Promoter CpG Island Hypermethylation in Dysplastic Nevus and Melanoma: CLDN11 as an Epigenetic Biomarker for Malignancy  Linda Gao, Karin van den Hurk, Peter T.M. Moerkerk, Jelle J. Goeman, Samuel Beck, Nelleke A. Gruis, Joost J. van den Oord, Véronique J. Winnepenninckx, Manon van Engeland, Remco van Doorn  Journal of Investigative Dermatology  Volume 134, Issue 12, Pages 2957-2966 (December 2014) DOI: 10.1038/jid.2014.270 Copyright © 2014 The Society for Investigative Dermatology, Inc Terms and Conditions

Figure 1 Differential promoter methylation of HOXA9, C1orf106, MAPK13, CDH11, EFCAB1, CNTN1, GNMT, PLEKHG6, PPP1R3C, and CLDN11 in common nevi, dysplastic nevi, and primary melanomas. (a) Schematic depiction of the workflow used to select candidate genes for methylation analyses in large series of melanocytic biopsy samples. (b) The 12 most frequently methylated genes identified by comparative analysis of genome-wide methylation data from 24 primary melanomas and five common nevi. (c) Methylation frequency of 10 genes in an independent set of 10 common nevi, 20 dysplastic nevi, and 15 primary melanomas as assessed by bisulfite melting curve analysis (BMCA). Black triangles indicate the position of the melting curve peak for the respective positive (fully methylated) and negative (fully unmethylated) control. Journal of Investigative Dermatology 2014 134, 2957-2966DOI: (10.1038/jid.2014.270) Copyright © 2014 The Society for Investigative Dermatology, Inc Terms and Conditions

Figure 2 Methylation analysis of CLDN11, CDH11, PPP1R3C, MAPK13, and GNMT in large series of common nevi, dysplastic nevi, primary and metastatic melanomas. (a) CpG island promoter region of the five genes, with the location of the primers used for methylation-specific PCR (MSP) and bisulfite melting curve analysis (BMCA) in this study. (b) Electrophoretic analysis of MSP amplification products of CLDN11, CDH11, PPP1R3C, MAPK13, and GNMT. N, common nevus; DN, dysplastic nevus; M, melanoma; u, unmethylated; m, methylated; IVD, positive control for methylated alleles (lymphocyte DNA treated with Sss1 methyltransferase); HUV, negative control for unmethylated alleles (DNA from human umbilical vein endothelial cells); H2Oo, no template control for first amplification with flanking primers; H2Oi, no template control for second amplification with primers specific for methylated and unmethylated DNA. Journal of Investigative Dermatology 2014 134, 2957-2966DOI: (10.1038/jid.2014.270) Copyright © 2014 The Society for Investigative Dermatology, Inc Terms and Conditions

Figure 3 Pattern and frequency of CLDN11, CDH11, PPP1R3C, MAPK13, and GNMT promoter methylation in a large series of common nevi, dysplastic nevi, primary melanomas, and metastatic melanomas (series 1). (a) Heatmap depiction of CLDN11, CDH11, PPP1R3C, MAPK13, and GNMT promoter methylation status in 55 benign nevi, 57 dysplastic nevi, 79 primary melanomas, and 15 metastatic melanomas from series 1. White, unmethylated; red, methylated. (b) Percentage of methylation events (methylated genes) found in each sample within the groups of common nevus, dysplastic nevus, primary melanoma, and metastatic melanoma. **P<0.01 and ***P<0.001 by two-sided Fisher’s exact test. (c) Overview of total number of genes that were methylated in each sample within the groups of common nevus, dysplastic nevus, primary melanoma, and metastatic melanoma. NS, nonsignificant. Journal of Investigative Dermatology 2014 134, 2957-2966DOI: (10.1038/jid.2014.270) Copyright © 2014 The Society for Investigative Dermatology, Inc Terms and Conditions

Figure 4 Testing and validation of diagnostic models that incorporate CLDN11, CDH11, PPP1R3C, MAPK13, and GNMT promoter methylation. (a) Diagnostic value was tested in 57 dysplastic nevi and 79 primary melanomas from series 1 (training set), yielding diagnostic scores in the form of a three-gene model and a two-step model, followed by validation of these models in 72 dysplastic nevi and 82 primary melanomas from series 2 (test set). (b) Receiver operating characteristic curve of the two-step diagnostic model. (c) Percentage of methylation events within the dysplastic nevi and primary melanomas of series 2. ***P<0.001 by two-sided Fisher’s exact test. (d) Promoter methylation status of the five genes in 72 dysplastic nevi and 82 primary melanomas from series 2. White, unmethylated; red, methylated. Journal of Investigative Dermatology 2014 134, 2957-2966DOI: (10.1038/jid.2014.270) Copyright © 2014 The Society for Investigative Dermatology, Inc Terms and Conditions