Molecular classification and subtype-specific characterization of skin cutaneous melanoma by aggregating multiple genomic platform data

• Published in: Journal of cancer research and clinical oncology Vol. 144; no. 9; pp. 1635 - 1647
• Main Authors: Lu, Xiaofan, Zhang, Qianyuan, Wang, Yue, Zhang, Liya, Zhao, Huiling, Chen, Chen, Wang, Yaoyan, Liu, Shengjie, Lu, Tao, Wang, Fei, Yan, Fangrong
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.09.2018; Springer Nature B.V
• Subjects: Biomarkers, Tumor - genetics; Cancer; Cancer Research; Classification; Decision making; Epigenesis, Genetic - genetics; Gene expression; Gene Silencing - physiology; Genomics - methods; Hematology; Humans; Immune system; Interleukin 1; Internal Medicine; Medicine; Medicine & Public Health; Melanin; Melanoma; Melanoma - genetics; Melanoma, Cutaneous Malignant; Mutation; Mutation - genetics; Oncology; Original Article – Cancer Research; Pigmentation; Skin; Skin Neoplasms - genetics; Molecular classification; Epigenetically silencing; Skin cutaneous melanoma; Biomarker; Gene mutation; SNFCC
• ISSN: 0171-5216; 1432-1335
• DOI: 10.1007/s00432-018-2684-7

Purpose Traditional classification of melanoma is widely utilized with little apparent results making the development of robust classifiers that can guide therapies an urgency. Successful seminal research on classification has provided a wider understanding of cancer from multiple molecular profiles, respectively. However, it may ignore the complementary nature of the information provided by different types of data, which motivated us to subtype melanoma by aggregating multiple genomic platform data. Methods Aggregating three omics data of 328 melanoma samples, melanoma subtyping was performed by three clustering methods. Differences across subtypes were extracted by functional enrichment, epigenetically silencing, gene mutations and clinical features. Subtypes were further distinguished by putative biomarkers. Results Functional enrichment of the subtype-specific differential expression genes endowed subtypes new designation: immune, melanin and ion, in which the first subtype was enriched for immune system, the second was characterized by melanin and pigmentation, and the third was enriched for ion-involved transmission process. Subtypes also differed in age, Breslow thickness, tumor site, mutation frequency of BRAF, PTGS2, CDKN2A, CDKN2B and incidence of epigenetically silencing for IL15RA, EPSTI1, LXN, CDKN1B genes. Conclusions Skin cutaneous melanoma can be robustly divided into three subtypes by SNFCC + . Compared with the TCGA classification derived from gene expression, the subtypes we presented share concordance, but new traits are excavated. Such a genomic classification offers insights to further personalize therapeutic decision-making and melanoma management.