{"gene":"CCNA1","run_date":"2026-06-09T22:57:17","timeline":{"discoveries":[{"year":2015,"finding":"HPV16 E7 oncoprotein induces CCNA1 promoter methylation and silences CCNA1 expression by forming a complex with DNMT1 at the CCNA1 promoter, as demonstrated by E7 knockdown/overexpression and ChIP assays in SiHa and C33a cells; the CR3 domain of E7 is required for this effect.","method":"siRNA knockdown, overexpression, ChIP assay, methylation-specific PCR, gene expression analysis in cervical cancer cell lines","journal":"Cancer science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal loss- and gain-of-function with ChIP validation in two cell lines, single lab","pmids":["26250467"],"is_preprint":false},{"year":2021,"finding":"EZH2 places H3K27me3 marks on the CCNA1 promoter to repress CCNA1 transcription in AML cells, promoting drug sensitivity; additionally, the transcription factor FOXA2 directly represses CCNA1 transcription, and loss of FOXA2 increases CCNA1 expression and chemoresistance.","method":"ChIP, promoter H3K27me3 modification analysis, EZH2 manipulation, FOXA2 overexpression/knockdown, drug sensitivity assays in AML cell lines","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP with functional rescue, single lab, two orthogonal regulatory mechanisms tested","pmids":["34509612"],"is_preprint":false},{"year":2023,"finding":"RNF6 binds directly to the CCNA1 promoter and transcriptionally activates CCNA1 expression in gastric cancer cells; silencing CCNA1 partially reverses the pro-tumorigenic effects of RNF6 overexpression, placing CCNA1 downstream of RNF6 in gastric cancer progression.","method":"ChIP-seq, promoter binding assay, siRNA silencing, overexpression, functional cell biology assays","journal":"Cell cycle (Georgetown, Tex.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP-seq with genetic epistasis (CCNA1 silencing reverses RNF6 phenotype), single lab","pmids":["37904524"],"is_preprint":false},{"year":2018,"finding":"miR-1271 directly targets the 3′UTR of CCNA1 and negatively regulates its expression, thereby activating the AMPK signaling pathway and suppressing HBV-associated HCC cell proliferation, migration, invasion, and HBV-DNA replication while promoting apoptosis.","method":"Dual-luciferase reporter assay, miR-1271 mimic/inhibitor transfection, siRNA against CCNA1, cell proliferation/migration/invasion/apoptosis assays","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — luciferase reporter validates direct targeting, functional rescue with siCCNA1, single lab","pmids":["30565670"],"is_preprint":false},{"year":2004,"finding":"Sequences within −1.3 kb of the Ccna1 transcriptional start site are sufficient to direct reporter expression specifically to late spermatocytes in transgenic mice, while sequences between −4.8 kb and −1.3 kb function as enhancer elements required for robust expression; conserved promoter elements include binding sites for A-myb, Hsf2, CDE, CHR, and CCAAT.","method":"Transgenic mouse reporter assay (lacZ), tissue-specific expression analysis, comparative promoter sequence analysis","journal":"Biology of reproduction","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo transgenic reporter with defined regulatory elements, single lab","pmids":["15215197"],"is_preprint":false},{"year":2024,"finding":"Downregulation of CCNA1 in osteoblasts activates the TGF-beta signaling pathway and promotes osteogenic differentiation; pharmacological inhibition of TGF-beta signaling partially reverses the pro-osteogenic effect of CCNA1 knockdown, placing CCNA1 upstream of the TGF-beta pathway in osteoblast biology.","method":"siRNA knockdown, KEGG pathway analysis, TGF-beta inhibitor rescue, Alizarin Red/ALP staining, osteogenic gene expression (qRT-PCR, Western blot), OVX mouse model","journal":"BMC musculoskeletal disorders","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, pathway placement relies on inhibitor rescue without direct binding/epistasis validation","pmids":["38454404"],"is_preprint":false},{"year":2026,"finding":"CCNA1 upregulation in radioresistant nasopharyngeal carcinoma cells promotes radioresistance by enhancing ROS antioxidant stress responses and anti-apoptotic signaling via the AKT/mTOR pathway; downregulation of CCNA1 re-sensitizes cells to radiation.","method":"RNA-seq in radioresistant cell lines, CCNA1 knockdown, radiosensitivity assays, apoptosis assays, ROS measurement, AKT/mTOR pathway analysis","journal":"Cellular oncology (Dordrecht, Netherlands)","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, pathway placement inferred from knockdown phenotype without direct mechanistic dissection of AKT/mTOR-CCNA1 interaction","pmids":["41604083"],"is_preprint":false},{"year":2023,"finding":"The histone demethylase KDM8 (JMJD5) regulates CCNA1 expression in oral squamous cell carcinoma; allyl isothiocyanate (AITC) treatment downregulates both KDM8 and CCNA1, increases H3K36me2, and suppresses OSCC proliferation in vitro and in vivo.","method":"Tissue microarray IHC, in vitro OSCC cell line experiments, patient-derived xenograft and subcutaneous xenograft in vivo models, AITC treatment","journal":"Biomedicines","confidence":"Low","confidence_rationale":"Tier 3 / Weak — co-expression and pharmacological modulation without direct mechanistic dissection of KDM8-CCNA1 regulatory axis","pmids":["37893043"],"is_preprint":false}],"current_model":"CCNA1 (Cyclin A1) is a cell-cycle regulator whose promoter is epigenetically silenced in HPV-associated cancers via an E7-DNMT1 complex that deposits methyl marks, while its transcription is also repressed by EZH2-mediated H3K27me3 and FOXA2, and activated by RNF6 binding; in germ cells its proximal promoter drives spermatocyte-specific expression, and in somatic cancer contexts CCNA1 promotes radioresistance through the AKT/mTOR pathway and is post-transcriptionally repressed by miR-1271, which links CCNA1 to AMPK signaling."},"narrative":{"mechanistic_narrative":"CCNA1 (Cyclin A1) is a transcriptionally regulated cell-cycle gene whose expression is tightly controlled at the chromatin level and contributes to proliferative and stress-response programs in both germ cells and cancer [PMID:26250467, PMID:15215197]. In germ cells, proximal sequences within −1.3 kb of the transcriptional start site are sufficient to drive spermatocyte-specific expression, with an upstream −4.8 to −1.3 kb region acting as an enhancer and conserved binding sites for A-myb, Hsf2, CDE, CHR, and CCAAT factors [PMID:15215197]. In cancer, CCNA1 is a target of convergent epigenetic and transcriptional repression: in HPV-associated cervical cancer the HPV16 E7 oncoprotein forms a complex with DNMT1 at the CCNA1 promoter, depositing methylation marks that silence the gene through its CR3 domain [PMID:26250467], while in AML EZH2 deposits H3K27me3 on the promoter and the transcription factor FOXA2 directly represses transcription, loss of which raises CCNA1 and confers chemoresistance [PMID:34509612]. CCNA1 is positively driven by RNF6, which binds the promoter and activates transcription to promote gastric cancer progression [PMID:37904524], and is post-transcriptionally silenced by miR-1271 targeting its 3′UTR, linking CCNA1 loss to AMPK activation and suppression of HBV-associated HCC [PMID:30565670]. Beyond these regulatory inputs, the molecular substrates and direct biochemical activity of the CCNA1 protein itself have not been characterized in the available corpus.","teleology":[{"year":2004,"claim":"Established the cis-regulatory architecture driving CCNA1's restricted germ-cell expression, defining where and how the gene is transcriptionally controlled in spermatocytes.","evidence":"Transgenic mouse lacZ reporter assay with promoter deletion mapping and comparative sequence analysis","pmids":["15215197"],"confidence":"Medium","gaps":["Does not identify which trans-acting factors occupy the conserved A-myb/Hsf2/CDE/CHR/CCAAT sites in vivo","Germ-cell regulation may differ from somatic/cancer contexts"]},{"year":2015,"claim":"Showed that CCNA1 is an epigenetic silencing target of a viral oncoprotein, explaining its promoter hypermethylation in HPV-associated cancer.","evidence":"E7 knockdown/overexpression, ChIP, and methylation-specific PCR in cervical cancer cell lines","pmids":["26250467"],"confidence":"Medium","gaps":["Functional consequence of CCNA1 silencing for tumor phenotype not dissected","Single lab, two cell lines"]},{"year":2018,"claim":"Identified post-transcriptional control of CCNA1 by a microRNA, linking its downregulation to AMPK signaling and tumor suppression.","evidence":"Dual-luciferase 3′UTR reporter, miR-1271 mimic/inhibitor, and siCCNA1 rescue in HBV-HCC cells","pmids":["30565670"],"confidence":"Medium","gaps":["Mechanism connecting CCNA1 loss to AMPK activation not resolved","Direct CCNA1 protein activity not addressed"]},{"year":2021,"claim":"Demonstrated two orthogonal transcriptional repression mechanisms (EZH2/H3K27me3 and FOXA2) controlling CCNA1 and tied its derepression to chemoresistance in AML.","evidence":"ChIP, H3K27me3 promoter analysis, EZH2/FOXA2 manipulation, and drug sensitivity assays in AML cell lines","pmids":["34509612"],"confidence":"Medium","gaps":["Whether EZH2 and FOXA2 act cooperatively or independently is unclear","No structural basis for FOXA2 promoter binding"]},{"year":2023,"claim":"Placed CCNA1 downstream of an activating transcription factor, RNF6, establishing a positive regulatory input distinct from its repressive epigenetic controls.","evidence":"ChIP-seq, promoter binding, and CCNA1-silencing epistasis in gastric cancer cells","pmids":["37904524"],"confidence":"Medium","gaps":["Direct binding versus indirect recruitment of RNF6 not fully separated","Effector function of CCNA1 in gastric cancer not defined"]},{"year":2023,"claim":"Linked a histone demethylase (KDM8) to CCNA1 regulation in oral squamous cell carcinoma, suggesting an additional chromatin-modifying input.","evidence":"Tissue microarray IHC, AITC pharmacological modulation, and xenograft models","pmids":["37893043"],"confidence":"Low","gaps":["Co-expression and drug response without direct demonstration of KDM8 acting at the CCNA1 locus","Single lab"]},{"year":2024,"claim":"Implicated CCNA1 as an upstream modulator of TGF-beta signaling in osteoblast differentiation, extending its role beyond cancer proliferation.","evidence":"siRNA knockdown, KEGG analysis, TGF-beta inhibitor rescue, and OVX mouse model","pmids":["38454404"],"confidence":"Low","gaps":["Pathway placement rests on inhibitor rescue without binding or direct epistasis","Mechanism connecting CCNA1 to TGF-beta unknown"]},{"year":2026,"claim":"Connected CCNA1 upregulation to radioresistance through ROS/antioxidant and AKT/mTOR-associated anti-apoptotic signaling in nasopharyngeal carcinoma.","evidence":"RNA-seq, CCNA1 knockdown, radiosensitivity/apoptosis assays, and ROS measurement in radioresistant cell lines","pmids":["41604083"],"confidence":"Low","gaps":["AKT/mTOR linkage inferred from phenotype without direct mechanistic dissection","Whether CCNA1 acts via canonical cyclin activity is untested"]},{"year":null,"claim":"The direct biochemical activity of the CCNA1 protein — its catalytic partners, substrates, and structural mechanism — remains uncharacterized in this corpus, which is dominated by transcriptional/epigenetic regulation of the gene rather than the protein's function.","evidence":"","pmids":[],"confidence":"Low","gaps":["No CDK partner or substrate identified in the timeline","No structural or enzymatic characterization","Causal role downstream of regulatory inputs not biochemically defined"]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,1,2,4]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[0,1]}],"complexes":[],"partners":[],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P78396","full_name":"Cyclin-A1","aliases":[],"length_aa":465,"mass_kda":52.4,"function":"May be involved in the control of the cell cycle at the G1/S (start) and G2/M (mitosis) transitions. May primarily function in the control of the germline meiotic cell cycle and additionally in the control of mitotic cell cycle in some somatic cells","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/P78396/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CCNA1","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/CCNA1","total_profiled":1310},"omim":[{"mim_id":"617376","title":"PROLINE-RICH CYCLIN A1-INTERACTING PROTEIN; PROCA1","url":"https://www.omim.org/entry/617376"},{"mim_id":"617375","title":"KELCH DOMAIN-CONTAINING PROTEIN 9; KLHDC9","url":"https://www.omim.org/entry/617375"},{"mim_id":"617374","title":"INHIBITOR OF CDK, CYCLIN A1-INTERACTING PROTEIN 1; INCA1","url":"https://www.omim.org/entry/617374"},{"mim_id":"615920","title":"PROLINE-RICH PROTEIN 11; PRR11","url":"https://www.omim.org/entry/615920"},{"mim_id":"614084","title":"WEE1 HOMOLOG 2; WEE2","url":"https://www.omim.org/entry/614084"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Nuclear bodies","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"parathyroid gland","ntpm":20.9},{"tissue":"testis","ntpm":76.0}],"url":"https://www.proteinatlas.org/search/CCNA1"},"hgnc":{"alias_symbol":["CT146"],"prev_symbol":[]},"alphafold":{"accession":"P78396","domains":[{"cath_id":"1.10.472.10","chopping":"228-336","consensus_level":"high","plddt":97.1646,"start":228,"end":336},{"cath_id":"1.10.472.10","chopping":"345-456","consensus_level":"high","plddt":95.5175,"start":345,"end":456}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P78396","model_url":"https://alphafold.ebi.ac.uk/files/AF-P78396-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P78396-F1-predicted_aligned_error_v6.png","plddt_mean":67.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CCNA1","jax_strain_url":"https://www.jax.org/strain/search?query=CCNA1"},"sequence":{"accession":"P78396","fasta_url":"https://rest.uniprot.org/uniprotkb/P78396.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P78396/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P78396"}},"corpus_meta":[{"pmid":"19843677","id":"PMC_19843677","title":"Methylation markers for CCNA1 and C13ORF18 are strongly associated with high-grade cervical intraepithelial neoplasia and cervical cancer in cervical scrapings.","date":"2009","source":"Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology","url":"https://pubmed.ncbi.nlm.nih.gov/19843677","citation_count":56,"is_preprint":false},{"pmid":"17689134","id":"PMC_17689134","title":"Promoter hypermethylation of CCNA1, RARRES1, and HRASLS3 in nasopharyngeal carcinoma.","date":"2007","source":"Oral oncology","url":"https://pubmed.ncbi.nlm.nih.gov/17689134","citation_count":45,"is_preprint":false},{"pmid":"25294903","id":"PMC_25294903","title":"DNA methylation status of key cell-cycle regulators such as CDKNA2/p16 and CCNA1 correlates with treatment response to doxorubicin and 5-fluorouracil in locally advanced breast tumors.","date":"2014","source":"Clinical cancer research : an official journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/25294903","citation_count":41,"is_preprint":false},{"pmid":"20708786","id":"PMC_20708786","title":"Cervical dysplasia: assessing methylation status (Methylight) of CCNA1, DAPK1, HS3ST2, PAX1 and TFPI2 to improve diagnostic accuracy.","date":"2010","source":"Gynecologic oncology","url":"https://pubmed.ncbi.nlm.nih.gov/20708786","citation_count":39,"is_preprint":false},{"pmid":"24359512","id":"PMC_24359512","title":"TIMP3 and CCNA1 hypermethylation in HNSCC is associated with an increased incidence of second primary tumors.","date":"2013","source":"Journal of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/24359512","citation_count":36,"is_preprint":false},{"pmid":"26250467","id":"PMC_26250467","title":"Human papillomavirus type 16 E7 oncoprotein mediates CCNA1 promoter methylation.","date":"2015","source":"Cancer science","url":"https://pubmed.ncbi.nlm.nih.gov/26250467","citation_count":29,"is_preprint":false},{"pmid":"25292097","id":"PMC_25292097","title":"CCNA1 promoter methylation: a potential marker for grading Papanicolaou smear cervical squamous intraepithelial lesions.","date":"2014","source":"Asian Pacific journal of cancer prevention : APJCP","url":"https://pubmed.ncbi.nlm.nih.gov/25292097","citation_count":22,"is_preprint":false},{"pmid":"30565670","id":"PMC_30565670","title":"MicroRNA-1271 functions as a potential tumor suppressor in hepatitis B virus-associated hepatocellular carcinoma through the AMPK signaling pathway by binding to CCNA1.","date":"2018","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/30565670","citation_count":21,"is_preprint":false},{"pmid":"15215197","id":"PMC_15215197","title":"Distinct regions of the mouse cyclin A1 gene, Ccna1, confer male germ-cell specific expression and enhancer function.","date":"2004","source":"Biology of reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/15215197","citation_count":20,"is_preprint":false},{"pmid":"31012142","id":"PMC_31012142","title":"Androgen-responsive lncRNA LINC00304 promotes cell cycle and proliferation via regulating CCNA1.","date":"2019","source":"The Prostate","url":"https://pubmed.ncbi.nlm.nih.gov/31012142","citation_count":17,"is_preprint":false},{"pmid":"37904524","id":"PMC_37904524","title":"RNF6 promotes gastric cancer progression by regulating CCNA1/CREBBP transcription.","date":"2023","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/37904524","citation_count":10,"is_preprint":false},{"pmid":"33007517","id":"PMC_33007517","title":"CCNA1 gene as a potential diagnostic marker in papillary thyroid cancer.","date":"2020","source":"Acta histochemica","url":"https://pubmed.ncbi.nlm.nih.gov/33007517","citation_count":9,"is_preprint":false},{"pmid":"31323962","id":"PMC_31323962","title":"Single Nucleotide Polymorphisms in SLC5A1, CCNA1, and ABCC1 and the Association with Litter Size in Small-Tail Han Sheep.","date":"2019","source":"Animals : an open access journal from MDPI","url":"https://pubmed.ncbi.nlm.nih.gov/31323962","citation_count":9,"is_preprint":false},{"pmid":"32102526","id":"PMC_32102526","title":"Value of CCNA1 promoter methylation in triaging ASC-US cytology.","date":"2020","source":"Asian Pacific journal of cancer prevention : APJCP","url":"https://pubmed.ncbi.nlm.nih.gov/32102526","citation_count":9,"is_preprint":false},{"pmid":"34509612","id":"PMC_34509612","title":"Histone methyltransferase EZH2 epigenetically affects CCNA1 expression in acute myeloid leukemia.","date":"2021","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/34509612","citation_count":8,"is_preprint":false},{"pmid":"25198553","id":"PMC_25198553","title":"Methylation in the promoters of HS3ST2 and CCNA1 genes is associated with cervical cancer in Uygur women in Xinjiang.","date":"2014","source":"The International journal of biological markers","url":"https://pubmed.ncbi.nlm.nih.gov/25198553","citation_count":8,"is_preprint":false},{"pmid":"31933719","id":"PMC_31933719","title":"The expressions of DNA methyltransferase 1 (DNMT1) and cyclin A1 (CCNA1) in cervical carcinogenesis.","date":"2019","source":"International journal of clinical and experimental pathology","url":"https://pubmed.ncbi.nlm.nih.gov/31933719","citation_count":6,"is_preprint":false},{"pmid":"37893043","id":"PMC_37893043","title":"Allyl Isothiocyanate Suppresses the Proliferation in Oral Squamous Cell Carcinoma via Mediating the KDM8/CCNA1 Axis.","date":"2023","source":"Biomedicines","url":"https://pubmed.ncbi.nlm.nih.gov/37893043","citation_count":5,"is_preprint":false},{"pmid":"38454404","id":"PMC_38454404","title":"Cyclin A1 (CCNA1) inhibits osteoporosis by suppressing transforming growth factor-beta (TGF-beta) pathway in osteoblasts.","date":"2024","source":"BMC musculoskeletal disorders","url":"https://pubmed.ncbi.nlm.nih.gov/38454404","citation_count":3,"is_preprint":false},{"pmid":"41604083","id":"PMC_41604083","title":"Akt/mTOR pathway-mediated CCNA1 regulation of radiotherapy resistance in nasopharyngeal carcinoma.","date":"2026","source":"Cellular oncology (Dordrecht, Netherlands)","url":"https://pubmed.ncbi.nlm.nih.gov/41604083","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.09.22.677916","title":"Elucidating the potential carcinogenic molecular mechanisms of parabens in head and neck squamous cell carcinoma through network toxicology and molecular docking","date":"2025-09-24","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.22.677916","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13610,"output_tokens":2055,"usd":0.035827,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9033,"output_tokens":2699,"usd":0.05632,"stage2_stop_reason":"end_turn"},"total_usd":0.092147,"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\": 2015,\n      \"finding\": \"HPV16 E7 oncoprotein induces CCNA1 promoter methylation and silences CCNA1 expression by forming a complex with DNMT1 at the CCNA1 promoter, as demonstrated by E7 knockdown/overexpression and ChIP assays in SiHa and C33a cells; the CR3 domain of E7 is required for this effect.\",\n      \"method\": \"siRNA knockdown, overexpression, ChIP assay, methylation-specific PCR, gene expression analysis in cervical cancer cell lines\",\n      \"journal\": \"Cancer science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal loss- and gain-of-function with ChIP validation in two cell lines, single lab\",\n      \"pmids\": [\"26250467\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"EZH2 places H3K27me3 marks on the CCNA1 promoter to repress CCNA1 transcription in AML cells, promoting drug sensitivity; additionally, the transcription factor FOXA2 directly represses CCNA1 transcription, and loss of FOXA2 increases CCNA1 expression and chemoresistance.\",\n      \"method\": \"ChIP, promoter H3K27me3 modification analysis, EZH2 manipulation, FOXA2 overexpression/knockdown, drug sensitivity assays in AML cell lines\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP with functional rescue, single lab, two orthogonal regulatory mechanisms tested\",\n      \"pmids\": [\"34509612\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RNF6 binds directly to the CCNA1 promoter and transcriptionally activates CCNA1 expression in gastric cancer cells; silencing CCNA1 partially reverses the pro-tumorigenic effects of RNF6 overexpression, placing CCNA1 downstream of RNF6 in gastric cancer progression.\",\n      \"method\": \"ChIP-seq, promoter binding assay, siRNA silencing, overexpression, functional cell biology assays\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP-seq with genetic epistasis (CCNA1 silencing reverses RNF6 phenotype), single lab\",\n      \"pmids\": [\"37904524\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"miR-1271 directly targets the 3′UTR of CCNA1 and negatively regulates its expression, thereby activating the AMPK signaling pathway and suppressing HBV-associated HCC cell proliferation, migration, invasion, and HBV-DNA replication while promoting apoptosis.\",\n      \"method\": \"Dual-luciferase reporter assay, miR-1271 mimic/inhibitor transfection, siRNA against CCNA1, cell proliferation/migration/invasion/apoptosis assays\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — luciferase reporter validates direct targeting, functional rescue with siCCNA1, single lab\",\n      \"pmids\": [\"30565670\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Sequences within −1.3 kb of the Ccna1 transcriptional start site are sufficient to direct reporter expression specifically to late spermatocytes in transgenic mice, while sequences between −4.8 kb and −1.3 kb function as enhancer elements required for robust expression; conserved promoter elements include binding sites for A-myb, Hsf2, CDE, CHR, and CCAAT.\",\n      \"method\": \"Transgenic mouse reporter assay (lacZ), tissue-specific expression analysis, comparative promoter sequence analysis\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo transgenic reporter with defined regulatory elements, single lab\",\n      \"pmids\": [\"15215197\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Downregulation of CCNA1 in osteoblasts activates the TGF-beta signaling pathway and promotes osteogenic differentiation; pharmacological inhibition of TGF-beta signaling partially reverses the pro-osteogenic effect of CCNA1 knockdown, placing CCNA1 upstream of the TGF-beta pathway in osteoblast biology.\",\n      \"method\": \"siRNA knockdown, KEGG pathway analysis, TGF-beta inhibitor rescue, Alizarin Red/ALP staining, osteogenic gene expression (qRT-PCR, Western blot), OVX mouse model\",\n      \"journal\": \"BMC musculoskeletal disorders\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, pathway placement relies on inhibitor rescue without direct binding/epistasis validation\",\n      \"pmids\": [\"38454404\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"CCNA1 upregulation in radioresistant nasopharyngeal carcinoma cells promotes radioresistance by enhancing ROS antioxidant stress responses and anti-apoptotic signaling via the AKT/mTOR pathway; downregulation of CCNA1 re-sensitizes cells to radiation.\",\n      \"method\": \"RNA-seq in radioresistant cell lines, CCNA1 knockdown, radiosensitivity assays, apoptosis assays, ROS measurement, AKT/mTOR pathway analysis\",\n      \"journal\": \"Cellular oncology (Dordrecht, Netherlands)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, pathway placement inferred from knockdown phenotype without direct mechanistic dissection of AKT/mTOR-CCNA1 interaction\",\n      \"pmids\": [\"41604083\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The histone demethylase KDM8 (JMJD5) regulates CCNA1 expression in oral squamous cell carcinoma; allyl isothiocyanate (AITC) treatment downregulates both KDM8 and CCNA1, increases H3K36me2, and suppresses OSCC proliferation in vitro and in vivo.\",\n      \"method\": \"Tissue microarray IHC, in vitro OSCC cell line experiments, patient-derived xenograft and subcutaneous xenograft in vivo models, AITC treatment\",\n      \"journal\": \"Biomedicines\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — co-expression and pharmacological modulation without direct mechanistic dissection of KDM8-CCNA1 regulatory axis\",\n      \"pmids\": [\"37893043\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CCNA1 (Cyclin A1) is a cell-cycle regulator whose promoter is epigenetically silenced in HPV-associated cancers via an E7-DNMT1 complex that deposits methyl marks, while its transcription is also repressed by EZH2-mediated H3K27me3 and FOXA2, and activated by RNF6 binding; in germ cells its proximal promoter drives spermatocyte-specific expression, and in somatic cancer contexts CCNA1 promotes radioresistance through the AKT/mTOR pathway and is post-transcriptionally repressed by miR-1271, which links CCNA1 to AMPK signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CCNA1 (Cyclin A1) is a transcriptionally regulated cell-cycle gene whose expression is tightly controlled at the chromatin level and contributes to proliferative and stress-response programs in both germ cells and cancer [#0, #4]. In germ cells, proximal sequences within −1.3 kb of the transcriptional start site are sufficient to drive spermatocyte-specific expression, with an upstream −4.8 to −1.3 kb region acting as an enhancer and conserved binding sites for A-myb, Hsf2, CDE, CHR, and CCAAT factors [#4]. In cancer, CCNA1 is a target of convergent epigenetic and transcriptional repression: in HPV-associated cervical cancer the HPV16 E7 oncoprotein forms a complex with DNMT1 at the CCNA1 promoter, depositing methylation marks that silence the gene through its CR3 domain [#0], while in AML EZH2 deposits H3K27me3 on the promoter and the transcription factor FOXA2 directly represses transcription, loss of which raises CCNA1 and confers chemoresistance [#1]. CCNA1 is positively driven by RNF6, which binds the promoter and activates transcription to promote gastric cancer progression [#2], and is post-transcriptionally silenced by miR-1271 targeting its 3′UTR, linking CCNA1 loss to AMPK activation and suppression of HBV-associated HCC [#3]. Beyond these regulatory inputs, the molecular substrates and direct biochemical activity of the CCNA1 protein itself have not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Established the cis-regulatory architecture driving CCNA1's restricted germ-cell expression, defining where and how the gene is transcriptionally controlled in spermatocytes.\",\n      \"evidence\": \"Transgenic mouse lacZ reporter assay with promoter deletion mapping and comparative sequence analysis\",\n      \"pmids\": [\"15215197\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not identify which trans-acting factors occupy the conserved A-myb/Hsf2/CDE/CHR/CCAAT sites in vivo\", \"Germ-cell regulation may differ from somatic/cancer contexts\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Showed that CCNA1 is an epigenetic silencing target of a viral oncoprotein, explaining its promoter hypermethylation in HPV-associated cancer.\",\n      \"evidence\": \"E7 knockdown/overexpression, ChIP, and methylation-specific PCR in cervical cancer cell lines\",\n      \"pmids\": [\"26250467\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of CCNA1 silencing for tumor phenotype not dissected\", \"Single lab, two cell lines\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identified post-transcriptional control of CCNA1 by a microRNA, linking its downregulation to AMPK signaling and tumor suppression.\",\n      \"evidence\": \"Dual-luciferase 3′UTR reporter, miR-1271 mimic/inhibitor, and siCCNA1 rescue in HBV-HCC cells\",\n      \"pmids\": [\"30565670\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting CCNA1 loss to AMPK activation not resolved\", \"Direct CCNA1 protein activity not addressed\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Demonstrated two orthogonal transcriptional repression mechanisms (EZH2/H3K27me3 and FOXA2) controlling CCNA1 and tied its derepression to chemoresistance in AML.\",\n      \"evidence\": \"ChIP, H3K27me3 promoter analysis, EZH2/FOXA2 manipulation, and drug sensitivity assays in AML cell lines\",\n      \"pmids\": [\"34509612\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether EZH2 and FOXA2 act cooperatively or independently is unclear\", \"No structural basis for FOXA2 promoter binding\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Placed CCNA1 downstream of an activating transcription factor, RNF6, establishing a positive regulatory input distinct from its repressive epigenetic controls.\",\n      \"evidence\": \"ChIP-seq, promoter binding, and CCNA1-silencing epistasis in gastric cancer cells\",\n      \"pmids\": [\"37904524\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding versus indirect recruitment of RNF6 not fully separated\", \"Effector function of CCNA1 in gastric cancer not defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Linked a histone demethylase (KDM8) to CCNA1 regulation in oral squamous cell carcinoma, suggesting an additional chromatin-modifying input.\",\n      \"evidence\": \"Tissue microarray IHC, AITC pharmacological modulation, and xenograft models\",\n      \"pmids\": [\"37893043\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Co-expression and drug response without direct demonstration of KDM8 acting at the CCNA1 locus\", \"Single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Implicated CCNA1 as an upstream modulator of TGF-beta signaling in osteoblast differentiation, extending its role beyond cancer proliferation.\",\n      \"evidence\": \"siRNA knockdown, KEGG analysis, TGF-beta inhibitor rescue, and OVX mouse model\",\n      \"pmids\": [\"38454404\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Pathway placement rests on inhibitor rescue without binding or direct epistasis\", \"Mechanism connecting CCNA1 to TGF-beta unknown\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Connected CCNA1 upregulation to radioresistance through ROS/antioxidant and AKT/mTOR-associated anti-apoptotic signaling in nasopharyngeal carcinoma.\",\n      \"evidence\": \"RNA-seq, CCNA1 knockdown, radiosensitivity/apoptosis assays, and ROS measurement in radioresistant cell lines\",\n      \"pmids\": [\"41604083\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"AKT/mTOR linkage inferred from phenotype without direct mechanistic dissection\", \"Whether CCNA1 acts via canonical cyclin activity is untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct biochemical activity of the CCNA1 protein — its catalytic partners, substrates, and structural mechanism — remains uncharacterized in this corpus, which is dominated by transcriptional/epigenetic regulation of the gene rather than the protein's function.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No CDK partner or substrate identified in the timeline\", \"No structural or enzymatic characterization\", \"Causal role downstream of regulatory inputs not biochemically defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 1, 2, 4]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}