Identification of gene expression levels in primary melanoma associated with clinically meaningful characteristics

Factors influencing melanoma survival include sex, age, clinical stage, lymph node involvement, as well as Breslow thickness, presence of tumor-infiltrating lymphocytes based on histological analysis of primary melanoma, mitotic rate, and ulceration. Identification of genes whose expression in primary tumors is associated with these key tumor/patient characteristics can shed light on molecular mechanisms of melanoma survival. Here, we show results from a gene expression analysis of formalin-fixed paraffin-embedded primary melanomas with extensive clinical annotation. The Cancer Genome Atlas data on primary melanomas were used for validation of nominally significant associations. We identified five genes that were significantly associated with the presence of tumor-infiltrating lymphocytes in the joint analysis after adjustment for multiple testing: IL1R2, PPL, PLA2G3, RASAL1, and SGK2. We also identified two genes significantly associated with melanoma metastasis to the regional lymph nodes (PIK3CG and IL2RA), and two genes significantly associated with sex (KDM5C and KDM6A). We found that LEF1 was significantly associated with Breslow thickness and CCNA2 and UBE2T with mitosis. RAD50 was the gene most significantly associated with survival, with a higher level of expression associated with worse survival. *Marianne Berwickh and Christopher Amos contributed equally to the writing of this article. Correspondence to Marianne Berwick, MD, Department of Internal Medicine and Dermatology, MSC10-5550, 1 University of New Mexico, Albuquerque, NM 87131, USA Tel: +1 203 464 4117; fax: +1 505 272 2579; e-mail: mberwick@salud.unm.edu or Correspondence to Christopher Amos, PhD, Department of Medicine, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA Tel: +1 713 798 2102; fax: +1 713 798 3658; e-mail: christopher.i.amos@dartmouth.edu Received February 19, 2018 Accepted May 15, 2018 Copyright © 2018 Wolters Kluwer Health, Inc. All rights reserved.

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