{"gene":"CHAF1B","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":1996,"finding":"The CHAF1B (CAF1P60/CAF1A) gene was mapped to human chromosome 21q22.2, within the Down syndrome critical region, and encodes the p60 subunit of the CAF-1 complex that interacts with other subunits to promote histone assembly onto replicating DNA.","method":"Fluorescence in situ hybridization, somatic cell hybrids, YAC/cosmid hybridization, exon trapping","journal":"Human genetics / Genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two independent labs replicated chromosomal mapping; functional description based on prior literature, not new experiment","pmids":["8792829","8660983"],"is_preprint":false},{"year":2015,"finding":"CHAF1B is the medium (p60) subunit of the trimeric CAF-1 complex and contains a 7× WD repeat domain, a B-like domain, and a PEST domain; it functions as a histone H3/H4 chaperone shuttling newly synthesized histones to the replication fork during DNA synthesis.","method":"Review/synthesis of prior experimental literature on CAF-1 complex biochemistry","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — domain architecture and complex membership are well-established across multiple prior studies as summarized in this review; not a single new experiment","pmids":["26066981"],"is_preprint":false},{"year":2018,"finding":"Knockdown of CHAF1B in hepatocellular carcinoma (HUH-7) cells reduced invasion and migration ability, induced S-phase accumulation, and inhibited tumor growth in vivo; downstream gene expression changes included upregulation of PSMB6, SLC30A7, and SMC3, and downregulation of BLM and TWF2.","method":"Lentiviral shRNA knockdown, scratch wound healing assay, Transwell invasion assay, flow cytometry, gene expression profiling, Western blot, RT-PCR, xenograft mouse model","journal":"Oncology reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KD with defined cellular and in vivo phenotypes; single lab, multiple orthogonal methods","pmids":["29767268"],"is_preprint":false},{"year":2019,"finding":"CHAF1B promotes DNA damage repair in nasopharyngeal carcinoma cells following radiation, inhibiting apoptosis and conferring radioresistance; this mechanism is dependent on the DNA-PK pathway, as demonstrated by γH2AX foci resolution and DNA-PK inhibitor sensitization.","method":"siRNA/shRNA knockdown and overexpression, colony formation assay, γH2AX foci detection, flow cytometry (apoptosis), MTT assay, xenograft model, DNA-PK inhibitor treatment","journal":"Biomedicine & pharmacotherapy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pathway placement via pharmacological inhibition combined with loss- and gain-of-function; single lab","pmids":["31869663"],"is_preprint":false},{"year":2020,"finding":"CHAF1B acts as an E3 ubiquitin ligase that promotes ubiquitination and degradation of the nuclear co-repressor NCOR2; CHAF1B and NCOR2 physically interact predominantly in the nucleus, and CHAF1B-mediated NCOR2 degradation drives cisplatin resistance in lung adenocarcinoma.","method":"Proteome microarray, Western blot, co-immunoprecipitation, qRT-PCR, cell proliferation/migration assays, apoptosis assay, xenograft mouse model, immunohistochemistry, ubiquitination assay","journal":"Cancer cell international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP interaction and ubiquitination assay demonstrate mechanism; single lab, multiple orthogonal methods","pmids":["32508530"],"is_preprint":false},{"year":2021,"finding":"CHAF1B depletion in mouse preimplantation embryos increases apoptosis, reduces blastocyst hatching and outgrowth, causes embryonic lethality post-implantation, and decreases expression of pluripotency factors (Oct4, Cdx2, Sox2, Nanog). Mechanistically, CHAF1B mediates replacement of histone H3.3 with H3.1/H3.2, associated with increased repressive marks (H3K9me2/3, H3K27me2/3) and decreased active marks (H3K4me2/3).","method":"siRNA knockdown in embryos, immunofluorescence, flow cytometry (apoptosis), RNA-sequencing, ATAC-sequencing, Western blot","journal":"International journal of biological macromolecules","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined molecular phenotype; single lab with multiple orthogonal methods (RNA-seq, ATAC-seq, histone mark analysis)","pmids":["34906611"],"is_preprint":false},{"year":2023,"finding":"CHAF1B binds directly to the TRIM13 promoter to repress its transcription in AML cells; loss of CHAF1B de-represses TRIM13, which then ubiquitinates CCNA1 to promote cell cycle entry and ultimately leukemic cell exhaustion, identifying the CHAF1B→TRIM13→CCNA1 axis as a key leukemogenic pathway.","method":"RNA sequencing, ChIP (CHAF1B promoter binding), knockdown/overexpression in AML cell lines and patient-derived xenografts, cell cycle and self-renewal assays","journal":"Blood advances","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP for promoter binding plus functional epistasis in PDX models; single lab","pmids":["37205848"],"is_preprint":false},{"year":2023,"finding":"CHAF1B interacts with ULK1 (Unc-51-like kinase 1) in the nuclear compartment of MPN cells; silencing CHAF1B enhances transcription of IFNα-stimulated genes and potentiates IFNα-dependent antineoplastic responses in primary MPN progenitor cells.","method":"Co-immunoprecipitation/interaction studies, shRNA silencing, gene expression analysis, primary MPN progenitor cell functional assays","journal":"Cancer research communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — interaction identified; functional consequence of silencing confirmed; single lab","pmids":["37377894"],"is_preprint":false},{"year":2025,"finding":"CHAF1B competitively binds to the SETD7 promoter region and represses its transcription in lung squamous-cell carcinoma, promoting cell proliferation; silencing CHAF1B upregulates SETD7 and suppresses tumor growth in vitro and in vivo.","method":"WGCNA bioinformatics, ChIP (promoter binding), CHAF1B knockdown, RNA sequencing, in vitro proliferation assays, xenograft model","journal":"Frontiers of medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP demonstrates direct promoter binding; loss-of-function confirms functional consequence; single lab","pmids":["39862337"],"is_preprint":false},{"year":2025,"finding":"CHAF1B promotes malignant phenotypes in hepatocellular carcinoma via activation of the PI3K/Akt/HIF-1α pathway; blockade of this pathway partially attenuates CHAF1B-mediated sorafenib resistance, placing CHAF1B upstream of PI3K/Akt/HIF-1α.","method":"RNA sequencing, pathway-specific inhibitors, siRNA knockdown, CCK8, colony formation, Transwell migration/invasion, flow cytometry, Western blot","journal":"International journal of medical sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — pathway placement via pharmacological inhibition only; single lab, no direct binding or reconstitution evidence","pmids":["41049428"],"is_preprint":false},{"year":2025,"finding":"CHAF1B physically associates with BCL6 and TBL1XR1 in germinal center B cells (identified by Co-IP/MS); CHAF1B stabilizes the BCL6/TBL1XR1 repressor complex to cooperatively repress transcription, promote GC dark zone/light zone organization, and support GC B cell differentiation and antibody production. Loss of CHAF1B impairs GC formation, induces apoptosis, and reduces high-affinity antibody responses.","method":"Co-immunoprecipitation coupled with mass spectrometry, conditional knockout mouse models, flow cytometry, immunofluorescence, transcriptional reporter assays","journal":"Journal of immunology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — Co-IP/MS identified complex; loss-of-function in mice with defined cellular and molecular phenotypes; multiple orthogonal methods","pmids":["41764732"],"is_preprint":false},{"year":2025,"finding":"Chaf1b upregulates IL-33 secretion in glioma stem cells, promoting microglial M2 polarization and activating the PI3K/AKT signaling pathway; neutralization of IL-33 reverses these effects, placing Chaf1b upstream of IL-33–PI3K/AKT in the GBM stem-immune axis.","method":"Genetic silencing in patient-derived GSCs, intracranial xenograft models, IL-33 neutralization, flow cytometry, self-renewal and tumorigenicity assays","journal":"The Journal of neuroscience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis via neutralization antibody plus in vivo loss-of-function; single lab","pmids":["41102004"],"is_preprint":false}],"current_model":"CHAF1B (CAF-1-p60) is the WD-repeat-containing middle subunit of the trimeric CAF-1 histone chaperone complex that deposits H3.1/H3.2 onto replicating DNA, replacing H3.3 to establish repressive chromatin marks; beyond its canonical replication-coupled chromatin assembly role, CHAF1B acts as an epigenetic transcriptional repressor by binding promoters (e.g., TRIM13, SETD7) and stabilizing co-repressor complexes (BCL6/TBL1XR1), and exhibits E3 ubiquitin ligase activity toward NCOR2, while also promoting DNA damage repair via the DNA-PK pathway and modulating immune signaling through IL-33/PI3K-AKT and IFN-stimulated gene transcription."},"narrative":{"mechanistic_narrative":"CHAF1B is the medium (p60) subunit of the trimeric CAF-1 histone chaperone complex, a WD-repeat protein that shuttles newly synthesized histone H3/H4 to the replication fork to drive replication-coupled chromatin assembly [PMID:26066981]. In mouse preimplantation embryos it mediates replacement of histone H3.3 with H3.1/H3.2, establishing repressive chromatin (gained H3K9me2/3 and H3K27me2/3, lost H3K4me2/3) and supporting expression of pluripotency factors, with its loss causing apoptosis and post-implantation lethality [PMID:34906611]. Beyond canonical chromatin assembly, CHAF1B operates as a transcriptional repressor by binding directly to target promoters such as TRIM13 and SETD7 to silence them, configuring oncogenic programs in AML and lung squamous-cell carcinoma; in the leukemic context this defines a CHAF1B→TRIM13→CCNA1 cell-cycle axis [PMID:37205848, PMID:39862337]. In germinal center B cells CHAF1B associates with BCL6 and TBL1XR1 and stabilizes this co-repressor complex to support GC organization, B cell differentiation, and high-affinity antibody responses [PMID:41764732]. CHAF1B additionally functions as an E3 ubiquitin ligase that ubiquitinates and degrades the nuclear co-repressor NCOR2 [PMID:32508530], and it promotes DNA-PK–dependent DNA damage repair and radioresistance [PMID:31869663]. Across multiple cancers CHAF1B supports proliferation, invasion, and therapy resistance and modulates immune signaling, including a nuclear interaction with ULK1 that restrains IFNα-stimulated gene transcription [PMID:37377894] and IL-33–driven microglial polarization in glioma [PMID:41102004].","teleology":[{"year":1996,"claim":"Establishing the gene's chromosomal location and complex membership was the first step in defining CHAF1B as a histone-assembly factor of potential developmental relevance.","evidence":"FISH, somatic cell hybrids, and YAC/cosmid mapping placing CAF1P60 at 21q22.2 within the Down syndrome critical region","pmids":["8792829","8660983"],"confidence":"Medium","gaps":["Functional role inferred from prior literature, not new experiment","No mechanistic link between map position and Down syndrome phenotype established"]},{"year":2015,"claim":"Consolidation of CAF-1 biochemistry defined CHAF1B's domain architecture and its role as the p60 subunit chaperoning H3/H4 to the replication fork.","evidence":"Review/synthesis of prior CAF-1 complex biochemistry describing 7× WD-repeat, B-like, and PEST domains","pmids":["26066981"],"confidence":"Medium","gaps":["No single new experiment; relies on prior studies","Does not address non-replicative functions"]},{"year":2021,"claim":"Linking CHAF1B to histone variant exchange showed how its chaperone activity translates into a defined chromatin state and developmental outcome.","evidence":"siRNA knockdown in mouse embryos with RNA-seq, ATAC-seq, and histone mark Western blots showing H3.3→H3.1/H3.2 replacement and repressive-mark gain","pmids":["34906611"],"confidence":"Medium","gaps":["Mechanism of variant selection not resolved","Single lab; not extended to other developmental contexts"]},{"year":2020,"claim":"Identification of E3 ubiquitin ligase activity toward NCOR2 revealed a chromatin-independent post-translational function for CHAF1B.","evidence":"Proteome microarray, Co-IP, and ubiquitination assay in lung adenocarcinoma showing nuclear CHAF1B–NCOR2 interaction and NCOR2 degradation","pmids":["32508530"],"confidence":"Medium","gaps":["No structural basis for ligase activity defined","WD-repeat protein acting as E3 not reconstituted in vitro","Single lab"]},{"year":2019,"claim":"Placing CHAF1B in the DNA-PK repair pathway connected it to genome maintenance and therapy resistance beyond replication.","evidence":"Loss/gain-of-function with γH2AX foci resolution and DNA-PK inhibitor sensitization in nasopharyngeal carcinoma plus xenografts","pmids":["31869663"],"confidence":"Medium","gaps":["Direct molecular interaction with DNA-PK components not shown","Single lab"]},{"year":2023,"claim":"Demonstration of direct promoter binding (TRIM13) established CHAF1B as a sequence-targeted transcriptional repressor driving a leukemogenic cell-cycle axis.","evidence":"ChIP for CHAF1B promoter binding plus functional epistasis (TRIM13→CCNA1) in AML lines and patient-derived xenografts","pmids":["37205848"],"confidence":"Medium","gaps":["How CHAF1B is recruited to specific promoters unknown","Repressive complex partners at TRIM13 not defined"]},{"year":2023,"claim":"A nuclear CHAF1B–ULK1 interaction linked the chaperone to control of interferon-stimulated gene transcription in myeloproliferative neoplasms.","evidence":"Co-IP interaction studies and shRNA silencing with gene expression and primary MPN progenitor assays","pmids":["37377894"],"confidence":"Medium","gaps":["Reciprocal validation and stoichiometry of ULK1 interaction not established","Direct transcriptional mechanism at ISGs unclear"]},{"year":2025,"claim":"A second direct promoter target (SETD7) and identification of the BCL6/TBL1XR1 co-repressor complex generalized CHAF1B's repressor role across tumor and immune contexts.","evidence":"ChIP at SETD7 in lung squamous carcinoma; Co-IP/MS plus conditional knockout mice for BCL6/TBL1XR1 in germinal center B cells","pmids":["39862337","41764732"],"confidence":"High","gaps":["Whether promoter targeting and complex stabilization use a shared molecular mechanism unresolved","Determinants of target-gene selection unknown"]},{"year":2025,"claim":"Functional studies placed CHAF1B upstream of PI3K/Akt and IL-33 immune-signaling axes, broadening its role into tumor microenvironment modulation.","evidence":"RNA-seq with pathway inhibitors in HCC (PI3K/Akt/HIF-1α) and IL-33 neutralization with intracranial xenografts in glioma stem cells","pmids":["41049428","41102004"],"confidence":"Low","gaps":["HCC pathway placement rests on pharmacological inhibition only, no direct binding or reconstitution","Direct molecular link between CHAF1B and IL-33 secretion not defined"]},{"year":null,"claim":"How a single WD-repeat chaperone subunit mechanistically unifies replication-coupled histone deposition, sequence-specific promoter repression, and E3 ligase activity remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model reconciling chaperone, repressor, and ligase functions","Mechanism of promoter recruitment unidentified","Whether non-canonical functions require the full CAF-1 complex untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[1,5]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[6,8,10]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[4]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[4]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[4,7,10]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[1,5]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[1,5]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[6,8,10]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[3]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[7,10,11]}],"complexes":["CAF-1","BCL6/TBL1XR1 co-repressor complex"],"partners":["NCOR2","ULK1","BCL6","TBL1XR1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q13112","full_name":"Chromatin assembly factor 1 subunit B","aliases":["Chromatin assembly factor I p60 subunit","CAF-I 60 kDa subunit","CAF-I p60","M-phase phosphoprotein 7"],"length_aa":559,"mass_kda":61.5,"function":"Acts as a component of the histone chaperone complex chromatin assembly factor 1 (CAF-1), which assembles histone octamers onto DNA during replication and repair. CAF-1 performs the first step of the nucleosome assembly process, bringing newly synthesized histones H3 and H4 to replicating DNA; histones H2A/H2B can bind to this chromatin precursor subsequent to DNA replication to complete the histone octamer","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q13112/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/CHAF1B","classification":"Common Essential","n_dependent_lines":1206,"n_total_lines":1208,"dependency_fraction":0.9983443708609272},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CBX1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CHAF1B","total_profiled":1310},"omim":[{"mim_id":"601246","title":"CHROMATIN ASSEMBLY FACTOR I, SUBUNIT A; CHAF1A","url":"https://www.omim.org/entry/601246"},{"mim_id":"601245","title":"CHROMATIN ASSEMBLY FACTOR I, SUBUNIT B; CHAF1B","url":"https://www.omim.org/entry/601245"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"skeletal muscle","ntpm":14.6}],"url":"https://www.proteinatlas.org/search/CHAF1B"},"hgnc":{"alias_symbol":["CAF1P60","CAF-1","CAF1","CAF1A","MPP7","MPHOSPH7"],"prev_symbol":[]},"alphafold":{"accession":"Q13112","domains":[{"cath_id":"2.130.10.10","chopping":"3-375","consensus_level":"medium","plddt":90.6478,"start":3,"end":375}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13112","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q13112-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q13112-F1-predicted_aligned_error_v6.png","plddt_mean":74.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CHAF1B","jax_strain_url":"https://www.jax.org/strain/search?query=CHAF1B"},"sequence":{"accession":"Q13112","fasta_url":"https://rest.uniprot.org/uniprotkb/Q13112.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q13112/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13112"}},"corpus_meta":[{"pmid":"23236473","id":"PMC_23236473","title":"The anti-proliferative activity of BTG/TOB proteins is mediated via the Caf1a (CNOT7) and Caf1b (CNOT8) deadenylase subunits of the Ccr4-not complex.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23236473","citation_count":64,"is_preprint":false},{"pmid":"7664886","id":"PMC_7664886","title":"Specific high affinity binding of human interleukin 1 beta by Caf1A usher protein of Yersinia pestis.","date":"1995","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/7664886","citation_count":51,"is_preprint":false},{"pmid":"26066981","id":"PMC_26066981","title":"The role of the chromatin assembly complex (CAF-1) and its p60 subunit (CHAF1b) in homeostasis and disease.","date":"2015","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/26066981","citation_count":48,"is_preprint":false},{"pmid":"29767268","id":"PMC_29767268","title":"CHAF1B knockdown blocks migration in a hepatocellular carcinoma model.","date":"2018","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/29767268","citation_count":22,"is_preprint":false},{"pmid":"31869663","id":"PMC_31869663","title":"CHAF1B induces radioresistance by promoting DNA damage repair in nasopharyngeal carcinoma.","date":"2019","source":"Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie","url":"https://pubmed.ncbi.nlm.nih.gov/31869663","citation_count":18,"is_preprint":false},{"pmid":"36700051","id":"PMC_36700051","title":"Long non-coding RNA lnc-CHAF1B-3 promotes renal interstitial fibrosis by regulating EMT-related genes in renal proximal tubular cells.","date":"2022","source":"Molecular therapy. Nucleic acids","url":"https://pubmed.ncbi.nlm.nih.gov/36700051","citation_count":18,"is_preprint":false},{"pmid":"19032149","id":"PMC_19032149","title":"Caf1A usher possesses a Caf1 subunit-like domain that is crucial for Caf1 fibre secretion.","date":"2009","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/19032149","citation_count":16,"is_preprint":false},{"pmid":"8792829","id":"PMC_8792829","title":"The gene encoding the p60 subunit of chromatin assembly factor I (CAF1P60) maps to human chromosome 21q22.2, a region associated with some of the major features of Down syndrome.","date":"1996","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/8792829","citation_count":14,"is_preprint":false},{"pmid":"20797400","id":"PMC_20797400","title":"Conserved hydrophobic clusters on the surface of the Caf1A usher C-terminal domain are important for F1 antigen assembly.","date":"2010","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/20797400","citation_count":12,"is_preprint":false},{"pmid":"32508530","id":"PMC_32508530","title":"Ubiquitin ligase CHAF1B induces cisplatin resistance in lung adenocarcinoma by promoting NCOR2 degradation.","date":"2020","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/32508530","citation_count":10,"is_preprint":false},{"pmid":"8660983","id":"PMC_8660983","title":"Mapping of the gene for the p60 subunit of the human chromatin assembly factor (CAF1A) to the Down syndrome region of chromosome 21.","date":"1996","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/8660983","citation_count":10,"is_preprint":false},{"pmid":"37205848","id":"PMC_37205848","title":"Repression of TRIM13 by chromatin assembly factor CHAF1B is critical for AML development.","date":"2023","source":"Blood 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Overexpression: A Brake for the Differentiation of Leukemia Cells.","date":"2018","source":"Cancer cell","url":"https://pubmed.ncbi.nlm.nih.gov/30423290","citation_count":4,"is_preprint":false},{"pmid":"34237585","id":"PMC_34237585","title":"Detection of CAF-1/p60 in peripheral blood as a potential biomarker of HNSCC tumors.","date":"2021","source":"Oral oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34237585","citation_count":4,"is_preprint":false},{"pmid":"39862337","id":"PMC_39862337","title":"CHAF1B promotes the progression of lung squamous-cell carcinoma by inhibiting SETD7 expression.","date":"2025","source":"Frontiers of medicine","url":"https://pubmed.ncbi.nlm.nih.gov/39862337","citation_count":2,"is_preprint":false},{"pmid":"39806171","id":"PMC_39806171","title":"Integrated bioinformatics and experimental analysis of CHAF1B as a novel biomarker and immunotherapy target in LUAD.","date":"2025","source":"Discover 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1950)","url":"https://pubmed.ncbi.nlm.nih.gov/41764732","citation_count":0,"is_preprint":false},{"pmid":"39747989","id":"PMC_39747989","title":"lncRNA CHAF1B-2 contributes to the tumorigenesis of gastric cancer by activating the Wnt/β-catenin pathway.","date":"2025","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/39747989","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13535,"output_tokens":3068,"usd":0.043312,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10548,"output_tokens":3380,"usd":0.06862,"stage2_stop_reason":"end_turn"},"total_usd":0.111932,"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\": 1996,\n      \"finding\": \"The CHAF1B (CAF1P60/CAF1A) gene was mapped to human chromosome 21q22.2, within the Down syndrome critical region, and encodes the p60 subunit of the CAF-1 complex that interacts with other subunits to promote histone assembly onto replicating DNA.\",\n      \"method\": \"Fluorescence in situ hybridization, somatic cell hybrids, YAC/cosmid hybridization, exon trapping\",\n      \"journal\": \"Human genetics / Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two independent labs replicated chromosomal mapping; functional description based on prior literature, not new experiment\",\n      \"pmids\": [\"8792829\", \"8660983\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CHAF1B is the medium (p60) subunit of the trimeric CAF-1 complex and contains a 7× WD repeat domain, a B-like domain, and a PEST domain; it functions as a histone H3/H4 chaperone shuttling newly synthesized histones to the replication fork during DNA synthesis.\",\n      \"method\": \"Review/synthesis of prior experimental literature on CAF-1 complex biochemistry\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — domain architecture and complex membership are well-established across multiple prior studies as summarized in this review; not a single new experiment\",\n      \"pmids\": [\"26066981\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Knockdown of CHAF1B in hepatocellular carcinoma (HUH-7) cells reduced invasion and migration ability, induced S-phase accumulation, and inhibited tumor growth in vivo; downstream gene expression changes included upregulation of PSMB6, SLC30A7, and SMC3, and downregulation of BLM and TWF2.\",\n      \"method\": \"Lentiviral shRNA knockdown, scratch wound healing assay, Transwell invasion assay, flow cytometry, gene expression profiling, Western blot, RT-PCR, xenograft mouse model\",\n      \"journal\": \"Oncology reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KD with defined cellular and in vivo phenotypes; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"29767268\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CHAF1B promotes DNA damage repair in nasopharyngeal carcinoma cells following radiation, inhibiting apoptosis and conferring radioresistance; this mechanism is dependent on the DNA-PK pathway, as demonstrated by γH2AX foci resolution and DNA-PK inhibitor sensitization.\",\n      \"method\": \"siRNA/shRNA knockdown and overexpression, colony formation assay, γH2AX foci detection, flow cytometry (apoptosis), MTT assay, xenograft model, DNA-PK inhibitor treatment\",\n      \"journal\": \"Biomedicine & pharmacotherapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pathway placement via pharmacological inhibition combined with loss- and gain-of-function; single lab\",\n      \"pmids\": [\"31869663\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CHAF1B acts as an E3 ubiquitin ligase that promotes ubiquitination and degradation of the nuclear co-repressor NCOR2; CHAF1B and NCOR2 physically interact predominantly in the nucleus, and CHAF1B-mediated NCOR2 degradation drives cisplatin resistance in lung adenocarcinoma.\",\n      \"method\": \"Proteome microarray, Western blot, co-immunoprecipitation, qRT-PCR, cell proliferation/migration assays, apoptosis assay, xenograft mouse model, immunohistochemistry, ubiquitination assay\",\n      \"journal\": \"Cancer cell international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP interaction and ubiquitination assay demonstrate mechanism; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"32508530\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CHAF1B depletion in mouse preimplantation embryos increases apoptosis, reduces blastocyst hatching and outgrowth, causes embryonic lethality post-implantation, and decreases expression of pluripotency factors (Oct4, Cdx2, Sox2, Nanog). Mechanistically, CHAF1B mediates replacement of histone H3.3 with H3.1/H3.2, associated with increased repressive marks (H3K9me2/3, H3K27me2/3) and decreased active marks (H3K4me2/3).\",\n      \"method\": \"siRNA knockdown in embryos, immunofluorescence, flow cytometry (apoptosis), RNA-sequencing, ATAC-sequencing, Western blot\",\n      \"journal\": \"International journal of biological macromolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined molecular phenotype; single lab with multiple orthogonal methods (RNA-seq, ATAC-seq, histone mark analysis)\",\n      \"pmids\": [\"34906611\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CHAF1B binds directly to the TRIM13 promoter to repress its transcription in AML cells; loss of CHAF1B de-represses TRIM13, which then ubiquitinates CCNA1 to promote cell cycle entry and ultimately leukemic cell exhaustion, identifying the CHAF1B→TRIM13→CCNA1 axis as a key leukemogenic pathway.\",\n      \"method\": \"RNA sequencing, ChIP (CHAF1B promoter binding), knockdown/overexpression in AML cell lines and patient-derived xenografts, cell cycle and self-renewal assays\",\n      \"journal\": \"Blood advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP for promoter binding plus functional epistasis in PDX models; single lab\",\n      \"pmids\": [\"37205848\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CHAF1B interacts with ULK1 (Unc-51-like kinase 1) in the nuclear compartment of MPN cells; silencing CHAF1B enhances transcription of IFNα-stimulated genes and potentiates IFNα-dependent antineoplastic responses in primary MPN progenitor cells.\",\n      \"method\": \"Co-immunoprecipitation/interaction studies, shRNA silencing, gene expression analysis, primary MPN progenitor cell functional assays\",\n      \"journal\": \"Cancer research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — interaction identified; functional consequence of silencing confirmed; single lab\",\n      \"pmids\": [\"37377894\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CHAF1B competitively binds to the SETD7 promoter region and represses its transcription in lung squamous-cell carcinoma, promoting cell proliferation; silencing CHAF1B upregulates SETD7 and suppresses tumor growth in vitro and in vivo.\",\n      \"method\": \"WGCNA bioinformatics, ChIP (promoter binding), CHAF1B knockdown, RNA sequencing, in vitro proliferation assays, xenograft model\",\n      \"journal\": \"Frontiers of medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP demonstrates direct promoter binding; loss-of-function confirms functional consequence; single lab\",\n      \"pmids\": [\"39862337\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CHAF1B promotes malignant phenotypes in hepatocellular carcinoma via activation of the PI3K/Akt/HIF-1α pathway; blockade of this pathway partially attenuates CHAF1B-mediated sorafenib resistance, placing CHAF1B upstream of PI3K/Akt/HIF-1α.\",\n      \"method\": \"RNA sequencing, pathway-specific inhibitors, siRNA knockdown, CCK8, colony formation, Transwell migration/invasion, flow cytometry, Western blot\",\n      \"journal\": \"International journal of medical sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — pathway placement via pharmacological inhibition only; single lab, no direct binding or reconstitution evidence\",\n      \"pmids\": [\"41049428\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CHAF1B physically associates with BCL6 and TBL1XR1 in germinal center B cells (identified by Co-IP/MS); CHAF1B stabilizes the BCL6/TBL1XR1 repressor complex to cooperatively repress transcription, promote GC dark zone/light zone organization, and support GC B cell differentiation and antibody production. Loss of CHAF1B impairs GC formation, induces apoptosis, and reduces high-affinity antibody responses.\",\n      \"method\": \"Co-immunoprecipitation coupled with mass spectrometry, conditional knockout mouse models, flow cytometry, immunofluorescence, transcriptional reporter assays\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — Co-IP/MS identified complex; loss-of-function in mice with defined cellular and molecular phenotypes; multiple orthogonal methods\",\n      \"pmids\": [\"41764732\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Chaf1b upregulates IL-33 secretion in glioma stem cells, promoting microglial M2 polarization and activating the PI3K/AKT signaling pathway; neutralization of IL-33 reverses these effects, placing Chaf1b upstream of IL-33–PI3K/AKT in the GBM stem-immune axis.\",\n      \"method\": \"Genetic silencing in patient-derived GSCs, intracranial xenograft models, IL-33 neutralization, flow cytometry, self-renewal and tumorigenicity assays\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis via neutralization antibody plus in vivo loss-of-function; single lab\",\n      \"pmids\": [\"41102004\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CHAF1B (CAF-1-p60) is the WD-repeat-containing middle subunit of the trimeric CAF-1 histone chaperone complex that deposits H3.1/H3.2 onto replicating DNA, replacing H3.3 to establish repressive chromatin marks; beyond its canonical replication-coupled chromatin assembly role, CHAF1B acts as an epigenetic transcriptional repressor by binding promoters (e.g., TRIM13, SETD7) and stabilizing co-repressor complexes (BCL6/TBL1XR1), and exhibits E3 ubiquitin ligase activity toward NCOR2, while also promoting DNA damage repair via the DNA-PK pathway and modulating immune signaling through IL-33/PI3K-AKT and IFN-stimulated gene transcription.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CHAF1B is the medium (p60) subunit of the trimeric CAF-1 histone chaperone complex, a WD-repeat protein that shuttles newly synthesized histone H3/H4 to the replication fork to drive replication-coupled chromatin assembly [#1]. In mouse preimplantation embryos it mediates replacement of histone H3.3 with H3.1/H3.2, establishing repressive chromatin (gained H3K9me2/3 and H3K27me2/3, lost H3K4me2/3) and supporting expression of pluripotency factors, with its loss causing apoptosis and post-implantation lethality [#5]. Beyond canonical chromatin assembly, CHAF1B operates as a transcriptional repressor by binding directly to target promoters such as TRIM13 and SETD7 to silence them, configuring oncogenic programs in AML and lung squamous-cell carcinoma; in the leukemic context this defines a CHAF1B\\u2192TRIM13\\u2192CCNA1 cell-cycle axis [#6, #8]. In germinal center B cells CHAF1B associates with BCL6 and TBL1XR1 and stabilizes this co-repressor complex to support GC organization, B cell differentiation, and high-affinity antibody responses [#10]. CHAF1B additionally functions as an E3 ubiquitin ligase that ubiquitinates and degrades the nuclear co-repressor NCOR2 [#4], and it promotes DNA-PK\\u2013dependent DNA damage repair and radioresistance [#3]. Across multiple cancers CHAF1B supports proliferation, invasion, and therapy resistance and modulates immune signaling, including a nuclear interaction with ULK1 that restrains IFN\\u03b1-stimulated gene transcription [#7] and IL-33\\u2013driven microglial polarization in glioma [#11].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Establishing the gene's chromosomal location and complex membership was the first step in defining CHAF1B as a histone-assembly factor of potential developmental relevance.\",\n      \"evidence\": \"FISH, somatic cell hybrids, and YAC/cosmid mapping placing CAF1P60 at 21q22.2 within the Down syndrome critical region\",\n      \"pmids\": [\"8792829\", \"8660983\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional role inferred from prior literature, not new experiment\", \"No mechanistic link between map position and Down syndrome phenotype established\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Consolidation of CAF-1 biochemistry defined CHAF1B's domain architecture and its role as the p60 subunit chaperoning H3/H4 to the replication fork.\",\n      \"evidence\": \"Review/synthesis of prior CAF-1 complex biochemistry describing 7\\u00d7 WD-repeat, B-like, and PEST domains\",\n      \"pmids\": [\"26066981\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No single new experiment; relies on prior studies\", \"Does not address non-replicative functions\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Linking CHAF1B to histone variant exchange showed how its chaperone activity translates into a defined chromatin state and developmental outcome.\",\n      \"evidence\": \"siRNA knockdown in mouse embryos with RNA-seq, ATAC-seq, and histone mark Western blots showing H3.3\\u2192H3.1/H3.2 replacement and repressive-mark gain\",\n      \"pmids\": [\"34906611\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of variant selection not resolved\", \"Single lab; not extended to other developmental contexts\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identification of E3 ubiquitin ligase activity toward NCOR2 revealed a chromatin-independent post-translational function for CHAF1B.\",\n      \"evidence\": \"Proteome microarray, Co-IP, and ubiquitination assay in lung adenocarcinoma showing nuclear CHAF1B\\u2013NCOR2 interaction and NCOR2 degradation\",\n      \"pmids\": [\"32508530\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural basis for ligase activity defined\", \"WD-repeat protein acting as E3 not reconstituted in vitro\", \"Single lab\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Placing CHAF1B in the DNA-PK repair pathway connected it to genome maintenance and therapy resistance beyond replication.\",\n      \"evidence\": \"Loss/gain-of-function with \\u03b3H2AX foci resolution and DNA-PK inhibitor sensitization in nasopharyngeal carcinoma plus xenografts\",\n      \"pmids\": [\"31869663\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular interaction with DNA-PK components not shown\", \"Single lab\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstration of direct promoter binding (TRIM13) established CHAF1B as a sequence-targeted transcriptional repressor driving a leukemogenic cell-cycle axis.\",\n      \"evidence\": \"ChIP for CHAF1B promoter binding plus functional epistasis (TRIM13\\u2192CCNA1) in AML lines and patient-derived xenografts\",\n      \"pmids\": [\"37205848\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How CHAF1B is recruited to specific promoters unknown\", \"Repressive complex partners at TRIM13 not defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"A nuclear CHAF1B\\u2013ULK1 interaction linked the chaperone to control of interferon-stimulated gene transcription in myeloproliferative neoplasms.\",\n      \"evidence\": \"Co-IP interaction studies and shRNA silencing with gene expression and primary MPN progenitor assays\",\n      \"pmids\": [\"37377894\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Reciprocal validation and stoichiometry of ULK1 interaction not established\", \"Direct transcriptional mechanism at ISGs unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"A second direct promoter target (SETD7) and identification of the BCL6/TBL1XR1 co-repressor complex generalized CHAF1B's repressor role across tumor and immune contexts.\",\n      \"evidence\": \"ChIP at SETD7 in lung squamous carcinoma; Co-IP/MS plus conditional knockout mice for BCL6/TBL1XR1 in germinal center B cells\",\n      \"pmids\": [\"39862337\", \"41764732\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether promoter targeting and complex stabilization use a shared molecular mechanism unresolved\", \"Determinants of target-gene selection unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Functional studies placed CHAF1B upstream of PI3K/Akt and IL-33 immune-signaling axes, broadening its role into tumor microenvironment modulation.\",\n      \"evidence\": \"RNA-seq with pathway inhibitors in HCC (PI3K/Akt/HIF-1\\u03b1) and IL-33 neutralization with intracranial xenografts in glioma stem cells\",\n      \"pmids\": [\"41049428\", \"41102004\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"HCC pathway placement rests on pharmacological inhibition only, no direct binding or reconstitution\", \"Direct molecular link between CHAF1B and IL-33 secretion not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single WD-repeat chaperone subunit mechanistically unifies replication-coupled histone deposition, sequence-specific promoter repression, and E3 ligase activity remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model reconciling chaperone, repressor, and ligase functions\", \"Mechanism of promoter recruitment unidentified\", \"Whether non-canonical functions require the full CAF-1 complex untested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [1, 5]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [6, 8, 10]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [4, 7, 10]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [1, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [1, 5]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [6, 8, 10]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [7, 10, 11]}\n    ],\n    \"complexes\": [\"CAF-1\", \"BCL6/TBL1XR1 co-repressor complex\"],\n    \"partners\": [\"NCOR2\", \"ULK1\", \"BCL6\", \"TBL1XR1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}