DNA methylation aberrancy is a reliable prognostic tool in uveal melanoma

Abstract

Background: Despite outstanding advances in understanding the genetic background of uveal melanoma (UM) development and prognosis, the role of DNA methylation reprogramming remains elusive. This study aims to clarify the extent of DNA methylation deregulation in the context of gene expression changes and its utility as a reliable prognostic biomarker. Methods: Transcriptomic and DNA methylation landscapes in 25 high- and low-risk UMs were interrogated by Agilent SurePrint G3 Human Gene Expression 8×60K v2 Microarray and Human Infinium Methylation EPIC Bead Chip array, respectively. DNA methylation and gene expression of the nine top discriminatory genes, selected by the integrative analysis, were validated by pyrosequencing and qPCR in 58 tissues. Results: Among 2,262 differentially expressed genes discovered in UM samples differing in metastatic risk, 60 were epigenetic regulators, mostly histone modifiers and chromatin remodelers. A total of 44,398 CpGs were differentially methylated, 27,810 hypomethylated, and 16,588 hypermethylated in high-risk tumors, with Δβ values ranging between -0.78 and 0.79. By integrative analysis, 944 differentially expressed DNA methylation-regulated genes were revealed, 635 hypomethylated/upregulated, and 309 hypermethylated/downregulated. Aberrant DNA methylation in high-risk tumors was associated with the deregulation of key oncogenic pathways such as EGFR tyrosine kinase inhibitor resistance, focal adhesion, proteoglycans in cancer, PI3K-Akt signaling, or ECM-receptor interaction. Notably, the DNA methylation values of nine genes, HTR2B, AHNAK2, CALHM2, SLC25A38, EDNRB, TLR1, RNF43, IL12RB2, and MEGF10, validated by pyrosequencing, demonstrated excellent risk group prediction accuracies (AUCs ranging between 0.870 and 0.956). Moreover, CALHM2 hypomethylation and MEGF10, TLR1 hypermethylation, as well as two three-gene methylation signatures, Signature 1 combining AHNAK2, CALHM2, and IL12RB and Signature 2 AHNAK2, CALHM2, and SLC25A38 genes, correlated with shorter overall survival (HR = 4.38, 95% CI 1.30-16.41, HR = 5.59, 95% CI 1.30-16.41; HR = 3.43, 95% CI 1.30-16.41, HR = 4.61, 95% CI 1.30-16.41 and HR = 4.95, 95% CI 1.39-17.58, respectively). Conclusions: Our results demonstrate a significant role of DNA methylation aberrancy in UM progression. The advantages of DNA as a biological material and the excellent prediction accuracies of methylation markers open the perspective for their more extensive clinical use.

Genetic and Epigenetic Features of Uveal Melanoma—An Overview and Clinical Implications

“…A recent study using UM tissue from 68 UM patients in Slovakia revealed that high-risk tumors had a total of 7810 CpGs that were hypomethylated and 16,588 that were hypermethylated. Three genes with hypomethylation or upregulation, HTR2B (FC 191.4), AHNAK2 (FC 12.6), and CALHM2 (FC 7.8), as well as six genes with hypermethylation or downregulation, SLC25A38 (FC-4.6), EDNRB (FC-4.7), TLR1 (FC-8.6), RNF43 (FC-10.8), IL12RB2 (FC-18.1), and MEGF10 (FC-25) were selected for validation and the number of CpGs inversely correlated with gene expression [ 108 ].…”

Caracterização genômica e funcional do lncRNA RMEL3 em melanoma

“…Ao buscar genes apoptóticos regulados por RMEL3, encontramos que como gene altamente aumentado no silenciamento de RMEL3 o MEGF10, que codifica uma proteína transmembrana tipo I altamente expressa no sistema nervoso central, que em melanoma uveal demonstrou ter papel crucial na inibição da progressão tumoral além de aumentar a apoptose celular (Yang et al, 2021). A expressão de MEGF10 é reprimida epigeneticamente pela hipermetilação do DNA ou pela metilação H3K27/K9 em linhas celulares de neuroblastoma e de melanoma uveal (Charlet et al, 2017;Soltysova et al, 2023), e pode ser por esse mecanismo que RMEL3 reprime a expressão de MEGF10 em A375, visto que análises anteriores do nosso grupo demonstraram alta expressão de RMEL3 correlaciona com uma hipermetilação do genoma em melanoma (Goedert, 2019).…”