{"gene":"CACUL1","run_date":"2026-06-09T22:57:17","timeline":{"discoveries":[{"year":2009,"finding":"CACUL1/CAC1 physically associates with CDK2 and promotes CDK2 kinase activity. The protein contains a Cullin domain and its expression is cell cycle-dependent, peaking in late G1 to S phase. Knockdown by RNAi induces G1/S arrest and inhibits cell proliferation.","method":"Co-immunoprecipitation, RNAi knockdown, cell cycle analysis, kinase activity assay","journal":"Cell cycle (Georgetown, Tex.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — physical association shown by co-IP, CDK2 kinase activity assay, and RNAi phenotype in single lab with multiple methods","pmids":["19829063"],"is_preprint":false},{"year":2012,"finding":"CACUL1/CAC1 functions as a corepressor of RARα by directly interacting with it via its CoRNR box and cooperating with HDACs to suppress RARα transcriptional activity. Depletion of CAC1 increases RA-induced neuronal differentiation of P19 cells with upregulation of the neuronal marker nestin.","method":"Co-immunoprecipitation, reporter assays, RNAi knockdown, differentiation assays","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — binding interaction via CoRNR box shown by Co-IP, functional repression confirmed by reporter assays and RNAi, single lab with multiple orthogonal methods","pmids":["22982681"],"is_preprint":false},{"year":2012,"finding":"CACUL1/CAC1 functions as a corepressor of ERα through its CoRNR box and associates with histone demethylase LSD1. CAC1 suppresses LSD1-enhanced ERα activity and impairs recruitment of ERα and LSD1 to ERα-responsive promoters, leading to increased H3K9me3 accumulation. CAC1 depletion reverses these effects.","method":"Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), reporter assays, RNAi knockdown","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal interactions shown by Co-IP, promoter occupancy by ChIP, functional activity by reporter assay, single lab with multiple orthogonal methods","pmids":["23178685"],"is_preprint":false},{"year":2015,"finding":"CACUL1 associates with the Cul3-Keap1 E3 ubiquitin ligase complex, leading to decreased Nrf2 ubiquitination and stabilization of Nrf2, thereby positively regulating the antioxidant stress response. CACUL1 is up-regulated by Nrf2-activating oxidative stresses, and its knockdown decreases Nrf2 activity and cell viability under stress.","method":"Co-immunoprecipitation, ubiquitination assays, RNAi knockdown, reporter assays","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — protein-complex association by Co-IP, direct ubiquitination measurement, functional knockdown phenotype, single lab with multiple orthogonal methods","pmids":["26238671"],"is_preprint":false},{"year":2015,"finding":"CACUL1 is a direct target of miR-106a* in esophageal carcinoma cells. Silencing CACUL1 blocks G1/S transition and suppresses cell proliferation by inhibiting CDK2 pathway cell cycle regulators Cyclin A and Cyclin E.","method":"Luciferase reporter assay, RNAi knockdown, flow cytometry, western blot","journal":"Cellular and molecular biology (Noisy-le-Grand, France)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct target validated by luciferase reporter, functional phenotype confirmed by RNAi with molecular pathway markers, single lab","pmids":["26314198"],"is_preprint":false},{"year":2016,"finding":"CACUL1 interacts with PML and suppresses PML SUMOylation, thereby regulating PML nuclear body (NB) size. SUMO-conjugating enzyme Ubc9 binds CACUL1 and antagonizes CACUL1-PML interaction. Through this mechanism CACUL1 attenuates p53 transcriptional activity.","method":"Co-immunoprecipitation, SUMOylation assays, fluorescence microscopy (NB size), reporter assays","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — protein interactions by Co-IP, direct SUMOylation measurement, functional p53 reporter assay, single lab with multiple orthogonal methods","pmids":["27889610"],"is_preprint":false},{"year":2016,"finding":"CACUL1 directly associates with androgen receptor (AR) and suppresses AR transcriptional activity. CACUL1 competes with LSD1 for AR binding, and depletion of CACUL1 enhances LSD1 occupancy at AR-target promoters with decreased H3K9me2 accumulation.","method":"Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), reporter assays, RNAi knockdown","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct protein interaction by Co-IP, promoter occupancy by ChIP, functional transcriptional assay, single lab with multiple orthogonal methods","pmids":["27085459"],"is_preprint":false},{"year":2017,"finding":"CACUL1 directly binds PPARγ via its CoRNR box 2 and represses PPARγ transcriptional activity and adipogenesis. CACUL1 recruits SIRT1 to PPARγ-responsive gene promoters; upon CACUL1 depletion, LSD1 replaces SIRT1, leading to increased H3K9 acetylation, decreased H3K9 methylation, and PPARγ activation in 3T3-L1 cells. This repressive function is reversed by fasting or resveratrol treatment.","method":"Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), RNAi knockdown, RNA sequencing, adipogenesis assays in 3T3-L1 cells and human adipose-derived stem cells","journal":"Cell death & disease","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct binding by Co-IP, promoter occupancy by ChIP, histone modification analysis, RNAi with transcriptomic validation, confirmed in two independent cell systems (3T3-L1 and human stem cells)","pmids":["29233982"],"is_preprint":false},{"year":2013,"finding":"CACUL1 upregulation via H. pylori-activated AP-1 transcription factor promotes expression of MMP-9 and Slug, enhancing invasion and metastasis of gastric cancer cells.","method":"Reporter assays (AP-1 activation), western blot, invasion/migration assays, RNAi knockdown","journal":"The international journal of biochemistry & cell biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, pathway linkage inferred from expression correlations and reporter assay without direct mechanistic reconstitution of CACUL1-MMP9/Slug axis","pmids":["24004834"],"is_preprint":false},{"year":2019,"finding":"CAC1/CACUL1 knockdown in 5-FU resistant colorectal cancer cells results in G1/S arrest, increased apoptosis, and decreased P-glycoprotein and MRP-1 protein expression, reversing drug resistance.","method":"Stable transfection/knockdown, flow cytometry, western blot, xenograft mouse model","journal":"PloS one","confidence":"Low","confidence_rationale":"Tier 3 / Weak — functional phenotype well-characterized but molecular mechanism connecting CACUL1 to P-gp/MRP-1 is not established, single lab","pmids":["31504073"],"is_preprint":false},{"year":2013,"finding":"CACUL1 expression is induced by DNA damage (UV radiation and chemotherapeutic drugs) in a p53-independent and post-transcriptional manner; high CACUL1 expression inhibits apoptosis and helps cells cross the G1/S checkpoint.","method":"Western blot, Northern blot, RNAi knockdown, UV/chemotherapy treatment, p53 wild-type and knockout cell lines","journal":"Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, mechanism inferred from expression kinetics and p53-null comparison without direct mechanistic reconstitution","pmids":["23643261"],"is_preprint":false}],"current_model":"CACUL1 (CAC1) is a Cullin-domain scaffold protein that physically associates with CDK2 to promote its kinase activity and cell cycle G1/S progression; acts as a nuclear receptor corepressor for PPARγ, ERα, AR, and RARα through its CoRNR box by differentially recruiting SIRT1 vs. LSD1 to regulate histone H3K9 modifications at target promoters; stabilizes Nrf2 by associating with the Cul3-Keap1 complex to inhibit Nrf2 ubiquitination; and suppresses p53 activity by binding PML and inhibiting its SUMOylation, thereby regulating PML nuclear body formation."},"narrative":{"mechanistic_narrative":"CACUL1 (CAC1) is a Cullin-domain scaffold protein that couples cell cycle progression to transcriptional repression and protein-stability control [PMID:19829063, PMID:29233982]. It physically associates with CDK2 and promotes CDK2 kinase activity, with expression peaking in late G1/S; its depletion arrests cells at the G1/S transition and inhibits proliferation through downregulation of Cyclin A and Cyclin E [PMID:19829063, PMID:26314198]. CACUL1 acts as a transcriptional corepressor of multiple nuclear receptors—RARα, ERα, AR, and PPARγ—engaging them directly through its CoRNR box motif [PMID:22982681, PMID:23178685, PMID:27085459, PMID:29233982]. At target promoters it represses receptor activity by differentially recruiting chromatin-modifying enzymes: it cooperates with HDACs and SIRT1 and competes with the demethylase LSD1, such that CACUL1 loss permits LSD1 occupancy and shifts the balance of histone H3K9 acetylation and methylation toward an active state, as shown most completely for PPARγ-driven adipogenesis [PMID:29233982], and for ERα and AR target genes [PMID:23178685, PMID:27085459]. Beyond transcription, CACUL1 controls two post-translational modification circuits: it associates with the Cul3-Keap1 E3 ligase complex to reduce Nrf2 ubiquitination and stabilize Nrf2, supporting the antioxidant stress response [PMID:26238671], and it binds PML to suppress PML SUMOylation, modulating PML nuclear body size and thereby attenuating p53 transcriptional activity [PMID:27889610].","teleology":[{"year":2009,"claim":"Established CACUL1 as a CDK2-associated cell cycle regulator, defining its first molecular function as a promoter of CDK2 activity required for G1/S progression.","evidence":"Co-IP, RNAi knockdown, cell cycle analysis and CDK2 kinase assays in cultured cells","pmids":["19829063"],"confidence":"Medium","gaps":["Does not resolve whether CACUL1 activates CDK2 directly via its Cullin domain or through an intermediary","No structural basis for the CDK2 interaction"]},{"year":2012,"claim":"Revealed CACUL1 as a CoRNR-box nuclear receptor corepressor, first for RARα and then ERα, linking it to histone-modifying machinery and showing it shapes differentiation and estrogen signaling outputs.","evidence":"Co-IP, reporter assays, ChIP, RNAi knockdown and differentiation assays (P19 cells)","pmids":["22982681","23178685"],"confidence":"Medium","gaps":["Whether HDAC versus LSD1 recruitment is context-dependent not resolved","No demonstration of a unified corepressor complex"]},{"year":2015,"claim":"Extended CACUL1 function beyond transcription by showing it engages the Cul3-Keap1 E3 ligase to stabilize Nrf2, placing CACUL1 in the oxidative stress response.","evidence":"Co-IP, ubiquitination assays, reporter assays and RNAi knockdown under oxidative stress","pmids":["26238671"],"confidence":"Medium","gaps":["Mechanism by which CACUL1 inhibits Keap1-directed Nrf2 ubiquitination is undefined","Whether CACUL1 is itself a Cul3 substrate adaptor not established"]},{"year":2016,"claim":"Defined the SIRT1/LSD1-switch logic of CACUL1 repression at AR target genes and uncovered a parallel role in regulating PML SUMOylation and p53 activity, broadening its scope to SUMO-dependent nuclear body control.","evidence":"Co-IP, ChIP, SUMOylation assays, fluorescence microscopy and reporter assays","pmids":["27085459","27889610"],"confidence":"Medium","gaps":["How CACUL1 mechanistically blocks Ubc9-mediated PML SUMOylation is unresolved","Connection between the transcriptional and SUMO-regulatory roles not integrated"]},{"year":2017,"claim":"Provided the most complete mechanistic model: CACUL1 binds PPARγ via CoRNR box 2, recruits SIRT1, and is displaced by LSD1 upon depletion, coupling H3K9 modification state to adipogenic gene activation.","evidence":"Co-IP, ChIP, histone modification analysis, RNA-seq and adipogenesis assays in 3T3-L1 cells and human adipose-derived stem cells","pmids":["29233982"],"confidence":"High","gaps":["Whether the SIRT1/LSD1 switch generalizes quantitatively to other receptors not tested in this system","In vivo physiological relevance to adipose tissue not addressed"]},{"year":null,"claim":"Whether CACUL1's distinct activities—CDK2 promotion, nuclear receptor corepression, Nrf2 stabilization, and PML/p53 regulation—reflect a single unifying biochemical mechanism of the Cullin domain or independent moonlighting functions remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of the Cullin domain or CoRNR box in complex with partners","No genetic loss-of-function model integrating the multiple pathways","Direct enzymatic activity of CACUL1, if any, undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[1,2,6,7]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,3,5]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,6,7]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2,5,6,7]}],"pathway":[{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0,4]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[1,2,6,7]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[3]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[2,6,7]}],"complexes":[],"partners":["CDK2","RARA","ESR1","AR","PPARG","PML","KEAP1","SIRT1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q86Y37","full_name":"CDK2-associated and cullin domain-containing protein 1","aliases":["Cdk-associated cullin 1"],"length_aa":369,"mass_kda":41.1,"function":"Cell cycle associated protein capable of promoting cell proliferation through the activation of CDK2 at the G1/S phase transition","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q86Y37/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CACUL1","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":[{"gene":"KPNA6","stoichiometry":4.0},{"gene":"PSMA2","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CACUL1","total_profiled":1310},"omim":[{"mim_id":"618764","title":"CDK2-ASSOCIATED CULLIN DOMAIN-CONTAINING PROTEIN 1; CACUL1","url":"https://www.omim.org/entry/618764"},{"mim_id":"180240","title":"RETINOIC ACID RECEPTOR, ALPHA; RARA","url":"https://www.omim.org/entry/180240"},{"mim_id":"133430","title":"ESTROGEN RECEPTOR 1; ESR1","url":"https://www.omim.org/entry/133430"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Uncertain","locations":[{"location":"Nucleoplasm","reliability":"Uncertain"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CACUL1"},"hgnc":{"alias_symbol":["FLJ40409","MGC33215","CAC1"],"prev_symbol":["C10orf46"]},"alphafold":{"accession":"Q86Y37","domains":[{"cath_id":"1.20.1310.10","chopping":"125-311","consensus_level":"medium","plddt":94.8209,"start":125,"end":311}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86Y37","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86Y37-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86Y37-F1-predicted_aligned_error_v6.png","plddt_mean":72.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CACUL1","jax_strain_url":"https://www.jax.org/strain/search?query=CACUL1"},"sequence":{"accession":"Q86Y37","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86Y37.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86Y37/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86Y37"}},"corpus_meta":[{"pmid":"16400172","id":"PMC_16400172","title":"Cryptococcus neoformans senses CO2 through the carbonic anhydrase Can2 and the adenylyl cyclase Cac1.","date":"2006","source":"Eukaryotic cell","url":"https://pubmed.ncbi.nlm.nih.gov/16400172","citation_count":133,"is_preprint":false},{"pmid":"9371803","id":"PMC_9371803","title":"The yeast Cac1 protein is required for the stable inheritance of transcriptionally repressed chromatin at telomeres.","date":"1997","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/9371803","citation_count":116,"is_preprint":false},{"pmid":"27690308","id":"PMC_27690308","title":"The Cac1 subunit of histone chaperone CAF-1 organizes CAF-1-H3/H4 architecture and tetramerizes histones.","date":"2016","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/27690308","citation_count":52,"is_preprint":false},{"pmid":"29233982","id":"PMC_29233982","title":"CACUL1 reciprocally regulates SIRT1 and LSD1 to repress PPARγ and inhibit adipogenesis.","date":"2017","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/29233982","citation_count":29,"is_preprint":false},{"pmid":"31077370","id":"PMC_31077370","title":"Screening the expression of several miRNAs from TaqMan Low Density Array in traumatic brain injury: miR-219a-5p regulates neuronal apoptosis by modulating CCNA2 and CACUL1.","date":"2019","source":"Journal of neurochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/31077370","citation_count":26,"is_preprint":false},{"pmid":"19829063","id":"PMC_19829063","title":"Identification and characterization of CAC1 as a novel CDK2-associated cullin.","date":"2009","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/19829063","citation_count":24,"is_preprint":false},{"pmid":"23178685","id":"PMC_23178685","title":"Negative regulation of ERα by a novel protein CAC1 through association with histone demethylase LSD1.","date":"2012","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/23178685","citation_count":20,"is_preprint":false},{"pmid":"24659785","id":"PMC_24659785","title":"Noncanonical Gβ Gib2 is a scaffolding protein promoting cAMP signaling through functions of Ras1 and Cac1 proteins in Cryptococcus neoformans.","date":"2014","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24659785","citation_count":18,"is_preprint":false},{"pmid":"31504073","id":"PMC_31504073","title":"CAC1 knockdown reverses drug resistance through the downregulation of P-gp and MRP-1 expression in colorectal cancer.","date":"2019","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/31504073","citation_count":17,"is_preprint":false},{"pmid":"22415352","id":"PMC_22415352","title":"Expression of the newly identified gene CAC1 in the hippocampus of Alzheimer's disease patients.","date":"2012","source":"Journal of molecular neuroscience : MN","url":"https://pubmed.ncbi.nlm.nih.gov/22415352","citation_count":13,"is_preprint":false},{"pmid":"27889610","id":"PMC_27889610","title":"CACUL1/CAC1 attenuates p53 activity through PML post-translational modification.","date":"2016","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/27889610","citation_count":12,"is_preprint":false},{"pmid":"24004834","id":"PMC_24004834","title":"Helicobacter pylori promotes invasion and metastasis of gastric cancer cells through activation of AP-1 and up-regulation of CACUL1.","date":"2013","source":"The international journal of biochemistry & cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/24004834","citation_count":11,"is_preprint":false},{"pmid":"22982681","id":"PMC_22982681","title":"CAC1 negatively regulates RARα activity through cooperation with HDAC.","date":"2012","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/22982681","citation_count":11,"is_preprint":false},{"pmid":"11115359","id":"PMC_11115359","title":"A newly characterized human endometrial adenocarcinoma cell line (CAC-1) differentiates in response to retinoic acid treatment.","date":"2000","source":"Experimental and molecular pathology","url":"https://pubmed.ncbi.nlm.nih.gov/11115359","citation_count":10,"is_preprint":false},{"pmid":"26238671","id":"PMC_26238671","title":"CACUL1/CAC1 Regulates the Antioxidant Response by Stabilizing Nrf2.","date":"2015","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/26238671","citation_count":8,"is_preprint":false},{"pmid":"15653329","id":"PMC_15653329","title":"Synthesis and evaluation of cis-hexahydropyrrolo[3,2-b]pyrrol-3-one peptidomimetic inhibitors of CAC1 cysteinyl proteinases.","date":"2005","source":"Bioorganic & medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15653329","citation_count":8,"is_preprint":false},{"pmid":"33025160","id":"PMC_33025160","title":"Cac1 WHD and PIP domains have distinct roles in replisome progression and genomic stability.","date":"2020","source":"Current genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33025160","citation_count":7,"is_preprint":false},{"pmid":"26314198","id":"PMC_26314198","title":"miR-106a* inhibits the proliferation of esophageal carcinoma cells by targeting CDK2-associated Cullin 1 (CACUL1).","date":"2015","source":"Cellular and molecular biology (Noisy-le-Grand, France)","url":"https://pubmed.ncbi.nlm.nih.gov/26314198","citation_count":7,"is_preprint":false},{"pmid":"36092343","id":"PMC_36092343","title":"Circular RNA ZFR promotes cell cycle arrest and apoptosis of colorectal cancer cells via the miR-147a/CACUL1 axis.","date":"2022","source":"Journal of gastrointestinal oncology","url":"https://pubmed.ncbi.nlm.nih.gov/36092343","citation_count":6,"is_preprint":false},{"pmid":"27085459","id":"PMC_27085459","title":"CACUL1 functions as a negative regulator of androgen receptor in prostate cancer cells.","date":"2016","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/27085459","citation_count":5,"is_preprint":false},{"pmid":"9500206","id":"PMC_9500206","title":"Cloning and characterization of a cDNA fragment coding beta-casein-like protein preferentially expressed in cervical adenocarcinoma cell line CAC-1.","date":"1998","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/9500206","citation_count":4,"is_preprint":false},{"pmid":"23643261","id":"PMC_23643261","title":"[Effect of cell cycle-related novel gene CACUL1 on the apoptosis of colorectal cancer cells in vitro].","date":"2013","source":"Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/23643261","citation_count":1,"is_preprint":false},{"pmid":"19663681","id":"PMC_19663681","title":"CA/C1 peptidases of the malaria parasites Plasmodium falciparum and P. berghei and their mammalian hosts--a bioinformatical analysis.","date":"2009","source":"Biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19663681","citation_count":1,"is_preprint":false},{"pmid":"38994075","id":"PMC_38994075","title":"Epigenetic silencing of miR-125a-3p promotes the progress of human cholangiocarcinoma via increasing CAC1 expression.","date":"2024","source":"Heliyon","url":"https://pubmed.ncbi.nlm.nih.gov/38994075","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12845,"output_tokens":2745,"usd":0.039855,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10086,"output_tokens":2514,"usd":0.05664,"stage2_stop_reason":"end_turn"},"total_usd":0.096495,"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\": 2009,\n      \"finding\": \"CACUL1/CAC1 physically associates with CDK2 and promotes CDK2 kinase activity. The protein contains a Cullin domain and its expression is cell cycle-dependent, peaking in late G1 to S phase. Knockdown by RNAi induces G1/S arrest and inhibits cell proliferation.\",\n      \"method\": \"Co-immunoprecipitation, RNAi knockdown, cell cycle analysis, kinase activity assay\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — physical association shown by co-IP, CDK2 kinase activity assay, and RNAi phenotype in single lab with multiple methods\",\n      \"pmids\": [\"19829063\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"CACUL1/CAC1 functions as a corepressor of RARα by directly interacting with it via its CoRNR box and cooperating with HDACs to suppress RARα transcriptional activity. Depletion of CAC1 increases RA-induced neuronal differentiation of P19 cells with upregulation of the neuronal marker nestin.\",\n      \"method\": \"Co-immunoprecipitation, reporter assays, RNAi knockdown, differentiation assays\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — binding interaction via CoRNR box shown by Co-IP, functional repression confirmed by reporter assays and RNAi, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"22982681\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"CACUL1/CAC1 functions as a corepressor of ERα through its CoRNR box and associates with histone demethylase LSD1. CAC1 suppresses LSD1-enhanced ERα activity and impairs recruitment of ERα and LSD1 to ERα-responsive promoters, leading to increased H3K9me3 accumulation. CAC1 depletion reverses these effects.\",\n      \"method\": \"Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), reporter assays, RNAi knockdown\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal interactions shown by Co-IP, promoter occupancy by ChIP, functional activity by reporter assay, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"23178685\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CACUL1 associates with the Cul3-Keap1 E3 ubiquitin ligase complex, leading to decreased Nrf2 ubiquitination and stabilization of Nrf2, thereby positively regulating the antioxidant stress response. CACUL1 is up-regulated by Nrf2-activating oxidative stresses, and its knockdown decreases Nrf2 activity and cell viability under stress.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, RNAi knockdown, reporter assays\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — protein-complex association by Co-IP, direct ubiquitination measurement, functional knockdown phenotype, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"26238671\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CACUL1 is a direct target of miR-106a* in esophageal carcinoma cells. Silencing CACUL1 blocks G1/S transition and suppresses cell proliferation by inhibiting CDK2 pathway cell cycle regulators Cyclin A and Cyclin E.\",\n      \"method\": \"Luciferase reporter assay, RNAi knockdown, flow cytometry, western blot\",\n      \"journal\": \"Cellular and molecular biology (Noisy-le-Grand, France)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct target validated by luciferase reporter, functional phenotype confirmed by RNAi with molecular pathway markers, single lab\",\n      \"pmids\": [\"26314198\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"CACUL1 interacts with PML and suppresses PML SUMOylation, thereby regulating PML nuclear body (NB) size. SUMO-conjugating enzyme Ubc9 binds CACUL1 and antagonizes CACUL1-PML interaction. Through this mechanism CACUL1 attenuates p53 transcriptional activity.\",\n      \"method\": \"Co-immunoprecipitation, SUMOylation assays, fluorescence microscopy (NB size), reporter assays\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — protein interactions by Co-IP, direct SUMOylation measurement, functional p53 reporter assay, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"27889610\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"CACUL1 directly associates with androgen receptor (AR) and suppresses AR transcriptional activity. CACUL1 competes with LSD1 for AR binding, and depletion of CACUL1 enhances LSD1 occupancy at AR-target promoters with decreased H3K9me2 accumulation.\",\n      \"method\": \"Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), reporter assays, RNAi knockdown\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct protein interaction by Co-IP, promoter occupancy by ChIP, functional transcriptional assay, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"27085459\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"CACUL1 directly binds PPARγ via its CoRNR box 2 and represses PPARγ transcriptional activity and adipogenesis. CACUL1 recruits SIRT1 to PPARγ-responsive gene promoters; upon CACUL1 depletion, LSD1 replaces SIRT1, leading to increased H3K9 acetylation, decreased H3K9 methylation, and PPARγ activation in 3T3-L1 cells. This repressive function is reversed by fasting or resveratrol treatment.\",\n      \"method\": \"Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), RNAi knockdown, RNA sequencing, adipogenesis assays in 3T3-L1 cells and human adipose-derived stem cells\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct binding by Co-IP, promoter occupancy by ChIP, histone modification analysis, RNAi with transcriptomic validation, confirmed in two independent cell systems (3T3-L1 and human stem cells)\",\n      \"pmids\": [\"29233982\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"CACUL1 upregulation via H. pylori-activated AP-1 transcription factor promotes expression of MMP-9 and Slug, enhancing invasion and metastasis of gastric cancer cells.\",\n      \"method\": \"Reporter assays (AP-1 activation), western blot, invasion/migration assays, RNAi knockdown\",\n      \"journal\": \"The international journal of biochemistry & cell biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, pathway linkage inferred from expression correlations and reporter assay without direct mechanistic reconstitution of CACUL1-MMP9/Slug axis\",\n      \"pmids\": [\"24004834\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CAC1/CACUL1 knockdown in 5-FU resistant colorectal cancer cells results in G1/S arrest, increased apoptosis, and decreased P-glycoprotein and MRP-1 protein expression, reversing drug resistance.\",\n      \"method\": \"Stable transfection/knockdown, flow cytometry, western blot, xenograft mouse model\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — functional phenotype well-characterized but molecular mechanism connecting CACUL1 to P-gp/MRP-1 is not established, single lab\",\n      \"pmids\": [\"31504073\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"CACUL1 expression is induced by DNA damage (UV radiation and chemotherapeutic drugs) in a p53-independent and post-transcriptional manner; high CACUL1 expression inhibits apoptosis and helps cells cross the G1/S checkpoint.\",\n      \"method\": \"Western blot, Northern blot, RNAi knockdown, UV/chemotherapy treatment, p53 wild-type and knockout cell lines\",\n      \"journal\": \"Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, mechanism inferred from expression kinetics and p53-null comparison without direct mechanistic reconstitution\",\n      \"pmids\": [\"23643261\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CACUL1 (CAC1) is a Cullin-domain scaffold protein that physically associates with CDK2 to promote its kinase activity and cell cycle G1/S progression; acts as a nuclear receptor corepressor for PPARγ, ERα, AR, and RARα through its CoRNR box by differentially recruiting SIRT1 vs. LSD1 to regulate histone H3K9 modifications at target promoters; stabilizes Nrf2 by associating with the Cul3-Keap1 complex to inhibit Nrf2 ubiquitination; and suppresses p53 activity by binding PML and inhibiting its SUMOylation, thereby regulating PML nuclear body formation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CACUL1 (CAC1) is a Cullin-domain scaffold protein that couples cell cycle progression to transcriptional repression and protein-stability control [#0, #7]. It physically associates with CDK2 and promotes CDK2 kinase activity, with expression peaking in late G1/S; its depletion arrests cells at the G1/S transition and inhibits proliferation through downregulation of Cyclin A and Cyclin E [#0, #4]. CACUL1 acts as a transcriptional corepressor of multiple nuclear receptors\\u2014RAR\\u03b1, ER\\u03b1, AR, and PPAR\\u03b3\\u2014engaging them directly through its CoRNR box motif [#1, #2, #6, #7]. At target promoters it represses receptor activity by differentially recruiting chromatin-modifying enzymes: it cooperates with HDACs and SIRT1 and competes with the demethylase LSD1, such that CACUL1 loss permits LSD1 occupancy and shifts the balance of histone H3K9 acetylation and methylation toward an active state, as shown most completely for PPAR\\u03b3-driven adipogenesis [#7], and for ER\\u03b1 and AR target genes [#2, #6]. Beyond transcription, CACUL1 controls two post-translational modification circuits: it associates with the Cul3-Keap1 E3 ligase complex to reduce Nrf2 ubiquitination and stabilize Nrf2, supporting the antioxidant stress response [#3], and it binds PML to suppress PML SUMOylation, modulating PML nuclear body size and thereby attenuating p53 transcriptional activity [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Established CACUL1 as a CDK2-associated cell cycle regulator, defining its first molecular function as a promoter of CDK2 activity required for G1/S progression.\",\n      \"evidence\": \"Co-IP, RNAi knockdown, cell cycle analysis and CDK2 kinase assays in cultured cells\",\n      \"pmids\": [\"19829063\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not resolve whether CACUL1 activates CDK2 directly via its Cullin domain or through an intermediary\", \"No structural basis for the CDK2 interaction\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Revealed CACUL1 as a CoRNR-box nuclear receptor corepressor, first for RAR\\u03b1 and then ER\\u03b1, linking it to histone-modifying machinery and showing it shapes differentiation and estrogen signaling outputs.\",\n      \"evidence\": \"Co-IP, reporter assays, ChIP, RNAi knockdown and differentiation assays (P19 cells)\",\n      \"pmids\": [\"22982681\", \"23178685\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether HDAC versus LSD1 recruitment is context-dependent not resolved\", \"No demonstration of a unified corepressor complex\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Extended CACUL1 function beyond transcription by showing it engages the Cul3-Keap1 E3 ligase to stabilize Nrf2, placing CACUL1 in the oxidative stress response.\",\n      \"evidence\": \"Co-IP, ubiquitination assays, reporter assays and RNAi knockdown under oxidative stress\",\n      \"pmids\": [\"26238671\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which CACUL1 inhibits Keap1-directed Nrf2 ubiquitination is undefined\", \"Whether CACUL1 is itself a Cul3 substrate adaptor not established\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Defined the SIRT1/LSD1-switch logic of CACUL1 repression at AR target genes and uncovered a parallel role in regulating PML SUMOylation and p53 activity, broadening its scope to SUMO-dependent nuclear body control.\",\n      \"evidence\": \"Co-IP, ChIP, SUMOylation assays, fluorescence microscopy and reporter assays\",\n      \"pmids\": [\"27085459\", \"27889610\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How CACUL1 mechanistically blocks Ubc9-mediated PML SUMOylation is unresolved\", \"Connection between the transcriptional and SUMO-regulatory roles not integrated\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Provided the most complete mechanistic model: CACUL1 binds PPAR\\u03b3 via CoRNR box 2, recruits SIRT1, and is displaced by LSD1 upon depletion, coupling H3K9 modification state to adipogenic gene activation.\",\n      \"evidence\": \"Co-IP, ChIP, histone modification analysis, RNA-seq and adipogenesis assays in 3T3-L1 cells and human adipose-derived stem cells\",\n      \"pmids\": [\"29233982\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the SIRT1/LSD1 switch generalizes quantitatively to other receptors not tested in this system\", \"In vivo physiological relevance to adipose tissue not addressed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether CACUL1's distinct activities\\u2014CDK2 promotion, nuclear receptor corepression, Nrf2 stabilization, and PML/p53 regulation\\u2014reflect a single unifying biochemical mechanism of the Cullin domain or independent moonlighting functions remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of the Cullin domain or CoRNR box in complex with partners\", \"No genetic loss-of-function model integrating the multiple pathways\", \"Direct enzymatic activity of CACUL1, if any, undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [1, 2, 6, 7]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 3, 5]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 6, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2, 5, 6, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [1, 2, 6, 7]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [2, 6, 7]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"CDK2\", \"RARA\", \"ESR1\", \"AR\", \"PPARG\", \"PML\", \"KEAP1\", \"SIRT1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}