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Mittempergher L, Piskorz AM, Bosma AJ, Michaut M, Wisman GBA, Kluin RJC, Nieuwland M, Brugman W, van der Ven KJW, Marass F, Morris J, Rosenfeld N, Jimenez-Linan M, de Jong S, van der Zee AGJ, Brenton JD, Bernards R. Kinome capture sequencing of high-grade serous ovarian carcinoma reveals novel mutations in the JAK3 gene. PLoS One 2020; 15:e0235766. [PMID: 32639993 PMCID: PMC7343160 DOI: 10.1371/journal.pone.0235766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/22/2020] [Indexed: 01/22/2023] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) remains the deadliest form of epithelial ovarian cancer and despite major efforts little improvement in overall survival has been achieved. Identification of recurring "driver" genetic lesions has the potential to enable design of novel therapies for cancer. Here, we report on a study to find such new therapeutic targets for HGSOC using exome-capture sequencing approach targeting all kinase genes in 127 patient samples. Consistent with previous reports, the most frequently mutated gene was TP53 (97% mutation frequency) followed by BRCA1 (10% mutation frequency). The average mutation frequency of the kinase genes mutated from our panel was 1.5%. Intriguingly, after BRCA1, JAK3 was the most frequently mutated gene (4% mutation frequency). We tested the transforming properties of JAK3 mutants using the Ba/F3 cell-based in vitro functional assay and identified a novel gain-of-function mutation in the kinase domain of JAK3 (p.T1022I). Importantly, p.T1022I JAK3 mutants displayed higher sensitivity to the JAK3-selective inhibitor Tofacitinib compared to controls. For independent validation, we re-sequenced the entire JAK3 coding sequence using tagged amplicon sequencing (TAm-Seq) in 463 HGSOCs resulting in an overall somatic mutation frequency of 1%. TAm-Seq screening of CDK12 in the same population revealed a 7% mutation frequency. Our data confirms that the frequency of mutations in kinase genes in HGSOC is low and provides accurate estimates for the frequency of JAK3 and CDK12 mutations in a large well characterized cohort. Although p.T1022I JAK3 mutations are rare, our functional validation shows that if detected they should be considered as potentially actionable for therapy. The observation of CDK12 mutations in 7% of HGSOC cases provides a strong rationale for routine somatic testing, although more functional and clinical characterization is required to understand which nonsynonymous mutations alterations are associated with homologous recombination deficiency.
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Affiliation(s)
- Lorenza Mittempergher
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anna M. Piskorz
- Cancer Research UK Cambridge Institute University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Astrid J. Bosma
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Magali Michaut
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - G. Bea A. Wisman
- Department of Gynecologic Oncology, Cancer Research Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Roelof J. C. Kluin
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marja Nieuwland
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wim Brugman
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Francesco Marass
- Cancer Research UK Cambridge Institute University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
- Department of Biosystems Science and Engineering and Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - James Morris
- Cancer Research UK Cambridge Institute University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Mercedes Jimenez-Linan
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Steven de Jong
- Department of Medical Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ate G. J. van der Zee
- Department of Gynecologic Oncology, Cancer Research Center Groningen, University of Groningen, Groningen, The Netherlands
| | - James D. Brenton
- Cancer Research UK Cambridge Institute University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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Reinders J, Rozemuller EH, van der Ven KJW, Caillat-Zucman S, Slootweg PJ, de Weger RA, Tilanus MGJ. MHC Class I Chain-Related Gene A Diversity in Head and Neck Squamous Cell Carcinoma. Hum Immunol 2006; 67:196-203. [PMID: 16698442 DOI: 10.1016/j.humimm.2006.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2005] [Indexed: 11/23/2022]
Abstract
Many immune-related genes are located within the human leukocyte antigen (HLA) region on chromosome 6. The MHC class I chain-related gene A (MICA), located centromeric of HLA-B, is involved in the innate and adaptive immune response through activation of NK and T cells. Differences of MICA transmembrane repeat lengths have been associated with diseases and expression is observed on epithelial tumors. Head and neck squamous cell carcinoma (HNSCC) is an epithelial tumor. In the present study we evaluated the MICA repeat length diversity in relation to MICA expression in Dutch HNSCC patients. MICA short tandem repeat analysis indicated a significant decrease in the frequency for the MICA-A9 repeat in patients diagnosed with oral cavity squamous cell carcinoma (SCC) but not in patients with SCC in the hypoharynx, larynx, or oropharynx. Interestingly, the majority of patients expressed MICA as observed with immunohistochemical staining whereas no soluble MICA was detected in patients' sera by enzyme-linked immunosorbent assay. In conclusion, the length of the MICA transmembrane repeats in Dutch HNSCC patients does not influence the MICA expression on tumor cells.
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Affiliation(s)
- Judith Reinders
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
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Koene GJPA, Arts-Hilkes YHA, van Dijk AJG, van der Ven KJW, Slootweg PJ, de Weger RA, Tilanus MGJ. High level of aneuploidy of chromosome 6 by FISH analysis of head and neck squamous cell carcinoma: Limited applicability of LOH analysis to define HLA loss. Hum Immunol 2004; 65:1455-62. [PMID: 15603873 DOI: 10.1016/j.humimm.2004.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2004] [Revised: 06/28/2004] [Accepted: 06/30/2004] [Indexed: 01/16/2023]
Abstract
Human Leukocyte Antigen (HLA) class I molecules are essential for tumor cell recognition by cytotoxic T cells of the adaptive immune system. Loss of HLA expression provides tumor cells with an escape mechanism to evade the immune system and thus immune therapy. Therefore, HLA loss, and in particular loss of heterozygosity (LOH), is frequently studied in tumors using microsatellite marker LOH analysis. Because LOH analysis detects any allelic imbalance and not just allelic loss, we evaluated the LOH analysis in nine head and neck squamous cell carcinomas (HNSCCs) using fluorescence in situ hybridization (FISH). These tumors were selected from 53 HNSCCs based upon the HLA class I immunohistochemical staining and LOH data. FISH analysis showed that only two tumors with LOH and one without LOH indeed had loss and a normal chromosome 6 copy number, respectively. Strikingly, for the remaining six tumors, LOH analysis did not reflect the genome HLA copy number. We demonstrated that LOH analysis cannot distinguish loss from gain and that the HLA region is not homogeneously affected within a tumor. Tumor heterogeneity and complex aneuploidy in tumors hinder a straightforward interpretation of microsatellite marker analysis. For immune therapy strategies in cancer patients, knowledge of the HLA expression on tumor cells is essential, to which LOH analysis has a limited contribution.
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Affiliation(s)
- Geert J P A Koene
- Department of Pathology, University Medical Centre Utrecht, Utrecht, The Netherlands.
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