{"gene":"ZNF652","run_date":"2026-06-11T09:02:07","timeline":{"discoveries":[{"year":2006,"finding":"ZNF652 was identified as a novel C2H2 zinc finger protein that physically interacts with the ETO family transcriptional repressor CBFA2T3 (putative breast tumor suppressor). The interaction occurs through the C-terminal 109 amino acids of ZNF652. Weaker interactions were also detected with CBFA2T1 and CBFA2T2. ZNF652 functions as a transcriptional repressor in reporter assays.","method":"Yeast two-hybrid screen, co-immunoprecipitation, transcriptional reporter assays, deletion mapping","journal":"Molecular cancer research : MCR","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP with domain mapping and transcriptional reporter validation, single lab","pmids":["16966434"],"is_preprint":false},{"year":2008,"finding":"ZNF652 forms a corepressor complex with CBFA2T3 to repress transcription of the E-box gene HEB. The complex binds a single ZNF652 response element in the HEB promoter. The NHR3 and NHR4 domains of CBFA2T3 interact with a conserved proline-rich region in the C-terminus of ZNF652. The ZNF652 consensus DNA binding sequence was identified and validated in vitro.","method":"ChIP, transcriptional reporter assays, DNA binding assays, co-immunoprecipitation, domain mutagenesis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (ChIP, reporter assay, in vitro DNA binding, Co-IP with domain mapping) in a single rigorous study","pmids":["18456661"],"is_preprint":false},{"year":2010,"finding":"ZNF651, a paralogue of ZNF652, shares the same DNA binding sequence as ZNF652 and represses target gene expression through formation of a CBFA2T3-ZNF651 corepressor complex, indicating that CBFA2T3-ZNF651 and CBFA2T3-ZNF652 perform functionally similar roles, potentially in a tissue-specific manner.","method":"DNA binding assays, co-immunoprecipitation, transcriptional reporter assays","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple methods (DNA binding, Co-IP, reporter assay), single lab; finding is about ZNF652 function by comparison with ZNF651","pmids":["20116376"],"is_preprint":false},{"year":2010,"finding":"Modulation of AR expression in LNCaP prostate cancer cells did not alter ZNF652 expression levels, and conversely, ZNF652 knockdown did not alter AR expression levels, indicating that ZNF652 and AR transcription factors act independently of each other.","method":"siRNA knockdown, Western blot / expression analysis in LNCaP cells","journal":"Oncology reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single negative result from knockdown/expression analysis, single lab, single method","pmids":["20204290"],"is_preprint":false},{"year":2011,"finding":"Genome-wide ChIP-chip mapping of ZNF652 binding sites in breast cancer cells identified a novel ZNF652 recognition motif (a 10-nucleotide core of a 13-nucleotide in vitro binding site) and revealed that ZNF652 targets gene promoters involved in diverse cellular pathways including cancer development and progression.","method":"ChIP-chip (chromatin immunoprecipitation with microarray), de novo motif scanning","journal":"Journal of cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide ChIP-chip with motif validation, single lab","pmids":["21678463"],"is_preprint":false},{"year":2020,"finding":"ZNF652 protein localizes to the nucleus of 293T cells, consistent with its role as a transcription factor.","method":"Immunofluorescence assay in 293T cells","journal":"Nan fang yi ke da xue xue bao = Journal of Southern Medical University","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single localization experiment, single lab, single method, no functional consequence directly tied to localization","pmids":["33380394"],"is_preprint":false},{"year":2023,"finding":"ZNF652 physically associates with the NuRD transcription co-repressor complex and represses transcription of a cohort of genes including PD-L1. Overexpression of ZNF652 inhibits PD-L1 transcription, while depletion of ZNF652 upregulates PD-L1, leading to immune evasion in triple-negative breast cancer.","method":"Co-immunoprecipitation (ZNF652-NuRD complex), ChIP, overexpression/knockdown with gene expression and functional immune evasion assays in vitro and in vivo","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP demonstrating NuRD complex association, ChIP confirming promoter binding, orthogonal OE/KD experiments with functional readouts in vitro and in vivo","pmids":["37906592"],"is_preprint":false},{"year":2021,"finding":"ZNF652 binds to the circRHOT1 promoter and regulates its expression transcriptionally in bladder cancer cells, as demonstrated by ChIP and luciferase reporter assays.","method":"ChIP assay, luciferase reporter assay, RNA pull-down","journal":"Journal of immunology research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, ChIP and reporter assay without comprehensive mechanistic follow-up","pmids":["34926705"],"is_preprint":false},{"year":2024,"finding":"ZNF652 directly binds the promoter of cyclin D3 (CCND3) and inhibits its transcription, thereby arresting the cell cycle at G1 phase in lung cancer cells. Ectopic expression of cyclin D3 rescued decreased cell viability and cell cycle arrest induced by ZNF652 overexpression.","method":"ChIP, promoter reporter assay, RNA-seq, overexpression/knockdown with cell cycle analysis, rescue experiments with CCND3","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP plus promoter reporter assay plus genetic rescue, single lab","pmids":["39500884"],"is_preprint":false},{"year":2025,"finding":"In HCC cells, ZNF652 transcriptionally activates circRHOT1 expression (binding to its promoter) and recruits the histone acetyltransferase KAT5 to the SLC38A6 promoter, increasing H3K27ac enrichment and activating SLC38A6 expression to promote HCC cell proliferation and inhibit apoptosis.","method":"ChIP, promoter binding assays, gene silencing/overexpression, rescue experiments","journal":"The Kaohsiung journal of medical sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP demonstrating promoter binding and histone modification, plus rescue experiments, single lab","pmids":["41311269"],"is_preprint":false},{"year":2026,"finding":"In hepatocellular carcinoma cells, ZNF652 binds to the PD-L1 promoter and activates its transcription, in contrast to its previously described repressor role in breast cancer. ZNF652 overexpression partially reversed the suppressive effects of PEITC on PD-L1 expression, while ZNF652 knockdown enhanced these effects.","method":"Bioinformatics, ChIP/promoter binding validation, overexpression/knockdown with PD-L1 expression and T cell cytotoxicity assays","journal":"Phytotherapy research : PTR","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, limited mechanistic validation described in abstract; contradicts breast cancer NuRD-repressor finding","pmids":["41983254"],"is_preprint":false}],"current_model":"ZNF652 is a nuclear C2H2 zinc finger transcription factor that primarily forms corepressor complexes — notably with CBFA2T3 (ETO family) and the NuRD complex — to bind specific promoter elements and repress target genes including HEB and PD-L1 in breast cancer; it also directly binds the cyclin D3 (CCND3) promoter to repress transcription and arrest the cell cycle at G1 in lung cancer, and transcriptionally activates circRHOT1 and recruits KAT5/H3K27ac to activate SLC38A6 in hepatocellular carcinoma, indicating context-dependent activator or repressor activity."},"narrative":{"mechanistic_narrative":"ZNF652 is a nuclear C2H2 zinc finger transcription factor that recognizes a defined DNA element in target gene promoters and acts predominantly as a sequence-specific transcriptional repressor through assembly of corepressor complexes [PMID:18456661, PMID:21678463]. Its repressive activity is mediated by direct physical interaction with the ETO-family corepressor CBFA2T3, an association formed through the C-terminal ~109 residues of ZNF652 and a conserved proline-rich region that engages the NHR3/NHR4 domains of CBFA2T3, enabling repression of E-box target genes such as HEB [PMID:16966434, PMID:18456661]. ZNF652 also associates with the NuRD corepressor complex to silence a cohort of genes including PD-L1, and loss of ZNF652 derepresses PD-L1 to drive immune evasion in triple-negative breast cancer [PMID:37906592]. Through direct promoter binding it represses the cyclin D3 (CCND3) gene to enforce G1 cell-cycle arrest in lung cancer, a phenotype rescued by ectopic cyclin D3 [PMID:39500884]. In other tumor contexts ZNF652 instead acts as an activator, transcriptionally inducing circRHOT1 and recruiting the histone acetyltransferase KAT5 to deposit H3K27ac at the SLC38A6 promoter [PMID:41311269], indicating context-dependent repressor or activator activity. A paralogous protein, ZNF651, shares the ZNF652 DNA-binding consensus and forms an analogous CBFA2T3 corepressor complex [PMID:20116376].","teleology":[{"year":2006,"claim":"Establishing ZNF652 as a transcriptional repressor required identifying a binding partner and a functional output; the discovery that it interacts with the ETO-family repressor CBFA2T3 and represses reporter transcription defined its core molecular role.","evidence":"Yeast two-hybrid screen, reciprocal Co-IP with C-terminal deletion mapping, and transcriptional reporter assays","pmids":["16966434"],"confidence":"Medium","gaps":["No endogenous target gene identified at this stage","DNA-binding specificity of ZNF652 not yet defined"]},{"year":2008,"claim":"To connect ZNF652 to genuine gene regulation, its DNA consensus and a bona fide endogenous target were needed; ZNF652-CBFA2T3 was shown to bind a single response element in the HEB promoter and repress it, with the interaction interface mapped to a proline-rich C-terminal region engaging CBFA2T3 NHR3/NHR4.","evidence":"ChIP, in vitro DNA-binding assays with consensus identification, reporter assays, and Co-IP with domain mutagenesis","pmids":["18456661"],"confidence":"High","gaps":["Genome-wide target repertoire not yet defined","Whether other corepressors participate not addressed"]},{"year":2010,"claim":"The question of whether ZNF652 repression is paralog-redundant was addressed by showing ZNF651 shares the same DNA consensus and also forms a CBFA2T3 corepressor complex, indicating potentially tissue-specific functional overlap.","evidence":"DNA-binding assays, Co-IP, and reporter assays comparing ZNF651 and ZNF652","pmids":["20116376"],"confidence":"Medium","gaps":["Tissue-specific division of labor between paralogs not demonstrated in vivo","Distinct target genes for each paralog not resolved"]},{"year":2011,"claim":"Defining the breadth of ZNF652 regulation required genome-scale mapping; ChIP-chip identified a refined recognition motif and promoter targets across diverse pathways including cancer progression.","evidence":"Genome-wide ChIP-chip in breast cancer cells with de novo motif scanning","pmids":["21678463"],"confidence":"Medium","gaps":["Functional consequences of most identified binding sites not validated","Activator vs repressor outcome per target not resolved"]},{"year":2023,"claim":"Beyond CBFA2T3, ZNF652 was shown to act through the NuRD complex to repress PD-L1, establishing a mechanistic link between ZNF652 loss and tumor immune evasion in triple-negative breast cancer.","evidence":"Reciprocal Co-IP for NuRD association, ChIP, and overexpression/knockdown with functional immune-evasion readouts in vitro and in vivo","pmids":["37906592"],"confidence":"High","gaps":["Which NuRD subunit directly contacts ZNF652 not defined","Relationship between NuRD- and CBFA2T3-dependent repression not reconciled"]},{"year":2024,"claim":"A direct cell-cycle role was established by showing ZNF652 binds the CCND3 promoter and represses it to enforce G1 arrest, with ectopic cyclin D3 rescuing the phenotype.","evidence":"ChIP, promoter reporter assays, RNA-seq, and CCND3 rescue with cell-cycle analysis in lung cancer cells","pmids":["39500884"],"confidence":"Medium","gaps":["Corepressor complex used at the CCND3 promoter not identified","Whether this repression depends on CBFA2T3 or NuRD untested"]},{"year":2025,"claim":"ZNF652 was shown to function as an activator in hepatocellular carcinoma, recruiting the acetyltransferase KAT5 to deposit H3K27ac and activate SLC38A6, and inducing circRHOT1, expanding its role beyond repression.","evidence":"ChIP, promoter binding and histone-modification assays, and silencing/overexpression with rescue experiments in HCC cells","pmids":["41311269"],"confidence":"Medium","gaps":["Determinants that switch ZNF652 between activator and repressor modes unknown","Direct ZNF652-KAT5 physical interaction not established"]},{"year":null,"claim":"What dictates the context-dependent choice between corepressor assembly (CBFA2T3/NuRD) and coactivator recruitment (KAT5/H3K27ac), and the conflicting reports of PD-L1 repression versus activation, remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No mechanism reconciling repressor vs activator activity at the same target (PD-L1)","No structural model of ZNF652 DNA or partner interfaces","Post-translational or cofactor switches governing complex choice unidentified"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,1,6,8,9]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[1,4]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,6]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[5]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[1,6,8]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[6,9]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[8]}],"complexes":["NuRD complex","CBFA2T3-ZNF652 corepressor complex"],"partners":["CBFA2T3","CBFA2T1","CBFA2T2","KAT5"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y2D9","full_name":"Zinc finger protein 652","aliases":[],"length_aa":606,"mass_kda":69.7,"function":"DNA-binding transcription repressor that acts together with CBFA2T2 to repress expression of target genes, such as TCF12 (PubMed:16966434, PubMed:18456661, PubMed:21678463). Specifically binds the DNA consensus sequence 5'-CGAAAGGGTTAAT-3' (PubMed:18456661, PubMed:21678463)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9Y2D9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ZNF652","classification":"Not Classified","n_dependent_lines":3,"n_total_lines":1208,"dependency_fraction":0.0024834437086092716},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ZNF652","total_profiled":1310},"omim":[{"mim_id":"619969","title":"ZINC FINGER- AND BTB DOMAIN-CONTAINING PROTEIN 47; ZBTB47","url":"https://www.omim.org/entry/619969"},{"mim_id":"619289","title":"ZINC FINGER PROTEIN 91, ATYPICAL E3 UBIQUITIN LIGASE; ZFP91","url":"https://www.omim.org/entry/619289"},{"mim_id":"617387","title":"GLUTAMINE-RICH PROTEIN 1; QRICH1","url":"https://www.omim.org/entry/617387"},{"mim_id":"613907","title":"ZINC FINGER PROTEIN 652; ZNF652","url":"https://www.omim.org/entry/613907"},{"mim_id":"603870","title":"CORE-BINDING FACTOR, ALPHA SUBUNIT 2, TRANSLOCATED TO, 3; CBFA2T3","url":"https://www.omim.org/entry/603870"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ZNF652"},"hgnc":{"alias_symbol":["KIAA0924"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y2D9","domains":[{"cath_id":"3.30.160.60","chopping":"392-438","consensus_level":"medium","plddt":75.96,"start":392,"end":438},{"cath_id":"3.30.160.60","chopping":"440-493","consensus_level":"medium","plddt":85.865,"start":440,"end":493}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2D9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2D9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2D9-F1-predicted_aligned_error_v6.png","plddt_mean":56.03},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ZNF652","jax_strain_url":"https://www.jax.org/strain/search?query=ZNF652"},"sequence":{"accession":"Q9Y2D9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y2D9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y2D9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2D9"}},"corpus_meta":[{"pmid":"32943922","id":"PMC_32943922","title":"Exosomal Circ-ZNF652 Promotes Cell Proliferation, Migration, Invasion and Glycolysis in Hepatocellular Carcinoma via miR-29a-3p/GUCD1 Axis.","date":"2020","source":"Cancer management and research","url":"https://pubmed.ncbi.nlm.nih.gov/32943922","citation_count":51,"is_preprint":false},{"pmid":"16966434","id":"PMC_16966434","title":"ZNF652, a novel zinc finger protein, interacts with the putative breast tumor suppressor CBFA2T3 to repress transcription.","date":"2006","source":"Molecular cancer research : MCR","url":"https://pubmed.ncbi.nlm.nih.gov/16966434","citation_count":46,"is_preprint":false},{"pmid":"31000195","id":"PMC_31000195","title":"RETRACTED: A novel circular RNA circ-ZNF652 promotes hepatocellular carcinoma metastasis through inducing snail-mediated epithelial-mesenchymal transition by sponging miR-203/miR-502-5p.","date":"2019","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/31000195","citation_count":41,"is_preprint":false},{"pmid":"18456661","id":"PMC_18456661","title":"CBFA2T3-ZNF652 corepressor complex regulates transcription of the E-box gene HEB.","date":"2008","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/18456661","citation_count":33,"is_preprint":false},{"pmid":"37906592","id":"PMC_37906592","title":"PD-L1-mediated immune evasion in triple-negative breast cancer is linked to the loss of ZNF652.","date":"2023","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/37906592","citation_count":27,"is_preprint":false},{"pmid":"21678463","id":"PMC_21678463","title":"Genome-wide mapping of ZNF652 promoter binding sites in breast cancer cells.","date":"2011","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21678463","citation_count":20,"is_preprint":false},{"pmid":"32070139","id":"PMC_32070139","title":"Silencing circular RNA-ZNF652 represses proliferation and EMT process of renal carcinoma cells via raising miR-205.","date":"2020","source":"Artificial cells, nanomedicine, and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/32070139","citation_count":15,"is_preprint":false},{"pmid":"34926705","id":"PMC_34926705","title":"ZNF652-Induced circRHOT1 Promotes SMAD5 Expression to Modulate Tumorigenic Properties and Nature Killer Cell-Mediated Toxicity in Bladder Cancer via Targeting miR-3666.","date":"2021","source":"Journal of immunology research","url":"https://pubmed.ncbi.nlm.nih.gov/34926705","citation_count":14,"is_preprint":false},{"pmid":"20204290","id":"PMC_20204290","title":"Co-expression of the androgen receptor and the transcription factor ZNF652 is related to prostate cancer outcome.","date":"2010","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/20204290","citation_count":13,"is_preprint":false},{"pmid":"20116376","id":"PMC_20116376","title":"CBFA2T3-ZNF651, like CBFA2T3-ZNF652, functions as a transcriptional corepressor complex.","date":"2010","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/20116376","citation_count":12,"is_preprint":false},{"pmid":"34424826","id":"PMC_34424826","title":"Circular RNA circVRK1 suppresses the proliferation, migration and invasion of osteosarcoma cells by regulating zinc finger protein ZNF652 expression via microRNA miR-337-3p.","date":"2021","source":"Bioengineered","url":"https://pubmed.ncbi.nlm.nih.gov/34424826","citation_count":11,"is_preprint":false},{"pmid":"39500884","id":"PMC_39500884","title":"ZNF652 exerts a tumor suppressor role in lung cancer by transcriptionally downregulating cyclin D3.","date":"2024","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/39500884","citation_count":8,"is_preprint":false},{"pmid":"36552358","id":"PMC_36552358","title":"Genome-Wide Association Study Revealed the Effect of rs312715211 in ZNF652 Gene on Abdominal Fat Percentage of Chickens.","date":"2022","source":"Biology","url":"https://pubmed.ncbi.nlm.nih.gov/36552358","citation_count":5,"is_preprint":false},{"pmid":"35667544","id":"PMC_35667544","title":"Circ_ZNF652 regulates the proliferation and apoptosis of LPS-induced WI-38 cells via miR-302e/TLR4 axis.","date":"2022","source":"Transplant immunology","url":"https://pubmed.ncbi.nlm.nih.gov/35667544","citation_count":3,"is_preprint":false},{"pmid":"39649418","id":"PMC_39649418","title":"Identification of ZNF652 as a Diagnostic and Therapeutic Target in Osteoarthritis Using Machine Learning.","date":"2024","source":"Journal of inflammation research","url":"https://pubmed.ncbi.nlm.nih.gov/39649418","citation_count":3,"is_preprint":false},{"pmid":"33380394","id":"PMC_33380394","title":"[High expression of ZNF652 promotes carcinogenesis and progression of breast cancer].","date":"2020","source":"Nan fang yi ke da xue xue bao = Journal of Southern Medical University","url":"https://pubmed.ncbi.nlm.nih.gov/33380394","citation_count":2,"is_preprint":false},{"pmid":"41311269","id":"PMC_41311269","title":"Role of ZNF652 in Regulating Hepatocellular Carcinoma Cell Proliferation and Apoptosis via the circRHOT1/SLC38A6 Axis.","date":"2025","source":"The Kaohsiung journal of medical sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41311269","citation_count":0,"is_preprint":false},{"pmid":"41983254","id":"PMC_41983254","title":"Phenethyl Isothiocyanate Suppresses Hepatocellular Carcinoma Progression and Immune Evasion via ZNF652 Regulation of PD-L1.","date":"2026","source":"Phytotherapy research : PTR","url":"https://pubmed.ncbi.nlm.nih.gov/41983254","citation_count":0,"is_preprint":false},{"pmid":"36922340","id":"PMC_36922340","title":"Retraction notice to \"A novel circular RNA circ-ZNF652 promotes hepatocellular carcinoma metastasis through inducing snail-mediated epithelial-mesenchymal transition by sponging miR-203/miR-502-5p\" [YBBRC 513(4) (2019) 812-819].","date":"2023","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/36922340","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11924,"output_tokens":2559,"usd":0.037079,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9743,"output_tokens":2969,"usd":0.06147,"stage2_stop_reason":"end_turn"},"total_usd":0.098549,"stage1_batch_id":"msgbatch_01UT1AahFPCAyn2uVweS7A9z","stage2_batch_id":"msgbatch_01HuKWtKNT4Pqj1bc8eEP5RV","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2006,\n      \"finding\": \"ZNF652 was identified as a novel C2H2 zinc finger protein that physically interacts with the ETO family transcriptional repressor CBFA2T3 (putative breast tumor suppressor). The interaction occurs through the C-terminal 109 amino acids of ZNF652. Weaker interactions were also detected with CBFA2T1 and CBFA2T2. ZNF652 functions as a transcriptional repressor in reporter assays.\",\n      \"method\": \"Yeast two-hybrid screen, co-immunoprecipitation, transcriptional reporter assays, deletion mapping\",\n      \"journal\": \"Molecular cancer research : MCR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP with domain mapping and transcriptional reporter validation, single lab\",\n      \"pmids\": [\"16966434\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"ZNF652 forms a corepressor complex with CBFA2T3 to repress transcription of the E-box gene HEB. The complex binds a single ZNF652 response element in the HEB promoter. The NHR3 and NHR4 domains of CBFA2T3 interact with a conserved proline-rich region in the C-terminus of ZNF652. The ZNF652 consensus DNA binding sequence was identified and validated in vitro.\",\n      \"method\": \"ChIP, transcriptional reporter assays, DNA binding assays, co-immunoprecipitation, domain mutagenesis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (ChIP, reporter assay, in vitro DNA binding, Co-IP with domain mapping) in a single rigorous study\",\n      \"pmids\": [\"18456661\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"ZNF651, a paralogue of ZNF652, shares the same DNA binding sequence as ZNF652 and represses target gene expression through formation of a CBFA2T3-ZNF651 corepressor complex, indicating that CBFA2T3-ZNF651 and CBFA2T3-ZNF652 perform functionally similar roles, potentially in a tissue-specific manner.\",\n      \"method\": \"DNA binding assays, co-immunoprecipitation, transcriptional reporter assays\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple methods (DNA binding, Co-IP, reporter assay), single lab; finding is about ZNF652 function by comparison with ZNF651\",\n      \"pmids\": [\"20116376\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Modulation of AR expression in LNCaP prostate cancer cells did not alter ZNF652 expression levels, and conversely, ZNF652 knockdown did not alter AR expression levels, indicating that ZNF652 and AR transcription factors act independently of each other.\",\n      \"method\": \"siRNA knockdown, Western blot / expression analysis in LNCaP cells\",\n      \"journal\": \"Oncology reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single negative result from knockdown/expression analysis, single lab, single method\",\n      \"pmids\": [\"20204290\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Genome-wide ChIP-chip mapping of ZNF652 binding sites in breast cancer cells identified a novel ZNF652 recognition motif (a 10-nucleotide core of a 13-nucleotide in vitro binding site) and revealed that ZNF652 targets gene promoters involved in diverse cellular pathways including cancer development and progression.\",\n      \"method\": \"ChIP-chip (chromatin immunoprecipitation with microarray), de novo motif scanning\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide ChIP-chip with motif validation, single lab\",\n      \"pmids\": [\"21678463\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ZNF652 protein localizes to the nucleus of 293T cells, consistent with its role as a transcription factor.\",\n      \"method\": \"Immunofluorescence assay in 293T cells\",\n      \"journal\": \"Nan fang yi ke da xue xue bao = Journal of Southern Medical University\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single localization experiment, single lab, single method, no functional consequence directly tied to localization\",\n      \"pmids\": [\"33380394\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ZNF652 physically associates with the NuRD transcription co-repressor complex and represses transcription of a cohort of genes including PD-L1. Overexpression of ZNF652 inhibits PD-L1 transcription, while depletion of ZNF652 upregulates PD-L1, leading to immune evasion in triple-negative breast cancer.\",\n      \"method\": \"Co-immunoprecipitation (ZNF652-NuRD complex), ChIP, overexpression/knockdown with gene expression and functional immune evasion assays in vitro and in vivo\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP demonstrating NuRD complex association, ChIP confirming promoter binding, orthogonal OE/KD experiments with functional readouts in vitro and in vivo\",\n      \"pmids\": [\"37906592\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ZNF652 binds to the circRHOT1 promoter and regulates its expression transcriptionally in bladder cancer cells, as demonstrated by ChIP and luciferase reporter assays.\",\n      \"method\": \"ChIP assay, luciferase reporter assay, RNA pull-down\",\n      \"journal\": \"Journal of immunology research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, ChIP and reporter assay without comprehensive mechanistic follow-up\",\n      \"pmids\": [\"34926705\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ZNF652 directly binds the promoter of cyclin D3 (CCND3) and inhibits its transcription, thereby arresting the cell cycle at G1 phase in lung cancer cells. Ectopic expression of cyclin D3 rescued decreased cell viability and cell cycle arrest induced by ZNF652 overexpression.\",\n      \"method\": \"ChIP, promoter reporter assay, RNA-seq, overexpression/knockdown with cell cycle analysis, rescue experiments with CCND3\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP plus promoter reporter assay plus genetic rescue, single lab\",\n      \"pmids\": [\"39500884\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In HCC cells, ZNF652 transcriptionally activates circRHOT1 expression (binding to its promoter) and recruits the histone acetyltransferase KAT5 to the SLC38A6 promoter, increasing H3K27ac enrichment and activating SLC38A6 expression to promote HCC cell proliferation and inhibit apoptosis.\",\n      \"method\": \"ChIP, promoter binding assays, gene silencing/overexpression, rescue experiments\",\n      \"journal\": \"The Kaohsiung journal of medical sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP demonstrating promoter binding and histone modification, plus rescue experiments, single lab\",\n      \"pmids\": [\"41311269\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"In hepatocellular carcinoma cells, ZNF652 binds to the PD-L1 promoter and activates its transcription, in contrast to its previously described repressor role in breast cancer. ZNF652 overexpression partially reversed the suppressive effects of PEITC on PD-L1 expression, while ZNF652 knockdown enhanced these effects.\",\n      \"method\": \"Bioinformatics, ChIP/promoter binding validation, overexpression/knockdown with PD-L1 expression and T cell cytotoxicity assays\",\n      \"journal\": \"Phytotherapy research : PTR\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, limited mechanistic validation described in abstract; contradicts breast cancer NuRD-repressor finding\",\n      \"pmids\": [\"41983254\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ZNF652 is a nuclear C2H2 zinc finger transcription factor that primarily forms corepressor complexes — notably with CBFA2T3 (ETO family) and the NuRD complex — to bind specific promoter elements and repress target genes including HEB and PD-L1 in breast cancer; it also directly binds the cyclin D3 (CCND3) promoter to repress transcription and arrest the cell cycle at G1 in lung cancer, and transcriptionally activates circRHOT1 and recruits KAT5/H3K27ac to activate SLC38A6 in hepatocellular carcinoma, indicating context-dependent activator or repressor activity.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ZNF652 is a nuclear C2H2 zinc finger transcription factor that recognizes a defined DNA element in target gene promoters and acts predominantly as a sequence-specific transcriptional repressor through assembly of corepressor complexes [#1, #4]. Its repressive activity is mediated by direct physical interaction with the ETO-family corepressor CBFA2T3, an association formed through the C-terminal ~109 residues of ZNF652 and a conserved proline-rich region that engages the NHR3/NHR4 domains of CBFA2T3, enabling repression of E-box target genes such as HEB [#0, #1]. ZNF652 also associates with the NuRD corepressor complex to silence a cohort of genes including PD-L1, and loss of ZNF652 derepresses PD-L1 to drive immune evasion in triple-negative breast cancer [#6]. Through direct promoter binding it represses the cyclin D3 (CCND3) gene to enforce G1 cell-cycle arrest in lung cancer, a phenotype rescued by ectopic cyclin D3 [#8]. In other tumor contexts ZNF652 instead acts as an activator, transcriptionally inducing circRHOT1 and recruiting the histone acetyltransferase KAT5 to deposit H3K27ac at the SLC38A6 promoter [#9], indicating context-dependent repressor or activator activity. A paralogous protein, ZNF651, shares the ZNF652 DNA-binding consensus and forms an analogous CBFA2T3 corepressor complex [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Establishing ZNF652 as a transcriptional repressor required identifying a binding partner and a functional output; the discovery that it interacts with the ETO-family repressor CBFA2T3 and represses reporter transcription defined its core molecular role.\",\n      \"evidence\": \"Yeast two-hybrid screen, reciprocal Co-IP with C-terminal deletion mapping, and transcriptional reporter assays\",\n      \"pmids\": [\"16966434\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No endogenous target gene identified at this stage\", \"DNA-binding specificity of ZNF652 not yet defined\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"To connect ZNF652 to genuine gene regulation, its DNA consensus and a bona fide endogenous target were needed; ZNF652-CBFA2T3 was shown to bind a single response element in the HEB promoter and repress it, with the interaction interface mapped to a proline-rich C-terminal region engaging CBFA2T3 NHR3/NHR4.\",\n      \"evidence\": \"ChIP, in vitro DNA-binding assays with consensus identification, reporter assays, and Co-IP with domain mutagenesis\",\n      \"pmids\": [\"18456661\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Genome-wide target repertoire not yet defined\", \"Whether other corepressors participate not addressed\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"The question of whether ZNF652 repression is paralog-redundant was addressed by showing ZNF651 shares the same DNA consensus and also forms a CBFA2T3 corepressor complex, indicating potentially tissue-specific functional overlap.\",\n      \"evidence\": \"DNA-binding assays, Co-IP, and reporter assays comparing ZNF651 and ZNF652\",\n      \"pmids\": [\"20116376\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Tissue-specific division of labor between paralogs not demonstrated in vivo\", \"Distinct target genes for each paralog not resolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Defining the breadth of ZNF652 regulation required genome-scale mapping; ChIP-chip identified a refined recognition motif and promoter targets across diverse pathways including cancer progression.\",\n      \"evidence\": \"Genome-wide ChIP-chip in breast cancer cells with de novo motif scanning\",\n      \"pmids\": [\"21678463\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Functional consequences of most identified binding sites not validated\", \"Activator vs repressor outcome per target not resolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Beyond CBFA2T3, ZNF652 was shown to act through the NuRD complex to repress PD-L1, establishing a mechanistic link between ZNF652 loss and tumor immune evasion in triple-negative breast cancer.\",\n      \"evidence\": \"Reciprocal Co-IP for NuRD association, ChIP, and overexpression/knockdown with functional immune-evasion readouts in vitro and in vivo\",\n      \"pmids\": [\"37906592\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Which NuRD subunit directly contacts ZNF652 not defined\", \"Relationship between NuRD- and CBFA2T3-dependent repression not reconciled\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"A direct cell-cycle role was established by showing ZNF652 binds the CCND3 promoter and represses it to enforce G1 arrest, with ectopic cyclin D3 rescuing the phenotype.\",\n      \"evidence\": \"ChIP, promoter reporter assays, RNA-seq, and CCND3 rescue with cell-cycle analysis in lung cancer cells\",\n      \"pmids\": [\"39500884\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Corepressor complex used at the CCND3 promoter not identified\", \"Whether this repression depends on CBFA2T3 or NuRD untested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"ZNF652 was shown to function as an activator in hepatocellular carcinoma, recruiting the acetyltransferase KAT5 to deposit H3K27ac and activate SLC38A6, and inducing circRHOT1, expanding its role beyond repression.\",\n      \"evidence\": \"ChIP, promoter binding and histone-modification assays, and silencing/overexpression with rescue experiments in HCC cells\",\n      \"pmids\": [\"41311269\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Determinants that switch ZNF652 between activator and repressor modes unknown\", \"Direct ZNF652-KAT5 physical interaction not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"What dictates the context-dependent choice between corepressor assembly (CBFA2T3/NuRD) and coactivator recruitment (KAT5/H3K27ac), and the conflicting reports of PD-L1 repression versus activation, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No mechanism reconciling repressor vs activator activity at the same target (PD-L1)\", \"No structural model of ZNF652 DNA or partner interfaces\", \"Post-translational or cofactor switches governing complex choice unidentified\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 1, 6, 8, 9]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [1, 4]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [1, 6, 8]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [6, 9]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"complexes\": [\n      \"NuRD complex\",\n      \"CBFA2T3-ZNF652 corepressor complex\"\n    ],\n    \"partners\": [\n      \"CBFA2T3\",\n      \"CBFA2T1\",\n      \"CBFA2T2\",\n      \"KAT5\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":6,"faith_pct":83.33333333333333}}