{"gene":"CCNL1","run_date":"2026-06-09T22:57:17","timeline":{"discoveries":[{"year":2022,"finding":"CCNL1 is a substrate of the SCF-FBXW7 E3 ubiquitin ligase complex; the CCNL1-CDK11 complex is critical at the G2-M phase of the cell cycle, and defective CCNL1 accumulation due to FBXW7 mutation leads to shorter mitotic time. Cells with FBXW7 loss-of-function are hypersensitive to CDK11 inhibition.","method":"Genome-wide CRISPR screens (synthetic lethal interaction), biochemical characterization of ubiquitination substrate, cell cycle analysis with FBXW7 mutant cells, CDK11 inhibitor treatment","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal genetic and biochemical evidence, CRISPR screen plus functional validation, multiple orthogonal methods in single study","pmids":["36278408"],"is_preprint":false},{"year":2025,"finding":"OGT (O-GlcNAc transferase) interacts with and stabilizes CCNL1 via O-GlcNAcylation; this post-translational modification is critical for CCNL1-mediated cancer cell proliferation and G0/G1 cell cycle progression.","method":"Co-immunoprecipitation, molecular docking, CCK-8 proliferation assay, flow cytometry, western blot, rescue experiments with OGT or CCNL1 overexpression","journal":"Discover oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP and rescue experiments in single lab, no in vitro reconstitution of O-GlcNAcylation","pmids":["41348282"],"is_preprint":false},{"year":2022,"finding":"Loss of CCNL1 activates the ERK/AKT/STAT3 survival pathway, causing pancreatic cancer cell resistance to gemcitabine treatment.","method":"Genome-wide CRISPR/Cas9 knockout screening followed by targeted CCNL1 knockout in TB32047 and PANC1 cell lines, with pathway analysis","journal":"Cancers","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — CRISPR KO with pathway readout, single lab, limited mechanistic depth beyond pathway activation","pmids":["35804923"],"is_preprint":false},{"year":2008,"finding":"CCNL1 co-localizes with TFIP11 and EWSR1 in nuclear speckle domains, consistent with participation in pre-mRNA splicing events; CCNL1 was identified as an interacting partner of TFIP11 by yeast two-hybrid assay.","method":"Yeast two-hybrid assay (prior work cited), fluorescently-tagged protein expression and confocal co-localization microscopy","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — yeast two-hybrid plus confocal co-localization, two methods but no reciprocal Co-IP or functional assay","pmids":["19122807"],"is_preprint":false},{"year":2006,"finding":"CCNL1 protein localizes to nuclear speckles in tumor cells, compatible with a role in RNA splicing.","method":"Immunofluorescence with CCNL1-specific antibody in head and neck squamous cell carcinoma tumor cells","journal":"British journal of cancer","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single immunofluorescence method, no functional validation of splicing role","pmids":["16598186"],"is_preprint":false},{"year":2015,"finding":"CCNL1 is a direct target of miR-199b-5p in Ewing's sarcoma cells; forced miR-199b-5p expression suppressed cell proliferation, invasion, and cell cycle progression, and promoted apoptosis by downregulating CCNL1.","method":"miR-199b-5p mimic transfection in A673 and TC252 cells, bioinformatic target prediction, direct target validation (luciferase reporter assay implied), cell proliferation/invasion/apoptosis assays","journal":"Molecular medicine reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, target validation method not explicitly stated as luciferase in abstract, limited mechanistic depth","pmids":["26043836"],"is_preprint":false},{"year":2022,"finding":"CCNL1 is a direct target of miR-5195-3p in prostate cancer cells; miR-5195-3p overexpression suppressed proliferation and G1/S cell cycle transition, effects mimicked by CCNL1 knockdown and reversed by CCNL1 overexpression.","method":"Luciferase reporter assay for direct target validation, CCK-8 proliferation assay, flow cytometry for cell cycle, xenograft in vivo model, qRT-PCR and western blot","journal":"Cellular & molecular biology letters","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — luciferase reporter plus rescue experiments plus in vivo validation, single lab but multiple orthogonal methods","pmids":["35260070"],"is_preprint":false},{"year":2026,"finding":"CCNL1 directly interacts with DVL3 (a negative correlation), activating the NF-κB signaling pathway and promoting the PI3K/AKT pathway, thereby driving breast cancer cell invasion, migration, proliferation, and EMT, and affecting paclitaxel sensitivity.","method":"Co-immunoprecipitation (Co-IP) for CCNL1-DVL3 interaction, plasmid transfection for overexpression, Transwell assay, wound-healing assay, western blot, rescue assay, bioinformatics","journal":"Molecular carcinogenesis","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP for interaction, single lab, no reconstitution or epistasis","pmids":["41632921"],"is_preprint":false},{"year":2024,"finding":"CCNL1 is required for HBV gene expression and replication in primary human hepatocytes; mechanistically, CCNL1 phosphorylates the C-terminal domain (CTD) of RNA Polymerase II at serine 2 (S2), and its knockdown inhibits binding of total and phospho-RNAPII and histone marks (H3ac, H3K27ac) to HBV cccDNA, implicating CCNL1 in regulation of cccDNA-dependent viral transcription.","method":"RNAi knockdown in primary human hepatocytes, pull-down experiments, ChIP-PCR on HBV cccDNA, whole transcriptome sequencing","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, single lab, pull-down and ChIP-PCR without full in vitro reconstitution of CTD kinase activity","pmids":["bio_10.1101_2024.10.23.619969"],"is_preprint":true},{"year":2025,"finding":"CCNL1 inhibition or miR-199b-5p overexpression in lung cancer cells promotes proliferation and reduces apoptosis; CCNL1 overexpression inhibits cell motility. Mechanistically, miR-199b-5p targets CCNL1 to inhibit CDK11 and upregulate TCF-4 and β-catenin, implicating the Wnt/β-catenin signaling pathway downstream of CCNL1.","method":"Exosome-mediated miR-199b-5p delivery, wound scratch/Transwell assays, qRT-PCR, western blot, in vivo lung metastasis model, target gene prediction and validation","journal":"Translational oncology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, indirect pathway inference, no direct CCNL1-CDK11 interaction assay","pmids":["41106272"],"is_preprint":false}],"current_model":"CCNL1 (Cyclin L1) is a nuclear speckle-localized protein that forms a complex with CDK11 to regulate G2-M cell cycle progression; it is subject to proteasomal degradation via SCF-FBXW7-mediated ubiquitination and stabilization by OGT-mediated O-GlcNAcylation, and participates in pre-mRNA splicing through interaction with spliceosomal proteins (TFIP11, EWSR1), while also modulating cancer cell survival signaling (ERK/AKT/STAT3, NF-κB, PI3K/AKT) and, in the context of HBV infection, phosphorylating RNA Polymerase II CTD at Ser2 to support viral transcription."},"narrative":{"mechanistic_narrative":"CCNL1 (Cyclin L1) is a nuclear speckle-localized cyclin that partners with the kinase CDK11 to regulate cell cycle progression, particularly the G2-M transition, where defective CCNL1 accumulation shortens mitotic time [PMID:36278408]. Its abundance is controlled by opposing post-translational mechanisms: it is targeted for ubiquitination and degradation by the SCF-FBXW7 E3 ligase complex, such that FBXW7 loss-of-function cells accumulate CCNL1 and become hypersensitive to CDK11 inhibition [PMID:36278408], while OGT-mediated O-GlcNAcylation stabilizes CCNL1 to support proliferation and cell cycle progression [PMID:41348282]. Consistent with its nuclear speckle localization, CCNL1 co-localizes with the splicing-associated proteins TFIP11 and EWSR1, linking it to pre-mRNA splicing [PMID:19122807]. Across cancer contexts CCNL1 levels modulate proliferation and survival signaling: it is a direct target of repressive microRNAs that constrain cell cycle progression [PMID:35260070], and its perturbation influences ERK/AKT/STAT3 survival signaling and chemotherapy resistance [PMID:35804923]. Beyond these themes, the CCNL1-CDK11 link to RNA Polymerase II CTD phosphorylation and downstream transcriptional roles remains only partially characterized in the available corpus.","teleology":[{"year":2006,"claim":"Establishing where CCNL1 acts in the cell was the first step toward a functional hypothesis; localizing it to nuclear speckles tied it to RNA processing machinery rather than bulk nucleoplasm.","evidence":"Immunofluorescence with a CCNL1-specific antibody in head and neck squamous carcinoma cells","pmids":["16598186"],"confidence":"Low","gaps":["Single immunofluorescence method without functional validation of a splicing role","No identification of associated splicing factors"]},{"year":2008,"claim":"To connect speckle localization to a molecular function, CCNL1 was placed in physical proximity to splicing-associated proteins, supporting participation in pre-mRNA splicing.","evidence":"Yeast two-hybrid (cited prior work) and confocal co-localization with TFIP11 and EWSR1","pmids":["19122807"],"confidence":"Medium","gaps":["No reciprocal Co-IP or functional splicing assay","Direct splicing substrates of a CCNL1-containing complex not defined"]},{"year":2015,"claim":"Cancer-context loss-of-function studies began testing whether CCNL1 levels drive proliferation; microRNA targeting linked CCNL1 downregulation to suppressed growth and cell cycle progression.","evidence":"miR-199b-5p mimic transfection with proliferation/invasion/apoptosis assays in Ewing's sarcoma cells","pmids":["26043836"],"confidence":"Low","gaps":["Direct target validation method not explicitly established","Downstream effector mechanism not defined"]},{"year":2022,"claim":"The core cell cycle mechanism was defined: CCNL1 functions with CDK11 at G2-M and is degraded by SCF-FBXW7, establishing both a kinase partner and the ubiquitin-ligase controlling its turnover, and revealing a synthetic-lethal vulnerability.","evidence":"Genome-wide CRISPR synthetic-lethal screens, biochemical ubiquitination characterization, FBXW7-mutant cell cycle analysis, and CDK11 inhibitor treatment","pmids":["36278408"],"confidence":"High","gaps":["Structural basis of CCNL1-CDK11 complex not resolved","Direct enzymatic substrates of the CCNL1-CDK11 kinase not enumerated"]},{"year":2022,"claim":"CCNL1 was linked to chemotherapy response, showing that its loss rewires survival signaling and confers drug resistance.","evidence":"Genome-wide CRISPR knockout screening and targeted CCNL1 knockout with ERK/AKT/STAT3 pathway analysis in pancreatic cancer lines","pmids":["35804923"],"confidence":"Medium","gaps":["Mechanism connecting CCNL1 loss to pathway activation not resolved","Limited to gemcitabine context"]},{"year":2022,"claim":"A second microRNA axis reinforced CCNL1's role in promoting the G1/S transition via rescue experiments and in vivo validation.","evidence":"Luciferase reporter validation, CCK-8 and flow cytometry, plus xenograft model in prostate cancer cells","pmids":["35260070"],"confidence":"Medium","gaps":["Molecular effectors downstream of CCNL1 in G1/S not defined"]},{"year":2024,"claim":"A transcriptional role was probed by testing whether CCNL1 supports viral gene expression through RNA Polymerase II CTD phosphorylation.","evidence":"RNAi knockdown in primary human hepatocytes, pull-down, and ChIP-PCR on HBV cccDNA (preprint)","pmids":["bio_10.1101_2024.10.23.619969"],"confidence":"Low","gaps":["Preprint; CTD kinase activity not reconstituted in vitro","Direct versus indirect contribution of CCNL1 to RNAPII Ser2 phosphorylation unresolved"]},{"year":2025,"claim":"CCNL1 stability control was extended by identifying OGT-mediated O-GlcNAcylation as a stabilizing modification supporting proliferation.","evidence":"Co-IP, molecular docking, CCK-8, flow cytometry, and OGT/CCNL1 rescue experiments","pmids":["41348282"],"confidence":"Medium","gaps":["O-GlcNAcylation not reconstituted in vitro","Modified residues not mapped"]},{"year":2026,"claim":"A direct interaction with DVL3 was reported to couple CCNL1 to NF-kB and PI3K/AKT signaling in breast cancer invasion and chemosensitivity.","evidence":"Co-IP, overexpression, Transwell/wound-healing assays, and rescue in breast cancer cells","pmids":["41632921"],"confidence":"Low","gaps":["Single Co-IP without reciprocal validation or reconstitution","Epistasis linking interaction to pathway activation not established"]},{"year":null,"claim":"Whether CCNL1's cell cycle, splicing, and signaling activities are mechanistically unified through a single CCNL1-CDK11 catalytic output remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of the CCNL1-CDK11 complex","Direct catalytic substrates and splicing targets not defined","Mechanistic basis linking CCNL1 abundance to ERK/AKT/STAT3, NF-kB, and Wnt pathway outputs unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[3,4]}],"pathway":[{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0]}],"complexes":["CCNL1-CDK11"],"partners":["CDK11","FBXW7","OGT","TFIP11","EWSR1","DVL3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UK58","full_name":"Cyclin-L1","aliases":[],"length_aa":526,"mass_kda":59.6,"function":"Regulatory component of the cyclin-L-CDK11 complex that regulates transcription and pre-mRNA splicing (PubMed:11980906, PubMed:18216018, PubMed:38059508). Inhibited by the CDK-specific inhibitor CDKN1A/p21 (PubMed:11980906). May be a candidate proto-oncogene in head and neck squamous cell carcinomas (HNSCC) (PubMed:12414649, PubMed:15700036)","subcellular_location":"Nucleus speckle; Nucleus, nucleoplasm","url":"https://www.uniprot.org/uniprotkb/Q9UK58/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/CCNL1","classification":"Common Essential","n_dependent_lines":779,"n_total_lines":1208,"dependency_fraction":0.6448675496688742},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CSNK2B","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CCNL1","total_profiled":1310},"omim":[{"mim_id":"613460","title":"FASTING PLASMA GLUCOSE LEVEL QUANTITATIVE TRAIT LOCUS 6; FGQTL6","url":"https://www.omim.org/entry/613460"},{"mim_id":"613459","title":"BIRTH WEIGHT QUANTITATIVE TRAIT LOCUS 2; BWQTL2","url":"https://www.omim.org/entry/613459"},{"mim_id":"613384","title":"CYCLIN L1; CCNL1","url":"https://www.omim.org/entry/613384"},{"mim_id":"613219","title":"FASTING PLASMA GLUCOSE LEVEL QUANTITATIVE TRAIT LOCUS 2; FGQTL2","url":"https://www.omim.org/entry/613219"},{"mim_id":"176873","title":"CYCLIN-DEPENDENT KINASE 11B; CDK11B","url":"https://www.omim.org/entry/176873"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CCNL1"},"hgnc":{"alias_symbol":["ania-6a"],"prev_symbol":[]},"alphafold":{"accession":"Q9UK58","domains":[{"cath_id":"1.10.472.10","chopping":"61-198","consensus_level":"medium","plddt":93.5643,"start":61,"end":198},{"cath_id":"1.10.472.10","chopping":"199-291","consensus_level":"medium","plddt":94.8928,"start":199,"end":291}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UK58","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UK58-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UK58-F1-predicted_aligned_error_v6.png","plddt_mean":68.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CCNL1","jax_strain_url":"https://www.jax.org/strain/search?query=CCNL1"},"sequence":{"accession":"Q9UK58","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UK58.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UK58/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UK58"}},"corpus_meta":[{"pmid":"33552682","id":"PMC_33552682","title":"Long non-coding RNA lnc-CCNL1-3:1 promotes granulosa cell apoptosis and suppresses glucose uptake in women with polycystic ovary syndrome.","date":"2020","source":"Molecular therapy. Nucleic acids","url":"https://pubmed.ncbi.nlm.nih.gov/33552682","citation_count":37,"is_preprint":false},{"pmid":"21586274","id":"PMC_21586274","title":"A fine balance between CCNL1 and TIMP1 contributes to the development of breast cancer cells.","date":"2011","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/21586274","citation_count":28,"is_preprint":false},{"pmid":"16598186","id":"PMC_16598186","title":"Cyclin L1 (CCNL1) gene alterations in human head and neck squamous cell carcinoma.","date":"2006","source":"British journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/16598186","citation_count":18,"is_preprint":false},{"pmid":"35804923","id":"PMC_35804923","title":"Genome-Wide CRISPR Screening Identifies DCK and CCNL1 as Genes That Contribute to Gemcitabine Resistance in Pancreatic Cancer.","date":"2022","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/35804923","citation_count":16,"is_preprint":false},{"pmid":"36278408","id":"PMC_36278408","title":"SCFFBXW7 regulates G2-M progression through control of CCNL1 ubiquitination.","date":"2022","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/36278408","citation_count":14,"is_preprint":false},{"pmid":"19122807","id":"PMC_19122807","title":"TFIP11, CCNL1 and EWSR1 Protein-protein Interactions, and Their Nuclear Localization.","date":"2008","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/19122807","citation_count":11,"is_preprint":false},{"pmid":"26043836","id":"PMC_26043836","title":"Overexpression of miR‑199b‑5p inhibits Ewing's sarcoma cell lines by targeting CCNL1.","date":"2015","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/26043836","citation_count":11,"is_preprint":false},{"pmid":"35260070","id":"PMC_35260070","title":"MiR-5195-3p functions as a tumor suppressor in prostate cancer via targeting CCNL1.","date":"2022","source":"Cellular & molecular biology letters","url":"https://pubmed.ncbi.nlm.nih.gov/35260070","citation_count":10,"is_preprint":false},{"pmid":"27607899","id":"PMC_27607899","title":"Association between LEKR1-CCNL1 and IGSF21-KLHDC7A gene polymorphisms and diabetic retinopathy of type 2 diabetes mellitus in the Chinese Han population.","date":"2016","source":"The journal of gene medicine","url":"https://pubmed.ncbi.nlm.nih.gov/27607899","citation_count":10,"is_preprint":false},{"pmid":"41348282","id":"PMC_41348282","title":"Lidocaine suppresses HER2-positive breast cancer cell proliferation by targeting the OGT-CCNL1 axis.","date":"2025","source":"Discover oncology","url":"https://pubmed.ncbi.nlm.nih.gov/41348282","citation_count":1,"is_preprint":false},{"pmid":"41106272","id":"PMC_41106272","title":"Tumor-derived exosomal miR-199b-5p promotes proliferation and epithelial-mesenchymal transition in non-small cell lung cancer by targeting CCNL1.","date":"2025","source":"Translational oncology","url":"https://pubmed.ncbi.nlm.nih.gov/41106272","citation_count":0,"is_preprint":false},{"pmid":"41632921","id":"PMC_41632921","title":"CCNL1 Activates the NF-κB Pathway Through DVL3 Inhibition and PI3K/AKT Pathway Promotion in Breast Cancer.","date":"2026","source":"Molecular carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/41632921","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.10.23.619969","title":"Identification of Cyclin L1 as a host factor regulating Hepatitis B Virus replication","date":"2024-10-24","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.23.619969","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.04.01.646534","title":"Cellular and molecular mechanism for reproductive capacity of male Mongolian cattle basing on single-cell sequencing for testis","date":"2025-04-03","source":"bioRxiv","url":"https://doi.org/10.1101/2025.04.01.646534","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9412,"output_tokens":2531,"usd":0.0331,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9608,"output_tokens":2912,"usd":0.06042,"stage2_stop_reason":"end_turn"},"total_usd":0.09352,"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\": 2022,\n      \"finding\": \"CCNL1 is a substrate of the SCF-FBXW7 E3 ubiquitin ligase complex; the CCNL1-CDK11 complex is critical at the G2-M phase of the cell cycle, and defective CCNL1 accumulation due to FBXW7 mutation leads to shorter mitotic time. Cells with FBXW7 loss-of-function are hypersensitive to CDK11 inhibition.\",\n      \"method\": \"Genome-wide CRISPR screens (synthetic lethal interaction), biochemical characterization of ubiquitination substrate, cell cycle analysis with FBXW7 mutant cells, CDK11 inhibitor treatment\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal genetic and biochemical evidence, CRISPR screen plus functional validation, multiple orthogonal methods in single study\",\n      \"pmids\": [\"36278408\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"OGT (O-GlcNAc transferase) interacts with and stabilizes CCNL1 via O-GlcNAcylation; this post-translational modification is critical for CCNL1-mediated cancer cell proliferation and G0/G1 cell cycle progression.\",\n      \"method\": \"Co-immunoprecipitation, molecular docking, CCK-8 proliferation assay, flow cytometry, western blot, rescue experiments with OGT or CCNL1 overexpression\",\n      \"journal\": \"Discover oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP and rescue experiments in single lab, no in vitro reconstitution of O-GlcNAcylation\",\n      \"pmids\": [\"41348282\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Loss of CCNL1 activates the ERK/AKT/STAT3 survival pathway, causing pancreatic cancer cell resistance to gemcitabine treatment.\",\n      \"method\": \"Genome-wide CRISPR/Cas9 knockout screening followed by targeted CCNL1 knockout in TB32047 and PANC1 cell lines, with pathway analysis\",\n      \"journal\": \"Cancers\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — CRISPR KO with pathway readout, single lab, limited mechanistic depth beyond pathway activation\",\n      \"pmids\": [\"35804923\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"CCNL1 co-localizes with TFIP11 and EWSR1 in nuclear speckle domains, consistent with participation in pre-mRNA splicing events; CCNL1 was identified as an interacting partner of TFIP11 by yeast two-hybrid assay.\",\n      \"method\": \"Yeast two-hybrid assay (prior work cited), fluorescently-tagged protein expression and confocal co-localization microscopy\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — yeast two-hybrid plus confocal co-localization, two methods but no reciprocal Co-IP or functional assay\",\n      \"pmids\": [\"19122807\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"CCNL1 protein localizes to nuclear speckles in tumor cells, compatible with a role in RNA splicing.\",\n      \"method\": \"Immunofluorescence with CCNL1-specific antibody in head and neck squamous cell carcinoma tumor cells\",\n      \"journal\": \"British journal of cancer\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single immunofluorescence method, no functional validation of splicing role\",\n      \"pmids\": [\"16598186\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CCNL1 is a direct target of miR-199b-5p in Ewing's sarcoma cells; forced miR-199b-5p expression suppressed cell proliferation, invasion, and cell cycle progression, and promoted apoptosis by downregulating CCNL1.\",\n      \"method\": \"miR-199b-5p mimic transfection in A673 and TC252 cells, bioinformatic target prediction, direct target validation (luciferase reporter assay implied), cell proliferation/invasion/apoptosis assays\",\n      \"journal\": \"Molecular medicine reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, target validation method not explicitly stated as luciferase in abstract, limited mechanistic depth\",\n      \"pmids\": [\"26043836\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CCNL1 is a direct target of miR-5195-3p in prostate cancer cells; miR-5195-3p overexpression suppressed proliferation and G1/S cell cycle transition, effects mimicked by CCNL1 knockdown and reversed by CCNL1 overexpression.\",\n      \"method\": \"Luciferase reporter assay for direct target validation, CCK-8 proliferation assay, flow cytometry for cell cycle, xenograft in vivo model, qRT-PCR and western blot\",\n      \"journal\": \"Cellular & molecular biology letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — luciferase reporter plus rescue experiments plus in vivo validation, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"35260070\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"CCNL1 directly interacts with DVL3 (a negative correlation), activating the NF-κB signaling pathway and promoting the PI3K/AKT pathway, thereby driving breast cancer cell invasion, migration, proliferation, and EMT, and affecting paclitaxel sensitivity.\",\n      \"method\": \"Co-immunoprecipitation (Co-IP) for CCNL1-DVL3 interaction, plasmid transfection for overexpression, Transwell assay, wound-healing assay, western blot, rescue assay, bioinformatics\",\n      \"journal\": \"Molecular carcinogenesis\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP for interaction, single lab, no reconstitution or epistasis\",\n      \"pmids\": [\"41632921\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CCNL1 is required for HBV gene expression and replication in primary human hepatocytes; mechanistically, CCNL1 phosphorylates the C-terminal domain (CTD) of RNA Polymerase II at serine 2 (S2), and its knockdown inhibits binding of total and phospho-RNAPII and histone marks (H3ac, H3K27ac) to HBV cccDNA, implicating CCNL1 in regulation of cccDNA-dependent viral transcription.\",\n      \"method\": \"RNAi knockdown in primary human hepatocytes, pull-down experiments, ChIP-PCR on HBV cccDNA, whole transcriptome sequencing\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, single lab, pull-down and ChIP-PCR without full in vitro reconstitution of CTD kinase activity\",\n      \"pmids\": [\"bio_10.1101_2024.10.23.619969\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CCNL1 inhibition or miR-199b-5p overexpression in lung cancer cells promotes proliferation and reduces apoptosis; CCNL1 overexpression inhibits cell motility. Mechanistically, miR-199b-5p targets CCNL1 to inhibit CDK11 and upregulate TCF-4 and β-catenin, implicating the Wnt/β-catenin signaling pathway downstream of CCNL1.\",\n      \"method\": \"Exosome-mediated miR-199b-5p delivery, wound scratch/Transwell assays, qRT-PCR, western blot, in vivo lung metastasis model, target gene prediction and validation\",\n      \"journal\": \"Translational oncology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, indirect pathway inference, no direct CCNL1-CDK11 interaction assay\",\n      \"pmids\": [\"41106272\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CCNL1 (Cyclin L1) is a nuclear speckle-localized protein that forms a complex with CDK11 to regulate G2-M cell cycle progression; it is subject to proteasomal degradation via SCF-FBXW7-mediated ubiquitination and stabilization by OGT-mediated O-GlcNAcylation, and participates in pre-mRNA splicing through interaction with spliceosomal proteins (TFIP11, EWSR1), while also modulating cancer cell survival signaling (ERK/AKT/STAT3, NF-κB, PI3K/AKT) and, in the context of HBV infection, phosphorylating RNA Polymerase II CTD at Ser2 to support viral transcription.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CCNL1 (Cyclin L1) is a nuclear speckle-localized cyclin that partners with the kinase CDK11 to regulate cell cycle progression, particularly the G2-M transition, where defective CCNL1 accumulation shortens mitotic time [#0]. Its abundance is controlled by opposing post-translational mechanisms: it is targeted for ubiquitination and degradation by the SCF-FBXW7 E3 ligase complex, such that FBXW7 loss-of-function cells accumulate CCNL1 and become hypersensitive to CDK11 inhibition [#0], while OGT-mediated O-GlcNAcylation stabilizes CCNL1 to support proliferation and cell cycle progression [#1]. Consistent with its nuclear speckle localization, CCNL1 co-localizes with the splicing-associated proteins TFIP11 and EWSR1, linking it to pre-mRNA splicing [#3]. Across cancer contexts CCNL1 levels modulate proliferation and survival signaling: it is a direct target of repressive microRNAs that constrain cell cycle progression [#6], and its perturbation influences ERK/AKT/STAT3 survival signaling and chemotherapy resistance [#2]. Beyond these themes, the CCNL1-CDK11 link to RNA Polymerase II CTD phosphorylation and downstream transcriptional roles remains only partially characterized in the available corpus.\"\n,\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Establishing where CCNL1 acts in the cell was the first step toward a functional hypothesis; localizing it to nuclear speckles tied it to RNA processing machinery rather than bulk nucleoplasm.\",\n      \"evidence\": \"Immunofluorescence with a CCNL1-specific antibody in head and neck squamous carcinoma cells\",\n      \"pmids\": [\"16598186\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single immunofluorescence method without functional validation of a splicing role\", \"No identification of associated splicing factors\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"To connect speckle localization to a molecular function, CCNL1 was placed in physical proximity to splicing-associated proteins, supporting participation in pre-mRNA splicing.\",\n      \"evidence\": \"Yeast two-hybrid (cited prior work) and confocal co-localization with TFIP11 and EWSR1\",\n      \"pmids\": [\"19122807\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No reciprocal Co-IP or functional splicing assay\", \"Direct splicing substrates of a CCNL1-containing complex not defined\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Cancer-context loss-of-function studies began testing whether CCNL1 levels drive proliferation; microRNA targeting linked CCNL1 downregulation to suppressed growth and cell cycle progression.\",\n      \"evidence\": \"miR-199b-5p mimic transfection with proliferation/invasion/apoptosis assays in Ewing's sarcoma cells\",\n      \"pmids\": [\"26043836\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Direct target validation method not explicitly established\", \"Downstream effector mechanism not defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"The core cell cycle mechanism was defined: CCNL1 functions with CDK11 at G2-M and is degraded by SCF-FBXW7, establishing both a kinase partner and the ubiquitin-ligase controlling its turnover, and revealing a synthetic-lethal vulnerability.\",\n      \"evidence\": \"Genome-wide CRISPR synthetic-lethal screens, biochemical ubiquitination characterization, FBXW7-mutant cell cycle analysis, and CDK11 inhibitor treatment\",\n      \"pmids\": [\"36278408\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of CCNL1-CDK11 complex not resolved\", \"Direct enzymatic substrates of the CCNL1-CDK11 kinase not enumerated\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"CCNL1 was linked to chemotherapy response, showing that its loss rewires survival signaling and confers drug resistance.\",\n      \"evidence\": \"Genome-wide CRISPR knockout screening and targeted CCNL1 knockout with ERK/AKT/STAT3 pathway analysis in pancreatic cancer lines\",\n      \"pmids\": [\"35804923\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting CCNL1 loss to pathway activation not resolved\", \"Limited to gemcitabine context\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"A second microRNA axis reinforced CCNL1's role in promoting the G1/S transition via rescue experiments and in vivo validation.\",\n      \"evidence\": \"Luciferase reporter validation, CCK-8 and flow cytometry, plus xenograft model in prostate cancer cells\",\n      \"pmids\": [\"35260070\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular effectors downstream of CCNL1 in G1/S not defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"A transcriptional role was probed by testing whether CCNL1 supports viral gene expression through RNA Polymerase II CTD phosphorylation.\",\n      \"evidence\": \"RNAi knockdown in primary human hepatocytes, pull-down, and ChIP-PCR on HBV cccDNA (preprint)\",\n      \"pmids\": [\"bio_10.1101_2024.10.23.619969\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Preprint; CTD kinase activity not reconstituted in vitro\", \"Direct versus indirect contribution of CCNL1 to RNAPII Ser2 phosphorylation unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"CCNL1 stability control was extended by identifying OGT-mediated O-GlcNAcylation as a stabilizing modification supporting proliferation.\",\n      \"evidence\": \"Co-IP, molecular docking, CCK-8, flow cytometry, and OGT/CCNL1 rescue experiments\",\n      \"pmids\": [\"41348282\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"O-GlcNAcylation not reconstituted in vitro\", \"Modified residues not mapped\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"A direct interaction with DVL3 was reported to couple CCNL1 to NF-kB and PI3K/AKT signaling in breast cancer invasion and chemosensitivity.\",\n      \"evidence\": \"Co-IP, overexpression, Transwell/wound-healing assays, and rescue in breast cancer cells\",\n      \"pmids\": [\"41632921\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single Co-IP without reciprocal validation or reconstitution\", \"Epistasis linking interaction to pathway activation not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether CCNL1's cell cycle, splicing, and signaling activities are mechanistically unified through a single CCNL1-CDK11 catalytic output remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of the CCNL1-CDK11 complex\", \"Direct catalytic substrates and splicing targets not defined\", \"Mechanistic basis linking CCNL1 abundance to ERK/AKT/STAT3, NF-kB, and Wnt pathway outputs unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"CCNL1-CDK11\"],\n    \"partners\": [\"CDK11\", \"FBXW7\", \"OGT\", \"TFIP11\", \"EWSR1\", \"DVL3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}