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Keppler S, Weiβbach S, Langer C, Knop S, Pischimarov J, Kull M, Stühmer T, Steinbrunn T, Bargou R, Einsele H, Rosenwald A, Leich E. Rare SNPs in receptor tyrosine kinases are negative outcome predictors in multiple myeloma. Oncotarget 2018; 7:38762-38774. [PMID: 27246973 PMCID: PMC5122427 DOI: 10.18632/oncotarget.9607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/04/2016] [Indexed: 12/25/2022] Open
Abstract
Multiple myeloma (MM) is a plasma cell disorder that is characterized by a great genetic heterogeneity. Recent next generation sequencing studies revealed an accumulation of tumor-associated mutations in receptor tyrosine kinases (RTKs) which may also contribute to the activation of survival pathways in MM. To investigate the clinical role of RTK-mutations in MM, we deep-sequenced the coding DNA-sequence of EGFR, EPHA2, ERBB3, IGF1R, NTRK1 and NTRK2 which were previously found to be mutated in MM, in 75 uniformly treated MM patients of the "Deutsche Studiengruppe Multiples Myelom". Subsequently, we correlated the detected mutations with common cytogenetic alterations and clinical parameters. We identified 11 novel non-synonymous SNVs or rare patient-specific SNPs, not listed in the SNP databases 1000 genomes and dbSNP, in 10 primary MM cases. The mutations predominantly affected the tyrosine-kinase and ligand-binding domains and no correlation with cytogenetic parameters was found. Interestingly, however, patients with RTK-mutations, specifically those with rare patient-specific SNPs, showed a significantly lower overall, event-free and progression-free survival. This indicates that RTK SNVs and rare patient-specific RTK SNPs are of prognostic relevance and suggests that MM patients with RTK-mutations could potentially profit from treatment with RTK-inhibitors.
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Affiliation(s)
- Sarah Keppler
- Institute of Pathology, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken (CCC MF), University Hospital Würzburg, Würzburg, Germany
| | - Susann Weiβbach
- Institute of Pathology, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken (CCC MF), University Hospital Würzburg, Würzburg, Germany
| | - Christian Langer
- Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Stefan Knop
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Jordan Pischimarov
- Institute of Pathology, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken (CCC MF), University Hospital Würzburg, Würzburg, Germany
| | - Miriam Kull
- Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Thorsten Stühmer
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Torsten Steinbrunn
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Ralf Bargou
- Comprehensive Cancer Center Mainfranken (CCC MF), University Hospital Würzburg, Würzburg, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken (CCC MF), University Hospital Würzburg, Würzburg, Germany
| | - Ellen Leich
- Institute of Pathology, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken (CCC MF), University Hospital Würzburg, Würzburg, Germany
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Wang Z, Rajaraman P, Melin BS, Chung CC, Zhang W, McKean-Cowdin R, Michaud D, Yeager M, Ahlbom A, Albanes D, Andersson U, Freeman LEB, Buring JE, Butler MA, Carreón T, Feychting M, Gapstur SM, Gaziano JM, Giles GG, Hallmans G, Henriksson R, Hoffman-Bolton J, Inskip PD, Kitahara CM, Marchand LL, Linet MS, Li S, Peters U, Purdue MP, Rothman N, Ruder AM, Sesso HD, Severi G, Stampfer M, Stevens VL, Visvanathan K, Wang SS, White E, Zeleniuch-Jacquotte A, Hoover R, Fraumeni JF, Chatterjee N, Hartge P, Chanock SJ. Further Confirmation of Germline Glioma Risk Variant rs78378222 in TP53 and Its Implication in Tumor Tissues via Integrative Analysis of TCGA Data. Hum Mutat 2015; 36:684-8. [PMID: 25907361 DOI: 10.1002/humu.22799] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/08/2015] [Indexed: 01/06/2023]
Abstract
We confirmed strong association of rs78378222:A>C (per allele odds ratio [OR] = 3.14; P = 6.48 × 10(-11) ), a germline rare single-nucleotide polymorphism (SNP) in TP53, via imputation of a genome-wide association study of glioma (1,856 cases and 4,955 controls). We subsequently performed integrative analyses on the Cancer Genome Atlas (TCGA) data for GBM (glioblastoma multiforme) and LUAD (lung adenocarcinoma). Based on SNP data, we imputed genotypes for rs78378222 and selected individuals carrying rare risk allele (C). Using RNA sequencing data, we observed aberrant transcripts with ∼3 kb longer than normal for those individuals. Using exome sequencing data, we further showed that loss of haplotype carrying common protective allele (A) occurred somatically in GBM but not in LUAD. Our bioinformatic analysis suggests rare risk allele (C) disrupts mRNA termination, and an allelic loss of a genomic region harboring common protective allele (A) occurs during tumor initiation or progression for glioma.
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Affiliation(s)
- Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, Maryland
| | - Preetha Rajaraman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Beatrice S Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, Maryland
| | - Weijia Zhang
- Department of Medicine Bioinformatics Core, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Roberta McKean-Cowdin
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Dominique Michaud
- Department of Epidemiology, Division of Biology and Medicine, Brown University, Providence, Rhode Island.,School of Public Health, Imperial College London, London, UK
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, Maryland
| | - Anders Ahlbom
- Division of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Ulrika Andersson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Mary Ann Butler
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio
| | - Tania Carreón
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio
| | - Maria Feychting
- Division of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia
| | - J Michael Gaziano
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,Massachusetts Veteran's Epidemiology, Research and Information Center, Geriatric Research Education and Clinical Center, VA Boston Healthcare System, Boston, Massachusetts
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council of Victoria, Melbourne, Australia.,Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Goran Hallmans
- Department of Public Health and Clinical Medicine/Nutritional Research, Umeå University, Umeå, Sweden
| | - Roger Henriksson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | | | - Peter D Inskip
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Cari M Kitahara
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | | | - Martha S Linet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Shengchao Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, Maryland
| | - Ulrike Peters
- Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Epidemiology, University of Washington, Seattle, Washington
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Avima M Ruder
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio
| | - Howard D Sesso
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Gianluca Severi
- Cancer Epidemiology Centre, Cancer Council of Victoria, Melbourne, Australia.,Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Meir Stampfer
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Departments of Epidemiology and Nutrition, Harvard School of Public Health, Boston, Massachusetts
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia
| | - Kala Visvanathan
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Sophia S Wang
- Division of Cancer Etiology, Department of Population Sciences, City of Hope and the Beckman Research Institute, Duarte, California
| | - Emily White
- Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Epidemiology, University of Washington, Seattle, Washington
| | - Anne Zeleniuch-Jacquotte
- Division of Epidemiology, Department of Environmental Medicine, NYU School of Medicine, New York, New York
| | - Robert Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
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