Higher Naevus Count Exhibits A Distinct DNA Methylation Signature in Healthy Human Skin: Implications for Melanoma

TY - JOUR

T1 - Higher Naevus Count Exhibits A Distinct DNA Methylation Signature in Healthy Human Skin

T2 - Implications for Melanoma

AU - Roos, Leonie

AU - Sandling, Johanna K

AU - Bell, Christopher G

AU - Glass, Daniel

AU - Mangino, Massimo

AU - Spector, Tim D

AU - Deloukas, Panos

AU - Bataille, Veronique

AU - Bell, Jordana T

N1 - Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

PY - 2016/12/18

Y1 - 2016/12/18

N2 - High naevus count is the strongest risk factor for melanoma and although gene variants have been discovered for both traits, epigenetic variation is unexplored. We investigated 322 healthy human skin DNA methylomes associated with total body naevi count, incorporating genetic and transcriptomic variation. DNA methylation changes were identified at genes involved in melanocyte biology, such as RAF1 (p = 1.2 x 10(-6)) and CTC1 (region: p = 6.3 x 10(-4)), and other genes including ARRDC1 (p = 3.1 x 10(-7)). A subset exhibited coordinated methylation and transcription changes within the same biopsy. The total analysis was also enriched for melanoma-associated DNA methylation variation (p = 6.33 x 10(-6)). Additionally, we show that skin DNA methylation is associated in cis with known GWAS SNPs for naevus count, at PLA2G6 (p = 1.7 x 10(-49)) and NID1 (p = 6.4 x 10(-14)), as well as melanoma risk, including in or near MC1R, MX2 and TERT/CLPTM1L (p < 1 x 10(-10)). Our analysis using a uniquely large dataset comprising healthy skin DNA methylomes identified known and additional regulatory loci and pathways in naevi and melanoma biology. This integrative study improves our understanding of predisposition to naevi and their potential contribution to melanoma pathogenesis.

AB - High naevus count is the strongest risk factor for melanoma and although gene variants have been discovered for both traits, epigenetic variation is unexplored. We investigated 322 healthy human skin DNA methylomes associated with total body naevi count, incorporating genetic and transcriptomic variation. DNA methylation changes were identified at genes involved in melanocyte biology, such as RAF1 (p = 1.2 x 10(-6)) and CTC1 (region: p = 6.3 x 10(-4)), and other genes including ARRDC1 (p = 3.1 x 10(-7)). A subset exhibited coordinated methylation and transcription changes within the same biopsy. The total analysis was also enriched for melanoma-associated DNA methylation variation (p = 6.33 x 10(-6)). Additionally, we show that skin DNA methylation is associated in cis with known GWAS SNPs for naevus count, at PLA2G6 (p = 1.7 x 10(-49)) and NID1 (p = 6.4 x 10(-14)), as well as melanoma risk, including in or near MC1R, MX2 and TERT/CLPTM1L (p < 1 x 10(-10)). Our analysis using a uniquely large dataset comprising healthy skin DNA methylomes identified known and additional regulatory loci and pathways in naevi and melanoma biology. This integrative study improves our understanding of predisposition to naevi and their potential contribution to melanoma pathogenesis.

U2 - 10.1016/j.jid.2016.11.029

DO - 10.1016/j.jid.2016.11.029

M3 - Article

C2 - 27993549

SN - 0022-202X

JO - Journal of Investigative Dermatology

JF - Journal of Investigative Dermatology

ER -