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Zhao X, Little P, Hoyle AP, Pegna GJ, Hayward MC, Ivanova A, Parker JS, Marron DL, Soloway MG, Jo H, Salazar AH, Papakonstantinou MP, Bouchard DM, Jefferys SR, Hoadley KA, Ollila DW, Frank JS, Thomas NE, Googe PB, Ezzell AJ, Collichio FA, Lee CB, Earp HS, Sharpless NE, Hugo W, Wilmott JS, Quek C, Waddell N, Johansson PA, Thompson JF, Hayward NK, Mann GJ, Lo RS, Johnson DB, Scolyer RA, Hayes DN, Moschos SJ. The Prognostic Significance of Low-Frequency Somatic Mutations in Metastatic Cutaneous Melanoma. Front Oncol 2019; 8:584. [PMID: 30662871 PMCID: PMC6329304 DOI: 10.3389/fonc.2018.00584] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022] Open
Abstract
Background: Little is known about the prognostic significance of somatically mutated genes in metastatic melanoma (MM). We have employed a combined clinical and bioinformatics approach on tumor samples from cutaneous melanoma (SKCM) as part of The Cancer Genome Atlas project (TCGA) to identify mutated genes with potential clinical relevance. Methods: After limiting our DNA sequencing analysis to MM samples (n = 356) and to the CANCER CENSUS gene list, we filtered out mutations with low functional significance (snpEFF). We performed Cox analysis on 53 genes that were mutated in ≥3% of samples, and had ≥50% difference in incidence of mutations in deceased subjects versus alive subjects. Results: Four genes were potentially prognostic [RAC1, FGFR1, CARD11, CIITA; false discovery rate (FDR) < 0.2]. We identified 18 additional genes (e.g., SPEN, PDGFRB, GNAS, MAP2K1, EGFR, TSC2) that were less likely to have prognostic value (FDR < 0.4). Most somatic mutations in these 22 genes were infrequent (< 10%), associated with high somatic mutation burden, and were evenly distributed across all exons, except for RAC1 and MAP2K1. Mutations in only 9 of these 22 genes were also identified by RNA sequencing in >75% of the samples that exhibited corresponding DNA mutations. The low frequency, UV signature type and RNA expression of the 22 genes in MM samples were confirmed in a separate multi-institution validation cohort (n = 413). An underpowered analysis within a subset of this validation cohort with available patient follow-up (n = 224) showed that somatic mutations in SPEN and RAC1 reached borderline prognostic significance [log-rank favorable (p = 0.09) and adverse (p = 0.07), respectively]. Somatic mutations in SPEN, and to a lesser extent RAC1, were not associated with definite gene copy number or RNA expression alterations. High (>2+) nuclear plus cytoplasmic expression intensity for SPEN was associated with longer melanoma-specific overall survival (OS) compared to lower (≤ 2+) nuclear intensity (p = 0.048). We conclude that expressed somatic mutations in infrequently mutated genes beyond the well-characterized ones (e.g., BRAF, RAS, CDKN2A, PTEN, TP53), such as RAC1 and SPEN, may have prognostic significance in MM.
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Affiliation(s)
- Xiaobei Zhao
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Paul Little
- Department of Biostatistics, Gillings School of Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Alan P. Hoyle
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Guillaume J. Pegna
- Division of Hematology/Oncology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Michele C. Hayward
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Anastasia Ivanova
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Biostatistics, Gillings School of Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Joel S. Parker
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - David L. Marron
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Matthew G. Soloway
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Heejoon Jo
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ashley H. Salazar
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Michael P. Papakonstantinou
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Deeanna M. Bouchard
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Stuart R. Jefferys
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Katherine A. Hoadley
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - David W. Ollila
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Division of Surgical Oncology, Department of Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Melanoma Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jill S. Frank
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Melanoma Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Nancy E. Thomas
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Melanoma Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Dermatology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Paul B. Googe
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Melanoma Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Dermatology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ashley J. Ezzell
- Department of Cell Biology & Physiology, Histology Research Core Facility, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Frances A. Collichio
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Division of Hematology/Oncology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Melanoma Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Carrie B. Lee
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Division of Hematology/Oncology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Melanoma Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - H. Shelton Earp
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Norman E. Sharpless
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Willy Hugo
- Division of Dermatology, Department of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, United States
| | - James S. Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Camelia Quek
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Nicola Waddell
- Queensland Institute of Medical Research-QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Peter A. Johansson
- Queensland Institute of Medical Research-QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - John F. Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Nicholas K. Hayward
- Queensland Institute of Medical Research-QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Graham J. Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Roger S. Lo
- Division of Dermatology, Department of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, United States
| | - Douglas B. Johnson
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN, United States
| | - Richard A. Scolyer
- Queensland Institute of Medical Research-QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - D. Neil Hayes
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Division of Hematology/Oncology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Stergios J. Moschos
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Division of Hematology/Oncology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Melanoma Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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