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    BIOMARKER:

    BAP1 mutation

    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
    Entrez ID:
    8314
    Related biomarkers:
    Expression
    Mutation
    CNA
    Others
    4d
    Recent Advances in Pathology of Intrahepatic Cholangiocarcinoma. (PubMed, Cancers (Basel))
    Accurate diagnosis of ICCA is essential for effective patient management and prognostic determination. This article provides an updated overview of ICCA pathology, focusing particularly on molecular features, histological subtypes, and diagnostic approaches.
    Review • Journal
    |
    EGFR (Epidermal growth factor receptor) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • TP53 (Tumor protein P53) • FGFR2 (Fibroblast growth factor receptor 2) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • ARID1A (AT-rich interaction domain 1A) • BAP1 (BRCA1 Associated Protein 1)
    |
    TP53 mutation • KRAS mutation • BRAF mutation • ARID1A mutation • FGFR2 mutation • FGFR2 fusion • BAP1 mutation
    5d
    Primary leptomeningeal melanocytic neoplasms: a clinicopathologic, immunohistochemical, and molecular study of 12 cases. (PubMed, Hum Pathol)
    SF3B1 mutation is first described in two cases of plaque-type blue nevus associated with LMM. Patients with SF3B1 mutation might be related to poor prognosis in LMN.
    Journal
    |
    CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • GNAQ (G Protein Subunit Alpha Q) • SF3B1 (Splicing Factor 3b Subunit 1) • BAP1 (BRCA1 Associated Protein 1) • GNA11 (G Protein Subunit Alpha 11) • EIF1AX (Eukaryotic Translation Initiation Factor 1A X-Linked) • PLCB4 (Phospholipase C Beta 4)
    |
    GNAQ mutation • SF3B1 mutation • BAP1 mutation
    6d
    Identification and validation of a costimulatory molecule-related signature to predict the prognosis for uveal melanoma patients. (PubMed, Sci Rep)
    Finally, based on the Genomics of Drug Sensitivity in Cancer 2 (GDSC2) dataset, drug sensitivity analysis found that high-risk patients may be potential beneficiaries of the treatment of crizotinib or temozolomide. Taken together, our CM-related prognostic signature is a reliable biomarker that may provide ideas for future treatments for the disease.
    Journal • Tumor mutational burden
    |
    TMB (Tumor Mutational Burden) • BAP1 (BRCA1 Associated Protein 1) • GNA11 (G Protein Subunit Alpha 11)
    |
    BAP1 mutation
    |
    Xalkori (crizotinib) • temozolomide
    7d
    Advances in Immunotherapy for Malignant Pleural Mesothelioma: From Emerging Strategies to Translational Insights. (PubMed, Open Respir Arch)
    Innovative combination regimens, exemplified by the concurrent administration of nivolumab and ipilimumab, have demonstrated marked improvement in survival and patient's benefits. This review accentuates the transformative capacity of immunotherapy in revolutionizing the therapeutic outlook for MPM, thereby potentially translating into augmented survival rates and offering glimpses of new approaches on the horizon. Despite the persisting challenges, the synergistic crossroads of interdisciplinary research and collaborative clinical endeavors portend a hopeful landscape for MPM treatment.
    Review • Journal • BRCA Biomarker • PD(L)-1 Biomarker • IO biomarker
    |
    CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • NF1 (Neurofibromin 1) • PD-1 (Programmed cell death 1) • BAP1 (BRCA1 Associated Protein 1) • NF2 (Neurofibromin 2) • CTLA4 (Cytotoxic T-Lymphocyte Associated Protein 4)
    |
    BAP1 mutation
    |
    Opdivo (nivolumab) • Yervoy (ipilimumab)
    7d
    MOICS, a novel classier deciphering immune heterogeneity and aid precise management of clear cell renal cell carcinoma at multiomics level. (PubMed, Cancer Biol Ther)
    Additionally, significant differences were observed in the genomic landscapes between the subtypes: MOICS1 exhibited mutations in TTN, BAP1, SETD2, MTOR, MUC16, CSMD3, and AKAP9, while MOICS2 was characterized by notable alterations in the TGF-β pathway. Overall, our work demonstrates that multi-immune omics remodeling analysis enhances the understanding of the immune heterogeneity in ccRCC and supports precise patient management.
    Journal
    |
    CD8 (cluster of differentiation 8) • mTOR (Mechanistic target of rapamycin kinase) • BAP1 (BRCA1 Associated Protein 1) • MUC16 (Mucin 16, Cell Surface Associated) • SETD2 (SET Domain Containing 2, Histone Lysine Methyltransferase) • CD4 (CD4 Molecule) • TGFB1 (Transforming Growth Factor Beta 1) • CSMD3 (CUB And Sushi Multiple Domains 3)
    |
    BAP1 mutation • MTOR mutation • TTN mutation • SETD2 mutation
    7d
    Genomic characterization and detection of potential therapeutic targets for peritoneal mesothelioma in current practice. (PubMed, Clin Exp Med)
    Extensive NGS analysis of PeM samples resulted in the identification of potentially effective targeted therapies for about one in four patients. Although these therapies are currently not available for patients with PeM, ongoing developments might result in new treatment options in the future.
    Journal • Tumor mutational burden • BRCA Biomarker
    |
    TMB (Tumor Mutational Burden) • ATM (ATM serine/threonine kinase) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • NF1 (Neurofibromin 1) • BAP1 (BRCA1 Associated Protein 1) • CDKN2B (Cyclin Dependent Kinase Inhibitor 2B) • NF2 (Neurofibromin 2)
    |
    BAP1 mutation • NF2 mutation
    |
    FoundationOne® CDx
    18d
    Low Exposures to Amphibole or Serpentine Asbestos in Germline Bap1-mutant Mice Induce Mesothelioma Characterized by an Immunosuppressive Tumor Microenvironment. (PubMed, Cancer Res Commun)
    Chrysotile induced a more profound immune tumor response than crocidolite in Bap1-mutant mice by upregulating CD39/CD73-adenosine and Ccl2/Ccr2 pathways and recruiting more M2 macrophages, which together contributed to an immunosuppressive tumor microenvironment. Interrogation of human MM RNA-seq data revealed interconnected immunosuppressive pathways consistent with our mouse findings.
    Preclinical • Journal • IO biomarker
    |
    BAP1 (BRCA1 Associated Protein 1) • IL6 (Interleukin 6) • CD73 (5'-Nucleotidase Ecto) • CD163 (CD163 Molecule) • IL10 (Interleukin 10) • CCL2 (Chemokine (C-C motif) ligand 2) • CCR2 (C-C Motif Chemokine Receptor 2) • ENTPD1 (Ectonucleoside Triphosphate Diphosphohydrolase 1)
    |
    BAP1 mutation
    23d
    The Pediatric and Young Adult Choroidal and Ciliary Body Melanoma Genetic Study, A Survey by the European Ophthalmic Oncology Group. (PubMed, Invest Ophthalmol Vis Sci)
    Males had a more favorable survival and disomy 3, and the absence of a BAP1 mutation in the tumor tissue predicted the most favorable metastasis-free survival. A BAP1 germline pathogenic variant was identified in one patient (1%), and a somatic variant based mainly on immunohistochemistry in 13 (42%).
    Retrospective data • Journal
    |
    GNAQ (G Protein Subunit Alpha Q) • SF3B1 (Splicing Factor 3b Subunit 1) • BAP1 (BRCA1 Associated Protein 1) • GNA11 (G Protein Subunit Alpha 11) • EIF1AX (Eukaryotic Translation Initiation Factor 1A X-Linked)
    |
    BAP1 mutation
    1m
    Complex Genomic Rearrangement Patterns in Malignant Pleural Mesothelioma due to Environmental Asbestos Exposure. (PubMed, J Environ Pathol Toxicol Oncol)
    We also discovered the SKA3-DDX10 fusion in two MPM genomes, which is a novel finding for MPM. We found that MPM genomes are very complex, suggesting that this highly rearranged pattern is strongly related to driver mutational status like BAP1, TP53 and RB1.
    Journal
    |
    TP53 (Tumor protein P53) • RB1 (RB Transcriptional Corepressor 1) • BAP1 (BRCA1 Associated Protein 1) • ERCC2 (Excision repair cross-complementation group 2) • KMT2C (Lysine Methyltransferase 2C) • XRCC1 (X-Ray Repair Cross Complementing 1) • DDX10 (DEAD-Box Helicase 10) • TGFBR1 (Transforming Growth Factor Beta Receptor 1)
    |
    TP53 mutation • BAP1 mutation
    2ms
    SYNERGY-AI: Artificial Intelligence Based Precision Oncology Clinical Trial Matching and Registry (clinicaltrials.gov)
    P=N/A, N=50000, Recruiting, Massive Bio, Inc. | Trial completion date: Jun 2025 --> Jun 2027 | Trial primary completion date: Dec 2024 --> Dec 2026
    Trial completion date • Trial primary completion date
    |
    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • PD-L1 (Programmed death ligand 1) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • ER (Estrogen receptor) • ALK (Anaplastic lymphoma kinase) • TP53 (Tumor protein P53) • TMB (Tumor Mutational Burden) • FLT3 (Fms-related tyrosine kinase 3) • ABL1 (ABL proto-oncogene 1) • NRAS (Neuroblastoma RAS viral oncogene homolog) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • FGFR2 (Fibroblast growth factor receptor 2) • PTEN (Phosphatase and tensin homolog) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • BCL2 (B-cell CLL/lymphoma 2) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2) • STK11 (Serine/threonine kinase 11) • NPM1 (Nucleophosmin 1) • HRAS (Harvey rat sarcoma viral oncogene homolog) • DNMT3A (DNA methyltransferase 1) • ERBB3 (V-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3) • RB1 (RB Transcriptional Corepressor 1) • CLDN18 (Claudin 18) • PDGFRA (Platelet Derived Growth Factor Receptor Alpha) • NF1 (Neurofibromin 1) • JAK2 (Janus kinase 2) • NRG1 (Neuregulin 1) • POLE (DNA Polymerase Epsilon) • AKT1 (V-akt murine thymoma viral oncogene homolog 1) • PD-1 (Programmed cell death 1) • CCND1 (Cyclin D1) • MCL1 (Myeloid cell leukemia 1) • KDR (Kinase insert domain receptor) • PBRM1 (Polybromo 1) • BAP1 (BRCA1 Associated Protein 1) • VEGFA (Vascular endothelial growth factor A) • BCL6 (B-cell CLL/lymphoma 6) • PDGFRB (Platelet Derived Growth Factor Receptor Beta) • PTCH1 (Patched 1) • FGFR4 (Fibroblast growth factor receptor 4) • MSH6 (MutS homolog 6) • CDK4 (Cyclin-dependent kinase 4) • MSH2 (MutS Homolog 2) • CTNNB1 (Catenin (cadherin-associated protein), beta 1) • MAP2K2 (Mitogen-activated protein kinase kinase 2) • FBXW7 (F-Box And WD Repeat Domain Containing 7) • WT1 (WT1 Transcription Factor) • ATRX (ATRX Chromatin Remodeler) • BRCA (Breast cancer early onset) • RAF1 (Raf-1 Proto-Oncogene Serine/Threonine Kinase) • TSC2 (TSC complex subunit 2) • CHEK2 (Checkpoint kinase 2) • PD-L2 (Programmed Cell Death 1 Ligand 2) • ERBB4 (erb-b2 receptor tyrosine kinase 4) • JAK1 (Janus Kinase 1) • FANCA (FA Complementation Group A) • TSC1 (TSC complex subunit 1) • MDM4 (The mouse double minute 4) • POLD1 (DNA Polymerase Delta 1) • CDK6 (Cyclin-dependent kinase 6) • CEBPA (CCAAT Enhancer Binding Protein Alpha) • PARP1 (Poly(ADP-Ribose) Polymerase 1) • AURKA (Aurora kinase A) • JAK3 (Janus Kinase 3) • RICTOR (RPTOR Independent Companion Of MTOR Complex 2) • CHEK1 (Checkpoint kinase 1) • GATA6 (GATA Binding Protein 6) • MSH3 (MutS Homolog 3) • TGFBR2 (Transforming Growth Factor Beta Receptor 2) • GNAS (GNAS Complex Locus) • MYCL (MYCL Proto-Oncogene BHLH Transcription Factor) • AKT2 (V-akt murine thymoma viral oncogene homolog 2) • CCND2 (Cyclin D2) • CCND3 (Cyclin D3) • CSF1R (Colony stimulating factor 1 receptor) • MAP3K1 (Mitogen-Activated Protein Kinase Kinase Kinase 1) • ERCC4 (ERCC Excision Repair 4, Endonuclease Catalytic Subunit) • HDAC1 (Histone Deacetylase 1) • PRDM1 (PR/SET Domain 1) • ZNF217 (Zinc Finger Protein 217) • CDKN1A (Cyclin-dependent kinase inhibitor 1A) • GATA3 (GATA binding protein 3) • PARP2 (Poly(ADP-Ribose) Polymerase 2) • PARP3 (Poly(ADP-Ribose) Polymerase Family Member 3) • SDHA (Succinate Dehydrogenase Complex Flavoprotein Subunit A) • ACVR1B (Activin A Receptor Type 1B) • ZNF703 (Zinc Finger Protein 703)
    |
    HER-2 mutation • BAP1 mutation • AKT1 mutation • FGFR3 fusion • JAK3 mutation
    2ms
    A centrosome-related gene signature for predicting the overall survival of uveal melanoma. (PubMed, Transl Cancer Res)
    Our study first investigated the role of centrosome-related genes in UVM overall survival (OS). We then constructed a centrosome-related gene signature for UVM, which provides new insights into the role of CA in UVM and identifies novel centrosome-related biomarkers.
    Journal • Gene Signature
    |
    SF3B1 (Splicing Factor 3b Subunit 1) • BAP1 (BRCA1 Associated Protein 1) • CCND3 (Cyclin D3)
    |
    SF3B1 mutation • BAP1 mutation
    2ms
    Evaluate the Safety and Clinical Activity of HH2853 (clinicaltrials.gov)
    P1/2, N=168, Recruiting, Haihe Biopharma Co., Ltd. | Trial completion date: Dec 2024 --> Dec 2025 | Trial primary completion date: Dec 2023 --> Dec 2025
    Trial completion date • Trial primary completion date • Metastases
    |
    ARID1A (AT-rich interaction domain 1A) • BAP1 (BRCA1 Associated Protein 1)
    |
    ARID1A mutation • BAP1 mutation • EZH2 mutation • SMARCA4 mutation
    |
    HH2853
    2ms
    The Prevalence and Radiologic Features of Renal Cancers Associated with FLCN, BAP1, SDH, and MET Germline Mutations. (PubMed, Radiol Imaging Cancer)
    Within the study sample size limits, imaging findings for hereditary RCC overlapped with those of nonhereditary RCC, and the prevalence of other associated benign solid renal lesions (other than complex cysts) was up to 11%. Keywords: Familial Renal Cell Carcinoma, Birt-Hogg-Dubé Syndrome, Carcinoma, Renal Cell, Paragangliomas, Urinary, Kidney
    Journal
    |
    MET (MET proto-oncogene, receptor tyrosine kinase) • BAP1 (BRCA1 Associated Protein 1) • FLCN (Folliculin)
    |
    BAP1 mutation • MET mutation • FLCN mutation
    2ms
    Whole-genome DNA methylation profiling of intrahepatic cholangiocarcinoma reveals prognostic subtypes with distinct biological drivers. (PubMed, Cancer Res)
    Further integrative and functional analyses identified GBP4 demethylation, which is highly prevalent in the S2 and S3 groups, as an epigenetic oncogenic factor that regulates iCCA proliferation, migration, and invasion. Together, this study identifies prognostic methylome alterations and epigenetic drivers in iCCA.
    Journal • Tumor mutational burden • Epigenetic controller
    |
    KRAS (KRAS proto-oncogene GTPase) • TMB (Tumor Mutational Burden) • FGFR2 (Fibroblast growth factor receptor 2) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • BAP1 (BRCA1 Associated Protein 1) • GBP4 (Guanylate Binding Protein 4)
    |
    TMB-H • FGFR2 mutation • FGFR2 fusion • BAP1 mutation
    2ms
    Genomic characterization of recurrent uRCC tumors (AUA 2024)
    uRCC demonstrates an aggressive disease course with 55% of patients recurring. We identified genomic alterations correlating with recurrence, which may help select patients for treatment intensification, though confirmatory studies are required.
    Tumor mutational burden
    |
    TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • PBRM1 (Polybromo 1) • BAP1 (BRCA1 Associated Protein 1) • SETD2 (SET Domain Containing 2, Histone Lysine Methyltransferase)
    |
    TMB-H • PBRM1 mutation • BAP1 mutation
    |
    MSK-IMPACT
    2ms
    Differences in genomic, transcriptomic and immune landscape of prostate cancer (PCa) based on site of metastasis (mets) (AUA 2024)
    This study highlights distinct molecular profiles in metastatic prostate cancer (PCa) based on metastasis site, underlining the importance of personalized treatment strategies. The findings, particularly the variations in gene mutations and AR signaling, are crucial in tailoring management approaches for advanced PCa.
    Tumor mutational burden • PD(L)-1 Biomarker • MSi-H Biomarker • IO biomarker
    |
    PD-L1 (Programmed death ligand 1) • KRAS (KRAS proto-oncogene GTPase) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • PTEN (Phosphatase and tensin homolog) • RB1 (RB Transcriptional Corepressor 1) • AKT1 (V-akt murine thymoma viral oncogene homolog 1) • BAP1 (BRCA1 Associated Protein 1) • IFNG (Interferon, gamma) • CTNNB1 (Catenin (cadherin-associated protein), beta 1) • KMT2C (Lysine Methyltransferase 2C) • APC (APC Regulator Of WNT Signaling Pathway) • SPOP (Speckle Type BTB/POZ Protein)
    |
    TP53 mutation • TMB-H • MSI-H/dMMR • PIK3CA mutation • PTEN mutation • BAP1 mutation • APC mutation • AR mutation • AR splice variant 7
    |
    VENTANA PD-L1 (SP142) Assay • MI Tumor Seek™
    2ms
    Emerging therapeutic strategies for metastatic uveal melanoma: Targeting driver mutations. (PubMed, Pigment Cell Melanoma Res)
    Furthermore, in preclinical studies, actionable targets associated with BAP1 loss or oncogenic mutant SF3B1 have been identified, offering promising avenues for UM treatment. This review aims to summarize the emerging targeted and epigenetic therapeutic strategies for metastatic UM carrying specific driver mutations and the potential of combining these approaches with immunotherapy, with particular focus on those in upcoming or ongoing clinical trials.
    Review • Journal • BRCA Biomarker • IO biomarker • Metastases
    |
    GNAQ (G Protein Subunit Alpha Q) • SF3B1 (Splicing Factor 3b Subunit 1) • BAP1 (BRCA1 Associated Protein 1) • GNA11 (G Protein Subunit Alpha 11)
    |
    BRCA1 mutation • GNAQ mutation • BAP1 mutation
    2ms
    IDENTHY-K: IDEntification of New Predisposition Genes in Differentiated THYroid Cancer (clinicaltrials.gov)
    P=N/A, N=34, Active, not recruiting, Nantes University Hospital | Recruiting --> Active, not recruiting | N=95 --> 34
    Enrollment closed • Enrollment change
    |
    BAP1 (BRCA1 Associated Protein 1) • DICER1 (Dicer 1 Ribonuclease III)
    |
    BAP1 mutation
    2ms
    Germline mutations of homologous recombination genes and clinical outcomes in pancreatic cancer: a multicenter study in Taiwan. (PubMed, J Biomed Sci)
    Our study showed that nearly 20% of Taiwanese PDAC patients carried germline P/LP variants. The longer survival observed in gHRmut patients treated with 1L platinum-based chemotherapy highlights the importance of germline testing for all patients with advanced PDAC at diagnosis.
    Clinical • Clinical data • Journal • BRCA Biomarker
    |
    BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • BAP1 (BRCA1 Associated Protein 1) • PALB2 (Partner and localizer of BRCA2) • CHEK2 (Checkpoint kinase 2) • FANCA (FA Complementation Group A) • BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1) • NBN (Nibrin Nijmegen Breakage Syndrome 1 (Nibrin)) • MUTYH (MutY homolog) • FANCC (FA Complementation Group C)
    |
    BRCA1 mutation • ATM mutation • PALB2 mutation • BAP1 mutation • CHEK2 mutation • BRIP1 mutation • FANCA mutation • BLM mutation • NBN mutation
    2ms
    Quantification of eosinophilic area and its potential molecular feature in clear cell renal cell carcinoma. (PubMed, Jpn J Clin Oncol)
    The quantification of the eosinophilic feature serves as a robust predictor of clinical prognosis in clear cell renal cell carcinoma. Furthermore, the manifestation of this feature may be linked to BAP1 mutations and the down-regulation of Erythroblast Transformation-Specific-Related Gene in clear cell renal cell carcinoma. Significantly, the expression levels of Erythroblast Transformation-Specific-Related Gene manifest as an exemplary prognostic marker, providing exceptional predictive accuracy for the clinical prognosis in clear cell renal cell carcinoma.
    Journal
    |
    BAP1 (BRCA1 Associated Protein 1)
    |
    BAP1 mutation
    3ms
    Integrated analyses of the genetic and clinicopathological features of cholangiolocarcinoma: cholangiolocarcinoma may be characterized by mismatch-repair deficiency. (PubMed, J Pathol)
    In contrast, CLC has characteristics of dMMR tumors that are not found in iCCA, suggesting that it should be treated distinctly from iCCA.
    Journal • Mismatch repair
    |
    IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • BAP1 (BRCA1 Associated Protein 1) • MLH1 (MutL homolog 1) • MSH6 (MutS homolog 6) • MSH2 (MutS Homolog 2) • PMS2 (PMS1 protein homolog 2) • NCAM1 (Neural cell adhesion molecule 1) • EPCAM (Epithelial cell adhesion molecule) • KRT19 (Keratin 19) • SALL4 (Spalt Like Transcription Factor 4)
    |
    MSI-H/dMMR • BAP1 mutation
    3ms
    Ovarian steroid cell tumors: what do we know so far? (PubMed, Front Oncol)
    In malignant SCT, the tumors generally show greater global genomic instability, copy number gains in oncogenes, and occasional BAP1 mutation. Future studies involving multi-institutional cohort and unbiased molecular profiling using whole exome/transcriptome sequencing are needed to help advance our molecular understanding of SCTs.
    Review • Journal
    |
    BAP1 (BRCA1 Associated Protein 1)
    |
    BAP1 mutation
    3ms
    Beyond typical histology of BAP1-inactivated melanocytoma. (PubMed, Pathol Res Pract)
    In the current article, we focus on some new histological features, attempting to explain and link them to certain mechanisms of tumor development, including senescence, endoreplication, endocycling, asymmetric cytokinesis, entosis and others. In light of the morphological and molecular findings observed in BIM, we postulated that this entity unmasks a fine mechanism of tumor in which both clonal/stochastic and hierarchical model can be unified.
    Review • Journal • BRCA Biomarker
    |
    BRAF (B-raf proto-oncogene) • BRCA1 (Breast cancer 1, early onset) • BAP1 (BRCA1 Associated Protein 1)
    |
    BRAF mutation • BAP1 mutation
    3ms
    Tissue genomic profiling of pleural mesothelioma patients treated with immunotherapy: Unraveling genetic alterations and complexity (ELCC 2024)
    Conclusions Our study did not identify predictive or prognostic factors for IO outcomes in unresectable PM, emphasizing the complexity and heterogeneity of PM. Further research with larger cohorts is crucial to unveil biomarkers in this setting.
    Clinical • Tumor mutational burden • IO biomarker
    |
    PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • TMB (Tumor Mutational Burden) • BAP1 (BRCA1 Associated Protein 1) • NF2 (Neurofibromin 2) • FANCA (FA Complementation Group A)
    |
    PIK3CA mutation • BAP1 mutation • NF2 mutation • FANCA mutation
    |
    FoundationOne® CDx • OmniSeq INSIGHT
    3ms
    Unveiling the hidden role of disulfidptosis in kidney renal clear cell carcinoma: a prognostic signature for personalized treatment. (PubMed, Apoptosis)
    Besides, the correlation between the DRPS score and the chemotherapy-response signature indicated the potential effect of Gefitinib for high-risk patients...The DRPS model enables improved clinical management and personalized KIRC therapy. The identified biomarkers and immune characteristics offer new mechanistic insight into disulfidptosis in KIRC.
    Journal • IO biomarker
    |
    BAP1 (BRCA1 Associated Protein 1) • AHNAK2 (AHNAK Nucleoprotein 2) • FOXM1 (Forkhead Box M1) • CHAC1 (ChaC Glutathione Specific Gamma-Glutamylcyclotransferase 1) • SHOX2 (SHOX Homeobox 2)
    |
    BAP1 mutation • AHNAK2 mutation
    |
    gefitinib
    3ms
    Molecular prognostication in grade 3 meningiomas and p16/MTAP immunohistochemistry for predicting CDKN2A/B status. (PubMed, Neurooncol Adv)
    Molecular alterations of grade 3 meningiomas stratify clinical outcomes more so than histologic features alone. Immunohistochemical loss of p16 and MTAP show promise in predicting CDKN2A/B status.
    Journal
    |
    CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • TERT (Telomerase Reverse Transcriptase) • MTAP (Methylthioadenosine Phosphorylase) • BAP1 (BRCA1 Associated Protein 1) • CDKN2B (Cyclin Dependent Kinase Inhibitor 2B)
    |
    CDKN2A deletion • CDKN2A mutation • BAP1 mutation • TERT mutation
    3ms
    Utilizing a novel model of PANoptosis-related genes for enhanced prognosis and immune status prediction in kidney renal clear cell carcinoma. (PubMed, Apoptosis)
    Finally, the risk model was predictive of response to immune checkpoint blockade, as well as sensitivity to sunitinib and paclitaxel. The PANoptosis-related risk model developed in this study enables accurate prognostic prediction in KIRC patients. Its associations with the tumor immune microenvironment and drug efficacy may offer potential therapeutic targets and inform clinical decisions.
    Journal
    |
    BAP1 (BRCA1 Associated Protein 1) • CD4 (CD4 Molecule)
    |
    BAP1 mutation • VHL mutation
    |
    paclitaxel • Sutent (sunitinib)
    4ms
    OPTIMUM: Olaparib With or Without Durvalumab for DDR Gene Mutated Biliary Tract Cancer Following Platinum-based Chemotherapy (clinicaltrials.gov)
    P2, N=62, Recruiting, Asan Medical Center | Trial completion date: Oct 2024 --> Dec 2025 | Trial primary completion date: Oct 2023 --> Dec 2024
    Trial completion date • Trial primary completion date • Metastases
    |
    BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • ATM (ATM serine/threonine kinase) • POLE (DNA Polymerase Epsilon) • BAP1 (BRCA1 Associated Protein 1) • MLH1 (MutL homolog 1) • MSH6 (MutS homolog 6) • MSH2 (MutS Homolog 2) • BRCA (Breast cancer early onset) • CHEK2 (Checkpoint kinase 2) • RAD51 (RAD51 Homolog A) • FANCA (FA Complementation Group A) • BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1) • RAD51C (RAD51 paralog C) • RAD50 (RAD50 Double Strand Break Repair Protein) • RAD51D (RAD51 paralog D) • CHEK1 (Checkpoint kinase 1) • BARD1 (BRCA1 Associated RING Domain 1) • NBN (Nibrin Nijmegen Breakage Syndrome 1 (Nibrin)) • XRCC2 (X-Ray Repair Cross Complementing 2) • FANCD2 (FA Complementation Group D2) • GEN1 (GEN1 Holliday junction 5' flap endonuclease)
    |
    ATM mutation • BAP1 mutation • CHEK2 mutation • BRIP1 mutation • FANCA mutation • RAD50 mutation • BARD1 mutation • BLM mutation • NBN mutation
    |
    Lynparza (olaparib) • Imfinzi (durvalumab)
    4ms
    Natural killer cells drive 4-1BBL positive uveal melanoma towards EMT and metastatic disease. (PubMed, J Exp Clin Cancer Res)
    Taken together, the present study demonstrates a role of NK cells in the aggravation of uveal melanoma towards metastatic disease.
    Journal • Metastases
    |
    BAP1 (BRCA1 Associated Protein 1) • TNFA (Tumor Necrosis Factor-Alpha) • CD73 (5'-Nucleotidase Ecto) • NT5E (5'-Nucleotidase Ecto) • ZEB1 (Zinc Finger E-box Binding Homeobox 1)
    |
    BAP1 mutation • CD73 expression • ZEB1 expression
    4ms
    Decitabine/Cedazuridine (INQOVI), an Oral DNA Demethylating Agent, in Subjects With BAP1 Cancer Predisposition Syndrome and Subclinical, Early-Stage Mesothelioma (clinicaltrials.gov)
    P2, N=15, Recruiting, National Cancer Institute (NCI) | Not yet recruiting --> Recruiting
    Enrollment open
    |
    BAP1 (BRCA1 Associated Protein 1)
    |
    BAP1 mutation
    |
    Inqovi (decitabine/cedazuridine)
    4ms
    8q Gain Has No Additional Predictive Value in SF3B1 Uveal Melanoma but Is Predictive for a Worse Prognosis in Patients with BAP1 Uveal Melanoma. (PubMed, Ophthalmol Sci)
    Thus, gain of chromosome 8q has additional predictive value for BAP1 tumors, but not for SF3B1 tumors. The author(s) have no proprietary or commercial interest in any materials discussed in this article.
    Journal • BRCA Biomarker
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    SF3B1 (Splicing Factor 3b Subunit 1) • BAP1 (BRCA1 Associated Protein 1)
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    SF3B1 mutation • BAP1 mutation
    4ms
    Complete clinical remission of malignant peritoneal mesothelioma with systemic pemetrexed and bevacizumab in a patient with a BAP1 mutation. (PubMed, BMJ Case Rep)
    We examine the unusual susceptibility of unresectable MPeM to systemic chemotherapy and attribute susceptibility to the molecular milieu created by mutations in multiple DNA repair pathways. We encourage increased testing for and analysis of mutations in DNA repair pathways to improve future treatment outcomes in this rare malignancy.
    Journal
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    BAP1 (BRCA1 Associated Protein 1)
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    BAP1 mutation
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    Avastin (bevacizumab) • pemetrexed
    4ms
    ITGB2-ICAM1 axis promotes liver metastasis in BAP1-mutated uveal melanoma with retained hypoxia and ECM signatures. (PubMed, Cell Oncol (Dordr))
    The inhibitors primarily inhibited hypoxia- and ECM-related pathways indicated by changes in the expression of genes such as ADAM8, CAV2, ENO1, PGK1, LOXL2, ITGA5, and VCAN. etc. This study suggested that the ITGB2-ICAM1 axis may play a crucial role for BAP1-associated UM metastasis by preserving hypoxia- and ECM- related signatures, which provide a potential strategy for preventing UM metastasis in patients with BAP1 mutation.
    Journal
    |
    CD8 (cluster of differentiation 8) • BAP1 (BRCA1 Associated Protein 1) • GDF15 (Growth differentiation factor 15) • ICAM1 (Intercellular adhesion molecule 1) • ENO1 (Enolase 1) • CAV2 (Caveolin 2) • CDKN1A (Cyclin-dependent kinase inhibitor 1A) • ITGB2 (Integrin Subunit Beta 2) • ADAM8 (ADAM Metallopeptidase Domain 8) • ATF3 (Activating Transcription Factor 3) • ITGA5 (Integrin Subunit Alpha 5) • PGK1 (Phosphoglycerate Kinase 1)
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    BAP1 mutation
    5ms
    Niraparib plus Dostarlimab in Pleural Mesothelioma or Non-Small Cell Lung Cancer harboring HRR mutations: interim results of the UNITO-001 phase 2 prospective trial. (PubMed, Clin Cancer Res)
    This preliminary analysis highlighted the lack of antitumor activity for the combination of niraparib and dostarlimab in patients with PM and/or advanced NSCLC harboring BAP1 somatic mutations. A potential antitumor activity emerged for PM with germline BAP1 and/or BRCA2 somatic mutations along with a good tolerability profile.
    P2 data • Journal • BRCA Biomarker • PARP Biomarker • PD(L)-1 Biomarker • IO biomarker
    |
    PD-L1 (Programmed death ligand 1) • BRCA2 (Breast cancer 2, early onset) • HRD (Homologous Recombination Deficiency) • BAP1 (BRCA1 Associated Protein 1)
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    BRCA2 mutation • BAP1 mutation
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    Zejula (niraparib) • Jemperli (dostarlimab-gxly)
    5ms
    The immune characteristic analysis of BAP1 mutated clear cell renal cell carcinoma. (ASCO-GU 2024)
    This study found that BAP1 and cytokines, cAMP pathway and immune inflammation-related pathways were significantly enriched at the transcriptome level. IHC results suggested that LAG3 was more highly expressed in patients with BAP1 mutation. Clinical treatment analysis found that PD-1 inhibitor-based immune combination therapy is not effective for patients with BAP1 mutations.
    PD(L)-1 Biomarker • IO biomarker
    |
    PD-L1 (Programmed death ligand 1) • CD8 (cluster of differentiation 8) • PBRM1 (Polybromo 1) • BAP1 (BRCA1 Associated Protein 1) • LAG3 (Lymphocyte Activating 3) • CD4 (CD4 Molecule)
    |
    PD-L1 expression • PBRM1 mutation • BAP1 mutation • CD8 expression • LAG3 expression • CD4 expression
    5ms
    Differences in genomic, transcriptomic, and immune landscape of prostate cancer (PCa) based on site of metastasis (mets). (ASCO-GU 2024)
    We elucidate molecular and immunologic mechanisms of metastatic tropism in advanced PCa. These data may facilitate future drug development.
    Tumor mutational burden • PD(L)-1 Biomarker • MSi-H Biomarker • IO biomarker
    |
    PD-L1 (Programmed death ligand 1) • KRAS (KRAS proto-oncogene GTPase) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • PTEN (Phosphatase and tensin homolog) • RB1 (RB Transcriptional Corepressor 1) • AKT1 (V-akt murine thymoma viral oncogene homolog 1) • BAP1 (BRCA1 Associated Protein 1) • IFNG (Interferon, gamma) • CTNNB1 (Catenin (cadherin-associated protein), beta 1) • KMT2C (Lysine Methyltransferase 2C) • APC (APC Regulator Of WNT Signaling Pathway) • SPOP (Speckle Type BTB/POZ Protein)
    |
    TP53 mutation • TMB-H • MSI-H/dMMR • PIK3CA mutation • PTEN mutation • BAP1 mutation • APC mutation • AR splice variant 7
    |
    VENTANA PD-L1 (SP142) Assay • MI Tumor Seek™
    5ms
    Mesothelioma in situ of the peritoneum: report of three cases and review of the literature. (PubMed, Histopathology)
    This work describes the histologic features and clinicopathologic characteristics of peritoneal MIS in three cases, highlights BAP1 somatic and germline mutations in peritoneal MIS, and strengthens the importance of ancillary studies (including immunohistochemical and molecular studies) in the diagnosis of MIS.
    Review • Journal • BRCA Biomarker
    |
    BRCA1 (Breast cancer 1, early onset) • MTAP (Methylthioadenosine Phosphorylase) • BAP1 (BRCA1 Associated Protein 1) • TET2 (Tet Methylcytosine Dioxygenase 2) • BRCA (Breast cancer early onset) • SMO (Smoothened Frizzled Class Receptor) • U2AF1 (U2 Small Nuclear RNA Auxiliary Factor 1) • ERCC3 (ERCC Excision Repair 3, TFIIH Core Complex Helicase Subunit)
    |
    TET2 mutation • BAP1 mutation • U2AF1 mutation • SMO mutation
    5ms
    Survival impact of homologous recombination deficiency in veterans with cholangiocarcinoma including mutual exclusivity with pathogenic KRAS and TP53. (ASCO-GI 2024)
    Across a diverse integrated healthcare system of Veterans, mutations associated with HRD were found to be common, however, not prognostic in OS across a diverse patient population of CCA. Further work is needed to clarify exposure to platinum containing chemotherapy. TP53 MT CCA remains a critical unmet need that drives worsened outcomes including here in patients with mutations in HRD.
    BRCA Biomarker
    |
    KRAS (KRAS proto-oncogene GTPase) • TP53 (Tumor protein P53) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • HRD (Homologous Recombination Deficiency) • ARID1A (AT-rich interaction domain 1A) • BAP1 (BRCA1 Associated Protein 1) • PALB2 (Partner and localizer of BRCA2) • CDK12 (Cyclin dependent kinase 12) • BRCA (Breast cancer early onset) • CHEK2 (Checkpoint kinase 2) • RAD51 (RAD51 Homolog A) • NBN (Nibrin Nijmegen Breakage Syndrome 1 (Nibrin))
    |
    KRAS mutation • BRCA1 mutation • HRD • ATM mutation • ARID1A mutation • PALB2 mutation • CDK12 mutation • BAP1 mutation • CHEK2 mutation • HRD + BRCA1 mutation • BRCA mutation • NBN mutation
    |
    FoundationOne® CDx
    5ms
    Genomic and immune landscape of biliary tract cancers with ARID1A, PBRM1, and BAP1 alterations. (ASCO-GI 2024)
    This is the largest known data set exploring the genomic and immune landscape of BTC with ARID1A, PBRM1 and BAP1 alterations. Macrophages were the dominant immune cell TME and may be a target of interest. Co-alteration profile is distinct between ARID1A- vs PBRM1- and/or BAP1-altered BTC.
    Tumor mutational burden • PD(L)-1 Biomarker • MSi-H Biomarker • IO biomarker
    |
    PD-L1 (Programmed death ligand 1) • KRAS (KRAS proto-oncogene GTPase) • TP53 (Tumor protein P53) • TMB (Tumor Mutational Burden) • NRAS (Neuroblastoma RAS viral oncogene homolog) • MSI (Microsatellite instability) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • ARID1A (AT-rich interaction domain 1A) • CD8 (cluster of differentiation 8) • PBRM1 (Polybromo 1) • BAP1 (BRCA1 Associated Protein 1) • SMAD4 (SMAD family member 4) • CD4 (CD4 Molecule) • ARID2 (AT-Rich Interaction Domain 2)
    |
    MSI-H/dMMR • PBRM1 mutation • BAP1 mutation
    |
    Tempus xT Assay • Tempus xR
    5ms
    Genetic insights into thymic carcinomas and thymic neuroendocrine neoplasms denote prognosis signatures and pathways. (PubMed, Chin Med J (Engl))
    We profiled the mutational features of 47 Chinese patients with thymic malignancy of diverse pathologic phenotypes to uncover the integrated genomic landscape of these rare tumors, and identified the pathology-specific mutational patterns, prognostic signatures, and potential therapeutic targets for TCs and TNENs.
    Journal
    |
    HER-2 (Human epidermal growth factor receptor 2) • BRAF (B-raf proto-oncogene) • TP53 (Tumor protein P53) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • RB1 (RB Transcriptional Corepressor 1) • mTOR (Mechanistic target of rapamycin kinase) • ASXL1 (ASXL Transcriptional Regulator 1) • BAP1 (BRCA1 Associated Protein 1) • KMT2D (Lysine Methyltransferase 2D) • PTCH1 (Patched 1) • CDKN2B (Cyclin Dependent Kinase Inhibitor 2B) • TSC2 (TSC complex subunit 2) • MLL2 (Myeloid/lymphoid or mixed-lineage leukemia 2)
    |
    BRAF mutation • HER-2 mutation • CDKN2A mutation • BAP1 mutation • PTCH1 mutation
    5ms
    Genomic Landscape of Pleural Mesothelioma and Therapeutic Aftermaths. (PubMed, Curr Oncol Rep)
    Similarly, the association between mutational profile and the immune microenvironment or immunotherapy response is not well characterised. Further research into the link between tumour mutational profile and response to therapy is critical for identifying targetable vulnerabilities and stratifying patients for therapy.
    Review • Journal • IO biomarker
    |
    CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • BAP1 (BRCA1 Associated Protein 1) • NF2 (Neurofibromin 2)
    |
    BAP1 mutation • NF2 mutation
    5ms
    Unveiling the immunogenomic landscape of cholangiocarcinoma: Identifying new prognostic markers and therapeutic targets based on CCL5 expression. (PubMed, J Gene Med)
    The present study provides an intricate depiction of the immunogenomic landscape of CCA based on CCL5 expression, thereby paving the way for novel immunotherapy strategies and prognostic assessment.
    Journal • IO biomarker
    |
    PBRM1 (Polybromo 1) • BAP1 (BRCA1 Associated Protein 1) • CCL5 (Chemokine (C-C motif) ligand 5)
    |
    PBRM1 mutation • BAP1 mutation