Original Articles: Basic ScienceMethylation of nonessential genes in cutaneous melanoma – Rule Out hypothesisGorlov, Ivan P.a; Conway, Kathleenb,c,d; Edmiston, Sharon N.b,c,d; Parrish, Eloise A.d,e; Hao, Honglinb; Amos, Christopher I.a; Tsavachidis, Spiridona; Gorlova, Olga Y.a; Begg, Colinf; Hernando, Evag; Cheng, Chaoa; Shen, Ronglaif; Orlow, Irenef; Luo, Lih; Ernstoff, Marc S.i; Kuan, Pei Fenj; Ollila, David W.d,k; Tsai, Yihsuan S.d; Berwick, Marianneh; Thomas, Nancy E.b,d Author Information aDepartment of Medicine, Baylor College of Medicine, Houston, Texas bDepartment of Dermatology, University of North Carolina cDepartment of Epidemiology dLineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina eDepartment of Applied Mathematics and Statistics, State University of New York, Stony Brook fDepartment of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York gDepartment of Pathology, New York University School of Medicine, New York hDepartment of Internal Medicine, University of New Mexico, Albuquerque, New Maxico iRoswell Park Comprehensive Cancer Center, Elm and Carlton, Buffalo jDepartment of Applied Mathematics and Statistics, State University of New York, Stony Brook and kDepartment of Surgery, University of North Carolina, Chapel Hill, North Carolina, USA Received 1 November 2022 Accepted 23 December 2022. Supplemental Digital Content is available for this article. Direct URL citations appear in the printed text and are provided in the HTML and PDF versions of this article on the journal’s website, www.melanomaresearch.com. Correspondence to Ivan Gorlov, PhD, Department of Medicine, Baylor College of Medicine, Institute for Clinical & Translational Research’ One Baylor Plaza, Mailstop: BCM451, Houston, TX 77030, USA, Tel: +1 713 798 8595; e-mail: [email protected] Melanoma Research 33(3):p 163-172, June 2023. | DOI: 10.1097/CMR.0000000000000881 Buy SDC Metrics Abstract Differential methylation plays an important role in melanoma development and is associated with survival, progression and response to treatment. However, the mechanisms by which methylation promotes melanoma development are poorly understood. The traditional explanation of selective advantage provided by differential methylation postulates that hypermethylation of regulatory 5’-cytosine-phosphate-guanine-3’ dinucleotides (CpGs) downregulates the expression of tumor suppressor genes and therefore promotes tumorigenesis. We believe that other (not necessarily alternative) explanations of the selective advantages of methylation are also possible. Here, we hypothesize that melanoma cells use methylation to shut down transcription of nonessential genes – those not required for cell survival and proliferation. Suppression of nonessential genes allows tumor cells to be more efficient in terms of energy and resource usage, providing them with a selective advantage over the tumor cells that transcribe and subsequently translate genes they do not need. We named the hypothesis the Rule Out (RO) hypothesis. The RO hypothesis predicts higher methylation of CpGs located in regulatory regions (CpG islands) of nonessential genes. It also predicts the higher methylation of regulatory CpGs linked to nonessential genes in melanomas compared to nevi and lower expression of nonessential genes in malignant (derived from melanoma) versus normal (derived from nonaffected skin) melanocytes. The analyses conducted using in-house and publicly available data found that all predictions derived from the RO hypothesis hold, providing observational support for the hypothesis. Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.