Cross-Platform Array Screening Identifies COL1A2, THBS1, TNFRSF10D and UCHL1 as Genes Frequently Silenced by Methylation in Melanoma

Abstract

Epigenetic regulation of tumor suppressor genes (TSGs) has been shown to play a central role in melanomagenesis. By integrating gene expression and methylation array analysis we identified novel candidate genes frequently methylated in melanoma. We validated the methylation status of the most promising genes using highly sensitive Sequenom Epityper assays in a large panel of melanoma cell lines and resected melanomas, and compared the findings with those from cultured melanocytes. We found transcript levels of UCHL1, COL1A2, THBS1 and TNFRSF10D were inversely correlated with promoter methylation. For THBS1 and UCHL1 the effect of this methylation on expression was confirmed at the protein level. Identification of these candidate TSGs and future research designed to understand how their silencing is related to melanoma development will increase our understanding of the etiology of this cancer and may provide tools for its early diagnosis.

Identification of COL1A1 and COL1A2 as candidate prognostic factors in gastric cancer

“…However, the expression levels of COL1A1 and COL1A2 in malignant tumors remain controversial. On one hand, frequent promoter methylation of COL1A1 was detected in renal cell carcinoma and hepatocellular carcinoma [9, 10], and COL1A2 was downregulated in melanoma [11], head and neck cancer [14], and bladder cancer [15]. On the other hand, COL1A1 and COL1A2 mRNA was upregulated in colorectal cancer and medulloblastoma [16, 17].…”

“…Typically, type I collagen is composed of two chains of collagen type I alpha 1 (COL1A1) and one chain of collagen type I alpha 2 (COL1A2) [5]. Recently, similar to the expressions of other members of the collagen family which is believed to be involved in carcinogenesis [6–8], abnormal expression of COL1A1 and COL1A2 has been reported in several cancers [9–11]. In addition, Zang et al [12] indentified that COL1A1 and COL1A2 were differentially expressed in gastric cancer by complementary DNA (cDNA) microarray.…”

Aberrant DNA methylation in melanoma: biomarker and therapeutic opportunities

“…Melanoma hypermethylation prevalence for ERα (50%), MGMT (50%), RARB2 (44%), RIL (88%), RASSF1A (69%), PAX7 (31%), PGRB (56%), PAX2 (38%), NKX2-3 (63%), OLIG2 (63%), HAND1 (63%), ECAD (88%), CDH13 (44%), MLH1 (0%), and p16 (6%) was reported [40]. Similarly, Bonazzi et al reported methylation of COL1A2 (24%), THBS1 (31%), TNFRSD10D (66%), and UCHL1 (42%) genes in 12 melanoma cell lines, relative to a reference pool of melanocytes [42]. More recent studies have integrated DNA methylation changes with transcriptional changes (RNA-Seq) and histone modifications (ChIP-Seq).…”

Constitutional promoter methylation and risk of familial melanoma

“…[16][17][18][19] In addition, aberrant promoter methylation of these genes in melanoma tissues, cultured melanocytes or serum from melanoma patients has also been described. 17,18,[20][21][22][23][24][25][26][27] Total genomic DNA extraction Deterioration of DNA methylation levels in cultured PBMC samples has previously been reported. 28 To avoid this problem, we extracted total genomic DNA directly from cryopreserved primary PBMC cells (3-5 × 10 6 cells) using TRIzol ® as per manufacturers' guidelines.…”