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Machnicki MM, Rzepakowska A, Janowska J, Pepek M, Krop A, Pruszczyk K, Stawinski P, Rydzanicz M, Grzybowski J, Gornicka B, Wnuk M, Ploski R, Osuch-Wojcikiewicz E, Stoklosa T. Analysis of Mutational Profile of Hypopharyngeal and Laryngeal Head and Neck Squamous Cell Carcinomas Identifies KMT2C as a Potential Tumor Suppressor. Front Oncol 2022; 12:768954. [PMID: 35664801 PMCID: PMC9160230 DOI: 10.3389/fonc.2022.768954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
Hypopharyngeal cancer is a poorly characterized type of head and neck squamous cell carcinoma (HNSCC) with bleak prognosis and only few studies focusing specifically on the genomic profile of this type of cancer. We performed molecular profiling of 48 HPV (Human Papilloma Virus)-negative tumor samples including 23 originating from the hypopharynx and 25 from the larynx using a targeted next-generation sequencing approach. Among genes previously described as significantly mutated, TP53, FAT1, NOTCH1, KMT2C, and CDKN2A were found to be most frequently mutated. We also found that more than three-quarters of our patients harbored candidate actionable or prognostic alterations in genes belonging to RTK/ERK/PI3K, cell-cycle, and DNA-damage repair pathways. Using previously published data we compared 67 hypopharyngeal cancers to 595 HNSCC from other sites and found no prominent differences in mutational frequency except for CASP8 and HRAS genes. Since we observed relatively frequent mutations of KTM2C (MLL3) in our dataset, we analyzed their role, in vitro, by generating a KMT2C-mutant hypopharyngeal cancer cell line FaDu with CRISPR-Cas9. We demonstrated that KMT2C loss-of-function mutations resulted in increased colony formation and proliferation, in concordance with previously published results. In summary, our results show that the mutational profile of hypopharyngeal cancers might be similar to the one observed for other head and neck cancers with respect to minor differences and includes multiple candidate actionable and prognostic genetic alterations. We also demonstrated, for the first time, that the KMT2C gene may play a role of tumor suppressor in HNSCC, which opens new possibilities in the search for new targeted treatment approaches.
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Affiliation(s)
- Marcin M. Machnicki
- Department of Tumor Biology and Genetics, Medical University of Warsaw, Warsaw, Poland
- *Correspondence: Marcin M. Machnicki, ; Tomasz Stoklosa,
| | - Anna Rzepakowska
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Warsaw, Warsaw, Poland
| | | | - Monika Pepek
- Department of Tumor Biology and Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Alicja Krop
- Department of Tumor Biology and Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Piotr Stawinski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Jakub Grzybowski
- Department of Pathology, Medical University of Warsaw, Warsaw, Poland
| | - Barbara Gornicka
- Department of Pathology, Medical University of Warsaw, Warsaw, Poland
| | - Maciej Wnuk
- Department of Biology, University of Rzeszow, Rzeszow, Poland
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Osuch-Wojcikiewicz
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Stoklosa
- Department of Tumor Biology and Genetics, Medical University of Warsaw, Warsaw, Poland
- *Correspondence: Marcin M. Machnicki, ; Tomasz Stoklosa,
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2
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Thomas C, Thierfelder F, Träger M, Soschinski P, Müther M, Edelmann D, Förster A, Geiler C, Kim HY, Filipski K, Harter PN, Schittenhelm J, Eckert F, Ntoulias G, May SA, Stummer W, Onken J, Vajkoczy P, Schüller U, Heppner FL, Capper D, Koch A, Kaul D, Paulus W, Hasselblatt M, Schweizer L. TERT promoter mutation and chromosome 6 loss define a high-risk subtype of ependymoma evolving from posterior fossa subependymoma. Acta Neuropathol 2021; 141:959-970. [PMID: 33755803 PMCID: PMC8113189 DOI: 10.1007/s00401-021-02300-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 02/06/2023]
Abstract
Subependymomas are benign tumors characteristically encountered in the posterior fossa of adults that show distinct epigenetic profiles assigned to the molecular group “subependymoma, posterior fossa” (PFSE) of the recently established DNA methylation-based classification of central nervous system tumors. In contrast, most posterior fossa ependymomas exhibit a more aggressive biological behavior and are allocated to the molecular subgroups PFA or PFB. A subset of ependymomas shows epigenetic similarities with subependymomas, but the precise biology of these tumors and their potential relationships remain unknown. We therefore set out to characterize epigenetic traits, mutational profiles, and clinical outcomes of 50 posterior fossa ependymal tumors of the PFSE group. On histo-morphology, these tumors comprised 12 ependymomas, 14 subependymomas and 24 tumors with mixed ependymoma–subependymoma morphology. Mixed ependymoma–subependymoma tumors varied in their extent of ependymoma differentiation (2–95%) but consistently exhibited global epigenetic profiles of the PFSE group. Selective methylome analysis of microdissected tumor components revealed CpG signatures in mixed tumors that coalesce with their pure counterparts. Loss of chr6 (20/50 cases), as well as TERT mutations (21/50 cases), were frequent events enriched in tumors with pure ependymoma morphology (p < 0.001) and confined to areas with ependymoma differentiation in mixed tumors. Clinically, pure ependymoma phenotype, chr6 loss, and TERT mutations were associated with shorter progression-free survival (each p < 0.001). In conclusion, our results suggest that subependymomas may acquire genetic and epigenetic changes throughout tumor evolution giving rise to subclones with ependymoma morphology (resulting in mixed tumors) that eventually overpopulate the subependymoma component (pure PFSE ependymomas).
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Affiliation(s)
- Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Felix Thierfelder
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Malte Träger
- Department of Radiation Oncology and Radiotherapy, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Patrick Soschinski
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Michael Müther
- Department of Neurosurgery, University Hospital Münster, Münster, Germany
| | - Dominic Edelmann
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Alexandra Förster
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Carola Geiler
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Hee-Yeong Kim
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katharina Filipski
- Neurological Institute (Edinger Institute), Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick N Harter
- Neurological Institute (Edinger Institute), Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Jens Schittenhelm
- Department of Neuropathology, Institute of Pathology and Neuropathology, University of Tübingen, Tübingen, Germany
| | - Franziska Eckert
- Department of Radiooncology, University Hospital Tübingen, Tübingen, Germany
| | - Georgios Ntoulias
- Department of Neurosurgery, Vivantes Klinikum Neukölln, Berlin, Germany
| | - Sven-Axel May
- Department of Neurosurgery, Klinikum Chemnitz, Chemnitz, Germany
| | - Walter Stummer
- Department of Neurosurgery, University Hospital Münster, Münster, Germany
| | - Julia Onken
- Department of Neurosurgery, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Peter Vajkoczy
- Department of Neurosurgery, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Ulrich Schüller
- Department of Neuropathology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Frank L Heppner
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Cluster of Excellence, NeuroCure, Charitéplatz 1, 10117, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117, Berlin, Germany
| | - David Capper
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Arend Koch
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - David Kaul
- Department of Radiation Oncology and Radiotherapy, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Leonille Schweizer
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany.
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Zhang C, Ostrom QT, Semmes EC, Ramaswamy V, Hansen HM, Morimoto L, de Smith AJ, Pekmezci M, Vaksman Z, Hakonarson H, Diskin SJ, Metayer C, Taylor MD, Wiemels JL, Bondy ML, Walsh KM. Genetic predisposition to longer telomere length and risk of childhood, adolescent and adult-onset ependymoma. Acta Neuropathol Commun 2020; 8:173. [PMID: 33115534 PMCID: PMC7592366 DOI: 10.1186/s40478-020-01038-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023] Open
Abstract
Ependymoma is the third most common brain tumor in children, with well-described molecular characterization but poorly understood underlying germline risk factors. To investigate whether genetic predisposition to longer telomere length influences ependymoma risk, we utilized case-control data from three studies: a population-based pediatric and adolescent ependymoma case-control sample from California (153 cases, 696 controls), a hospital-based pediatric posterior fossa type A (EPN-PF-A) ependymoma case-control study from Toronto's Hospital for Sick Children and the Children's Hospital of Philadelphia (83 cases, 332 controls), and a multicenter adult-onset ependymoma case-control dataset nested within the Glioma International Case-Control Consortium (GICC) (103 cases, 3287 controls). In the California case-control sample, a polygenic score for longer telomere length was significantly associated with increased risk of ependymoma diagnosed at ages 12-19 (P = 4.0 × 10-3), but not with ependymoma in children under 12 years of age (P = 0.94). Mendelian randomization supported this observation, identifying a significant association between genetic predisposition to longer telomere length and increased risk of adolescent-onset ependymoma (ORPRS = 1.67; 95% CI 1.18-2.37; P = 3.97 × 10-3) and adult-onset ependymoma (PMR-Egger = 0.042), but not with risk of ependymoma diagnosed before age 12 (OR = 1.12; 95% CI 0.94-1.34; P = 0.21), nor with EPN-PF-A (PMR-Egger = 0.59). These findings complement emerging literature suggesting that augmented telomere maintenance is important in ependymoma pathogenesis and progression, and that longer telomere length is a risk factor for diverse nervous system malignancies.
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Affiliation(s)
- Chenan Zhang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, USA
| | - Quinn T Ostrom
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, USA
| | - Eleanor C Semmes
- Medical Scientist Training Program, Duke University School of Medicine, Durham, USA
- Children's Health and Discovery Initiative, Department of Pediatrics, Duke University, Durham, USA
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Helen M Hansen
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, USA
| | - Libby Morimoto
- School of Public Health, University of California, Berkeley, Berkeley, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, USA
| | - Melike Pekmezci
- Department of Pathology, University of California, San Francisco, San Francisco, USA
| | - Zalman Vaksman
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Sharon J Diskin
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, USA
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, USA
| | - Melissa L Bondy
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
| | - Kyle M Walsh
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, USA.
- Medical Scientist Training Program, Duke University School of Medicine, Durham, USA.
- Department of Neurosurgery and Duke Cancer Institute, Duke University School of Medicine, DUMC Box 3050, Durham, NC, 27710, USA.
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Differential Regulation of Telomeric Complex by BCR-ABL1 Kinase in Human Cellular Models of Chronic Myeloid Leukemia-From Single Cell Analysis to Next-Generation Sequencing. Genes (Basel) 2020; 11:genes11101145. [PMID: 33003326 PMCID: PMC7601685 DOI: 10.3390/genes11101145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/15/2020] [Accepted: 09/25/2020] [Indexed: 11/17/2022] Open
Abstract
Telomeres are specialized nucleoprotein complexes, localized at the physical ends of chromosomes, that contribute to the maintenance of genome stability. One of the features of chronic myeloid leukemia (CML) cells is a reduction in telomere length which may result in increased genomic instability and progression of the disease. Aberrant telomere maintenance in CML is not fully understood and other mechanisms such as the alternative lengthening of telomeres (ALT) are involved. In this work, we employed five BCR-ABL1-positive cell lines, namely K562, KU-812, LAMA-84, MEG-A2, and MOLM-1, commonly used in the laboratories to study the link between mutation, copy number, and expression of telomere maintenance genes with the expression, copy number, and activity of BCR-ABL1. Our results demonstrated that the copy number and expression of BCR-ABL1 are crucial for telomere lengthening. We observed a correlation between BCR-ABL1 expression and telomere length as well as shelterins upregulation. Next-generation sequencing revealed pathogenic variants and copy number alterations in major tumor suppressors, such as TP53 and CDKN2A, but not in telomere-associated genes. Taken together, we showed that BCR-ABL1 kinase expression and activity play a crucial role in the maintenance of telomeres in CML cell lines. Our results may help to validate and properly interpret results obtained by many laboratories employing these in vitro models of CML.
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Hewer E, Prebil N, Berezowska S, Gutt-Will M, Schucht P, Dettmer MS, Vassella E. Diagnostic implications of TERT promoter mutation status in diffuse gliomas in a routine clinical setting. Virchows Arch 2017; 471:641-649. [PMID: 28823044 DOI: 10.1007/s00428-017-2216-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/21/2017] [Accepted: 08/07/2017] [Indexed: 12/24/2022]
Abstract
IDH (isocitrate dehydrogenase) gene mutations are present in most diffuse low-grade gliomas and define the clinico-pathological core of the respective morphologically defined entities. Conversely, according to the 2016 WHO classification, the majority of glioblastomas belong to the IDH-wildtype category, which is defined by exclusion. TERT (telomerase reverse transcriptase gene) promoter mutations have been suggested as a molecular marker for primary glioblastomas. We analyzed molecular, histopathological, and clinical profiles of a series of 110 consecutive diffuse gliomas (WHO grades II-IV) diagnosed at our institution, in which TERT promoter mutation analysis had been performed as part of diagnostic work-up. A diagnostic algorithm based on IDH, TERT, ATRX, H3F3A, and 1p19q co-deletion status resulted in a consistent molecular classification with only 14 (13%) marker-negative tumors. TERT promoter mutations were present in 77% of IDH-wildtype tumors. The TERT/IDH-wildtype category was highly enriched for tumors with unconventional clinical or histological features. Molecular classes were associated with distinct rates of MGMT promoter methylation. We conclude that, in a routine diagnostic setting, TERT promoter mutations define a relatively homogeneous core group among IDH-wildtype diffuse gliomas that includes the majority of primary glioblastomas as well as their putative precursor lesions.
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Affiliation(s)
- Ekkehard Hewer
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3010, Bern, Switzerland.
| | - Nadine Prebil
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3010, Bern, Switzerland
| | - Sabina Berezowska
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3010, Bern, Switzerland
| | - Marielena Gutt-Will
- Department of Neurosurgery, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
| | - Philippe Schucht
- Department of Neurosurgery, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
| | - Matthias S Dettmer
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3010, Bern, Switzerland
| | - Erik Vassella
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3010, Bern, Switzerland
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