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    GENE:

    BAP1 (BRCA1 Associated Protein 1)

    i
    Other names: BAP1, BRCA1 Associated Protein 1, BRCA1 Associated Protein-1 (Ubiquitin Carboxy-Terminal Hydrolase), Ubiquitin Carboxyl-Terminal Hydrolase BAP1, Cerebral Protein 6, Ubiquitin Carboxy-Terminal Hydrolase, BRCA1-Associated Protein 1, Cerebral Protein-13, HUCEP-13, KIAA0272, Hucep-6, UCHL2
    2d
    Update on pleural epithelioid mesothelioma: New insights for diagnosis and patient management. (PubMed, J Thorac Oncol)
    The emerging role of Artificial Intelligence in subtyping, grading and prediction of biomarkers for genomic subtyping is also discussed. [251 words].
    Review • Journal
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    MTAP (Methylthioadenosine Phosphorylase) • BAP1 (BRCA1 Associated Protein 1) • NF2 (Neurofibromin 2)
    2d
    Recently identified diagnostic markers in effusion cytology. (PubMed, Acta Cytol)
    Effusion diagnosis remains central to staging, and consequently prognosis of cancer patients. Effusions additionally constitute optimal material for predictive studies and thereby guide the choice of targeted therapy.  .
    Review • Journal
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    MTAP (Methylthioadenosine Phosphorylase) • BAP1 (BRCA1 Associated Protein 1) • NF2 (Neurofibromin 2) • NKX2-1 (NK2 Homeobox 1) • PAX8 (Paired box 8) • HEG1 (Heart Development Protein With EGF Like Domains 1) • TRPS1 (Transcriptional Repressor GATA Binding 1)
    3d
    Causal Prediction of TP53 Variant Pathogenicity Using a Perturbation-Informed Protein Language Model. (PubMed, Adv Sci (Weinh))
    Thus, by integrating protein language models with experimentally validated functional data, our approach enables accurate, interpretable VEP for TP53, overcoming limitations of predictors trained solely on evolutionary or clinical associations. We further extended this framework to five additional cancer-related genes (VHL, ATM, BRCA1, RAD51C, and BAP1), establishing a generalizable framework for gene-specific VEP with potential applications in precision medicine.
    Journal • BRCA Biomarker
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    TP53 (Tumor protein P53) • BRCA1 (Breast cancer 1, early onset) • ATM (ATM serine/threonine kinase) • BAP1 (BRCA1 Associated Protein 1) • RAD51C (RAD51 paralog C)
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    TP53 mutation
    3d
    Clinicopathological and molecular characteristics of rare ovarian sex cord stromal tumors with BAP1 mutation. (PubMed, Virchows Arch)
    Follow-up (32-37 months) showed two late recurrences, with all patients alive. These findings define a distinct BAP1-mutated ovarian SCST subset, linking specific mutations to characteristic phenotypes and expanding the BAP1-TPDS clinical-pathological spectrum.
    Journal
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    BAP1 (BRCA1 Associated Protein 1)
    4d
    Distinction of thymic carcinoma and type B3 thymoma using ancillary biomarkers. (PubMed, Pathologica)
    CD5 and CD117 are the best markers for TC. While the addition of other markers (i.e., BAP1 loss, MTAP loss and CDKN2A deletion) might be useful in cases negative for CD5 and CD117, rare cases of type B3 thymoma might harbor these alterations.
    Journal
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    KIT (KIT proto-oncogene, receptor tyrosine kinase) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • MTAP (Methylthioadenosine Phosphorylase) • BAP1 (BRCA1 Associated Protein 1) • CD5 (CD5 Molecule)
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    CDKN2A deletion • KIT expression
    4d
    Immunohistochemical and molecular profiling of uveal melanoma: clinicopathological correlations from an Italian cohort. (PubMed, Pathologica)
    This study highlights the heterogeneous molecular landscape of UM and underscores the importance of integrating histopathological and molecular data for improved prognostic stratification. The identification of potential therapeutic targets and atypical mutations typically associated with other melanoma subtypes suggests avenues for future research and tailored therapeutic strategies.
    Retrospective data • Journal • Tumor mutational burden • PD(L)-1 Biomarker • IO biomarker
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    PD-L1 (Programmed death ligand 1) • BRAF (B-raf proto-oncogene) • ER (Estrogen receptor) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • TMB (Tumor Mutational Burden) • PTEN (Phosphatase and tensin homolog) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • NOTCH1 (Notch 1) • GNAQ (G Protein Subunit Alpha Q) • KDR (Kinase insert domain receptor) • BAP1 (BRCA1 Associated Protein 1) • GNA11 (G Protein Subunit Alpha 11) • JAK3 (Janus Kinase 3) • H3-3A (H3.3 Histone A)
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    PD-L1 expression • TP53 mutation • TMB-H • BRAF mutation • PTEN mutation
    7d
    Spatial immune profiling complements genomic sequencing in biliary tract cancer: hypothesis-generating use cases. (PubMed, ESMO Gastrointest Oncol)
    In contrast, a patient with loss of BAP1 was linked to a CD8+ T-cell enriched tumor microenvironment, classified as spatially immune enriched and responded long-term to subsequent immune checkpoint inhibition and tyrosine kinase inhibition therapy. These observations provide a rationale for integrated genomic and spatial immune profiling in BTC, which will require further prospective validation.
    Journal • BRCA Biomarker • IO biomarker
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    BRCA2 (Breast cancer 2, early onset) • HRD (Homologous Recombination Deficiency) • CD8 (cluster of differentiation 8) • BAP1 (BRCA1 Associated Protein 1)
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    BRCA2 mutation • HRD
    8d
    Clinical and immunological significance of FOXO1 as a biomarker of improved response to immune checkpoint plus tyrosine kinase inhibitor therapy in metastatic renal cell carcinoma. (PubMed, Eur J Pharmacol)
    FOXO1 carries both prognostic and predictive relevance in mRCC and independently predicts greater benefit from IO+TKI therapy. Integration of FOXO1 with complementary immune gene features into an RF-based model provides a promising framework for precision immunotherapy in advanced RCC.
    Journal • IO biomarker
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    BRAF (B-raf proto-oncogene) • CD8 (cluster of differentiation 8) • BAP1 (BRCA1 Associated Protein 1) • CD4 (CD4 Molecule) • FOXO1 (Forkhead box O1)
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    BRAF mutation
    9d
    S100A6 promotes liver metastasis by activating FGFR3 signaling in BAP1-deficient uveal melanoma. (PubMed, Oncogene)
    Genetic or pharmacological targeting of S100A6-FGFR3 signaling effectively suppressed BAP1-deficient UM metastasis in preclinical models, highlighting the therapeutic potential of targeting this signaling pathway. Overall, our findings establish S100A6 as a critical mediator of hepatic metastasis in BAP1-deficient UM through FGFR3-dependent tumor microenvironment activation, revealing its therapeutic potential.
    Journal
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    FGFR3 (Fibroblast growth factor receptor 3) • BAP1 (BRCA1 Associated Protein 1) • S100A6 (S100 calcium binding protein A6)
    10d
    Concurrent Tissue and Circulating Tumor DNA analysis in Renal Cell Carcinoma: Insights from a Multimodal Database. (PubMed, Oncologist)
    ctDNA testing offers complementary insights to tissue NGS in RCC, particularly in metastatic disease, suggesting the potential utility of ctDNA in advanced RCC. Longitudinal analysis may enhance delineation of biomarkers of response and resistance at mutation and ctDNA fraction levels.
    Journal • Circulating tumor DNA
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    TP53 (Tumor protein P53) • PBRM1 (Polybromo 1) • BAP1 (BRCA1 Associated Protein 1) • SETD2 (SET Domain Containing 2, Histone Lysine Methyltransferase)
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    Tempus xT Assay • Tempus xF Assay
    11d
    When loss is gain: truncating mutations in additional sex combs (ASXL) gene family in cancer and neurodevelopment. (PubMed, Trends Genet)
    Sequence analysis suggests that such mechanisms require both escape from nonsense-mediated mRNA decay and removal of a putative C-terminal degron signal within ASXL proteins. We propose GOF as a generalized mechanism for ASXL mutations, resulting in increased protein stability and altered histone modifications, with implications for diagnosis and therapy for these medical conditions.
    Review • Journal
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    ASXL1 (ASXL Transcriptional Regulator 1) • BAP1 (BRCA1 Associated Protein 1)
    11d
    Uncovering BAP1 deubiquitination landscape enhances mechanism elucidation and therapeutic precision for BAP1-deficient pancancers. (PubMed, Sci Transl Med)
    Combined inhibition of LSD1 and PARP1, using SP2509/SP2577 and olaparib, respectively, synergistically hinders NER, induces apoptosis, reduces tumor burden, and prolongs the survival of multiple BAP1-deficient pancancer in vitro models and in vivo xenografts. In conclusion, our results provide a deubiquitination landscape of BAP1; elucidate the mechanisms of action of BAP1, LSD1, and PARP1 in pancancers; and describe a promising combination therapeutic strategy applicable across multiple cancers with BAP1 mutations.
    Journal • BRCA Biomarker • PARP Biomarker • Pan tumor
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    BAP1 (BRCA1 Associated Protein 1) • DDB1 (Damage Specific DNA Binding Protein 1) • RAD23B (RAD23 Homolog B)
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    BRCA1 mutation
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    Lynparza (olaparib) • seclidemstat (SP2577) • SP-2509