination; downstream consequences of CDKN3 activity include modulation of XIAP (via CDK2), RAD51 (DNA repair/cisplatin resistance), LDHA (glycolysis/chemoresistance), and CCNB2 (G2M progression), and its catalytic activity is absolutely required for all observed cell-cycle and tumor-suppressive functions.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CDKN3 (CDI1/KAP) is a dual-specificity protein phosphatase that regulates cell-cycle progression by directly binding and dephosphorylating cyclin-dependent kinases [#0]. It forms stable complexes with CDK2 and interacts with CDC2/CDK1 and CDK3 but not CDK4, and its phosphatase activity is strictly required for its cell-cycle function, since an active-site C\\u2192S mutant both abolishes catalysis and abolishes the cell-cycle delay caused by overexpression [#0]. During mitotic exit CDKN3 dephosphorylates Thr-161 of CDC2/CDK1, with its substrate concentrated at kinetochores and centrosomes in early mitosis, and it acts through downstream phosphotargets that control the spindle checkpoint [#1]. At centrosomes CDKN3 directly binds Mps1 kinase, by which it is recruited to the centrosome, and limits centrosomal Mps1 levels through proteasome-mediated degradation in a self-regulated feedback loop that restrains centrosome overduplication [#2]. In cancer contexts CDKN3 catalytic activity underlies a tumor-suppressive role in Bcr-Abl leukemogenesis, where wild-type but not phosphatase-dead CDKN3 dephosphorylates CDK2 to lower CDK2-dependent XIAP expression and delay G1/S transition [#3]; in other tumor settings CDKN3 supports proliferation and chemoresistance through downstream effectors including RAD51 in DNA-damage repair [#5], LDHA-dependent aerobic glycolysis [#4], and CCNB2-driven G2/M progression [#11]. CDKN3 expression is transcriptionally driven by N-Myc in neuroblastoma [#10] and by BACH1 in cardiomyocytes [#9], placed under an ER/E2F1 axis in UV-exposed epidermis [#8], and its protein level is stabilized by PSMD12 and GID2 through reduced ubiquitination [#6, #7].\",\n  \"teleology\": [\n    {\n      \"year\": 1993,\n      \"claim\": \"Established the founding biochemical identity of CDKN3 as a CDK-binding dual-specificity phosphatase whose catalytic activity is essential for cell-cycle control, answering what kind of molecule it is and how it acts.\",\n      \"evidence\": \"Yeast two-hybrid, in vitro phosphatase assay, active-site C\\u2192S mutagenesis, and overexpression with cell-cycle readout in HeLa cells\",\n      \"pmids\": [\"8242750\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the physiological CDK phospho-site dephosphorylated in vivo\", \"Did not resolve which CDK partner is the dominant cellular substrate\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identified the in vivo substrate and timing of CDKN3 action, showing it removes the Thr-161 phosphate from CDC2/CDK1 at mitotic exit and feeds into spindle-checkpoint control.\",\n      \"evidence\": \"Genome-wide siRNA phosphatase screen, phospho-specific immunofluorescence across the cell cycle, and phosphokinome-wide mass spectrometry\",\n      \"pmids\": [\"23775190\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism coupling CDKN3 relocalization to substrate access not fully resolved\", \"Direct enzyme-substrate kinetics for Thr-161 not reconstituted\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined a centrosomal function distinct from CDK dephosphorylation, showing CDKN3 binds Mps1 to control its proteasomal turnover and prevent centrosome overduplication.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation, siRNA knockdown with centrosome-number readout, immunofluorescence localization, and proteasome inhibitor experiments\",\n      \"pmids\": [\"26586430\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether phosphatase activity is required for Mps1 regulation not established\", \"E3 ligase mediating Mps1 degradation not identified\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Connected catalytic activity to tumor suppression, showing CDKN3 dephosphorylates CDK2 to suppress XIAP and delay G1/S in leukemic cells.\",\n      \"evidence\": \"C140S phosphatase-dead mutant, overexpression/knockdown in K562 cells, xenograft model, and Western blot for CDK2 phosphorylation and XIAP\",\n      \"pmids\": [\"25360622\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Mechanism linking CDK2 activity to XIAP expression not detailed\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Placed CDKN3 upstream of DNA-damage repair, identifying RAD51 as a downstream mediator of CDKN3-driven cisplatin resistance.\",\n      \"evidence\": \"siRNA knockdown, RAD51 overexpression rescue, xenograft assays, and \\u03b3H2AX DNA-damage readout in esophageal cancer cells\",\n      \"pmids\": [\"31114363\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct biochemical interaction between CDKN3 and RAD51 shown\", \"Mechanism by which CDKN3 controls RAD51 expression unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Linked CDKN3 to tumor metabolism, showing it supports aerobic glycolysis and chemoresistance through LDHA.\",\n      \"evidence\": \"siRNA knockdown, LDHA overexpression rescue, glucose-uptake/lactate measurements, and viability assays in bladder cancer cells\",\n      \"pmids\": [\"35388272\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct enzymatic connection to LDHA not established\", \"Single lab\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Revealed post-translational control of CDKN3 abundance, identifying PSMD12 and GID2 as physical partners that stabilize CDKN3 by reducing its ubiquitination.\",\n      \"evidence\": \"Co-immunoprecipitation, ubiquitination assays, and CDKN3-knockdown rescue of overexpression phenotypes with xenograft validation\",\n      \"pmids\": [\"37037907\", \"36828188\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitin ligase/deubiquitinase mechanism for CDKN3 not fully defined\", \"Single lab per partner\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined transcriptional regulators of CDKN3, showing N-Myc and BACH1 directly drive its expression in neuroblastoma and cardiomyocytes respectively, with phenotypic consequences for differentiation and stress responses.\",\n      \"evidence\": \"ChIP and luciferase reporter assays, siRNA knockdown, and differentiation/proliferation or apoptosis/ferroptosis readouts\",\n      \"pmids\": [\"38356706\", \"39060883\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Downstream AMPK link in cardiomyocytes not biochemically traced to CDKN3 activity\", \"CDKN3/CDC6/CDK4 network not reconstituted in vitro\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Positioned CDKN3 within a sex-specific tumor-protective circuit, showing estrogen receptors downregulate E2F1 and its target CDKN3 to limit UV-induced squamous cell carcinoma.\",\n      \"evidence\": \"UV-induced SCC mouse model with sex comparison, transcriptional profiling, ER perturbation, and CDKN3 siRNA depletion with S-phase and xenograft readouts\",\n      \"pmids\": [\"41876816\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct ER occupancy at the CDKN3 locus not shown\", \"Single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CDKN3's defined phosphatase activity mechanistically connects to the diverse downstream effectors (RAD51, LDHA, CCNB2, HSP90) reported in tumor models remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct enzyme-substrate link between CDKN3 and these effectors established\", \"Whether catalytic activity is required for the metabolic and chemoresistance phenotypes untested in most contexts\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0, 1, 3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"CDK2\", \"CDK1\", \"MPS1\", \"PSMD12\", \"GID2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}