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Birkeland E, Zhang S, Poduval D, Geisler J, Nakken S, Vodak D, Meza-Zepeda LA, Hovig E, Myklebost O, Knappskog S, Lønning PE. Patterns of genomic evolution in advanced melanoma. Nat Commun 2018; 9:2665. [PMID: 29991680 PMCID: PMC6039447 DOI: 10.1038/s41467-018-05063-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 06/07/2018] [Indexed: 01/30/2023] Open
Abstract
Genomic alterations occurring during melanoma progression and the resulting genomic heterogeneity between metastatic deposits remain incompletely understood. Analyzing 86 metastatic melanoma deposits from 53 patients with whole-exome sequencing (WES), we show a low branch to trunk mutation ratio and little intermetastatic heterogeneity, with driver mutations almost completely shared between lesions. Branch mutations consistent with UV damage indicate that metastases may arise from different subclones in the primary tumor. Selective gain of mutated BRAF alleles occurs as an early event, contrasting whole-genome duplication (WGD) occurring as a late truncal event in about 40% of cases. One patient revealed elevated mutational diversity, probably related to previous chemotherapy and DNA repair defects. In another patient having received radiotherapy toward a lymph node metastasis, we detected a radiotherapy-related mutational signature in two subsequent distant relapses, consistent with secondary metastatic seeding. Our findings add to the understanding of genomic evolution in metastatic melanomas. As melanoma progresses, it evolves. Here, in advanced melanoma the authors study genomic evolution, highlighting trunk mutations dominated by the ultraviolet damage signature, common late truncal whole-genome duplication events, as well as selective copy number gain of mutant BRAF.
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Affiliation(s)
- E Birkeland
- Section of Oncology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - S Zhang
- Section of Oncology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - D Poduval
- Section of Oncology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - J Geisler
- Institute of Clinical Medicine, University of Oslo, Campus Akershus University Hospital, 1478 Lørenskog, Oslo, Norway.,Department of Oncology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - S Nakken
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway.,Norwegian Cancer Genomics Consortium, Institute for Cancer Research, Oslo University Hospital -Radium Hospital, 0310 Oslo, Norway
| | - D Vodak
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway.,Norwegian Cancer Genomics Consortium, Institute for Cancer Research, Oslo University Hospital -Radium Hospital, 0310 Oslo, Norway
| | - L A Meza-Zepeda
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway.,Norwegian Cancer Genomics Consortium, Institute for Cancer Research, Oslo University Hospital -Radium Hospital, 0310 Oslo, Norway.,Genomics Core Facility, Department of Core Facilities, Institute of Cancer Research, the Norwegian Radium Hospital, 0310 Oslo, Norway
| | - E Hovig
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway.,Norwegian Cancer Genomics Consortium, Institute for Cancer Research, Oslo University Hospital -Radium Hospital, 0310 Oslo, Norway.,Department of Informatics, University of Oslo, 0316 Oslo, Norway.,Institute of Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway
| | - O Myklebost
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway.,Norwegian Cancer Genomics Consortium, Institute for Cancer Research, Oslo University Hospital -Radium Hospital, 0310 Oslo, Norway
| | - S Knappskog
- Section of Oncology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - P E Lønning
- Section of Oncology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway. .,Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway.
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Helland Å, Brustugun OT, Nakken S, Halvorsen AR, Dønnem T, Bremnes R, Busund LT, Sun J, Lorenz S, Solberg SK, Jørgensen LH, Vodak D, Myklebost O, Hovig E, Meza-Zepeda LA. High number of kinome-mutations in non-small cell lung cancer is associated with reduced immune response and poor relapse-free survival. Int J Cancer 2017; 141:184-190. [PMID: 28387924 PMCID: PMC5450131 DOI: 10.1002/ijc.30726] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 12/10/2016] [Accepted: 03/23/2017] [Indexed: 11/24/2022]
Abstract
Lung cancer is the leading cause of cancer related death, and the past years’ improved insight into underlying molecular events has significantly improved outcome for specific subsets of patients. In particular, several new therapies that target protein kinases have been implemented, and many more are becoming available. We have investigated lung cancer specimens for somatic mutations in a targeted panel of 612 human genes, the majority being protein kinases. The somatic mutation profiles were correlated to profiles of immune cell infiltration as well as relapse‐free survival. Targeted deep sequencing was performed on 117 tumour/normal pairs using the SureSelect Human Kinome kit (Agilent Technologies), with capture probes targeting 3.2 Mb of the human genome, including exons and untranslated regions of all known kinases, kinase receptors and selected cancer‐related genes (612 genes in total). CD8 staining was determined using Ventana Benchmark. Survival analyses were performed using SPSS. The number of mutations per sample ranged from 0 to 50 (within the 612 genes tested), with a median of nine. The prognosis was worse for patients with more than the median number of mutations. A significant correlation was found between mutations in one of selected DNA‐repair genes and the total number of mutations in that tumour (p < 0.001). There was a significant inverse correlation between the number of infiltrating stromal CD8+ lymphocytes and the presence of EGFR mutations. What's new? Lung carcinomas are among the tumours with highest mutation frequency. Here, the authors performed mutational analyses of 612 genes–including all known kinases and kinase receptors–in 117 non‐small cell lung cancer (NSCLC) tumours. They also investigated the relationship of mutation rate to number of infiltrating lymphocytes and to the clinical course of the disease. The number of mutations per sample varied, and the relapse‐free survival was worse for patients with more than the median number of mutations. Also, there was a significant inverse correlation between the number of infiltrating stromal CD8+ lymphocytes and the presence of EGFR mutations.
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Affiliation(s)
- Å Helland
- Department of Cancer Genetics, Oslo University Hospital - Radium Hospital, Oslo, Norway.,Department of Oncology, Oslo University Hospital - Radium Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Norway
| | - O T Brustugun
- Department of Cancer Genetics, Oslo University Hospital - Radium Hospital, Oslo, Norway.,Department of Oncology, Oslo University Hospital - Radium Hospital, Oslo, Norway
| | - S Nakken
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, Oslo University Hospital -Radium Hospital, Oslo, Norway.,Department of Tumor Biology, Oslo University Hospital, Radium Hospital, Oslo, Norway
| | - A R Halvorsen
- Department of Cancer Genetics, Oslo University Hospital - Radium Hospital, Oslo, Norway
| | - T Dønnem
- Institute of Clinical Medicine, UiT - The Arctic University of Tromsø, Norway.,Department of Oncology, University Hospital of Northern Norway, Tromsø, Norway
| | - R Bremnes
- Institute of Clinical Medicine, UiT - The Arctic University of Tromsø, Norway.,Department of Oncology, University Hospital of Northern Norway, Tromsø, Norway
| | - L T Busund
- Institute of Medical Biology, The Arctic University of Norway, Tromsø, Norway.,Department of Pathology, University Hospital of Northern Norway, Tromsø, Norway
| | - J Sun
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, Oslo University Hospital -Radium Hospital, Oslo, Norway.,Department of Tumor Biology, Oslo University Hospital, Radium Hospital, Oslo, Norway
| | - S Lorenz
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, Oslo University Hospital -Radium Hospital, Oslo, Norway.,Department of Tumor Biology, Oslo University Hospital, Radium Hospital, Oslo, Norway
| | - S K Solberg
- Departement of Thoracic Surgery, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - L H Jørgensen
- Departement of Thoracic Surgery, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - D Vodak
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, Oslo University Hospital -Radium Hospital, Oslo, Norway.,Department of Tumor Biology, Oslo University Hospital, Radium Hospital, Oslo, Norway
| | - O Myklebost
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, Oslo University Hospital -Radium Hospital, Oslo, Norway.,Department of Tumor Biology, Oslo University Hospital, Radium Hospital, Oslo, Norway
| | - E Hovig
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, Oslo University Hospital -Radium Hospital, Oslo, Norway.,Department of Tumor Biology, Oslo University Hospital, Radium Hospital, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway.,Institute of Cancer Genetics and informatics, Radium Hospital, Oslo, Norway
| | - L A Meza-Zepeda
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, Oslo University Hospital -Radium Hospital, Oslo, Norway.,Department of Tumor Biology, Oslo University Hospital, Radium Hospital, Oslo, Norway
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