Aberrantly hypermethylated tumor suppressor genes were identified in oral squamous cell carcinoma (OSCC)

Soo Yeon Kim,Joo Mi Yi,Jae Min Song,Keunsoo Kang,Hae Ryoun Park,Yu Kyeong Han,Chang Hun Lee

doi:10.1186/s13148-019-0715-0

Abstract

BackgroundOral squamous cell carcinoma (OSCC) is a genetic and epigenetic disease. There is growing evidence to suggest that environmental factors due to epigenetic changes can be involved in the OSCC pathogenesis. Although tumor suppressor genes (TSGs) are commonly inactivated by promoter hypermethylation in human cancers, the epigenetic changes and the mechanism of TSGs in human OSCC remain unclear. We therefore assessed the methylation status of the TSGs, which are associated with epigenetic silencing in human cancers, OSCC cell lines, primary tumors, and normal oral mucosa.ResultsWe used 14 TSGs that were originally identified in colon cancer to investigate the aberrant hypermethylation of these genes associated with transcriptional silencing in 10 OSCC cell lines. We found three TSGs, TFPI2, SOX17, and GATA4, that are robustly hypermethylated and are associated with transcriptional silencing in OSCC cell lines. The re-expression of the three genes was induced by 5-aza-2′-deoxycytidine (5-aza-dC) in cells in which these genes were not expressed or had a lack of expression. In 33 cases of primary OSCC tumors, promoter hypermethylation was detected for the TFPI2, SOX17, and GATA4 genes at (32/33) 97%, (22/33) 67%, and (11/33) 33%, respectively. Eleven normal oral mucosa samples showed no promoter hypermethylation for all three genes, which suggests that this promoter hypermethylation is cancer-specific. Bisulfite sequencing analysis confirmed the cancer-specific methylation of the TFPI2, SOX17, and GATA4 promoters in the OSCC cell lines and tumors but not in the normal oral mucosa samples. More importantly, the methylation status of TFPI2, GATA4, and SOX17 was significantly associated with OSCC patients’ overall survival through TCGA DNA methylation database.ConclusionsWe identified that TFPI2, SOX17, and GATA4 are frequently hypermethylated in human OSCC cells in a cancer-specific manner and that the transcriptional expression of these genes is regulated by promoter hypermethylation in OSCC. Our results highlight the great potential used as a synergistic biomarker set to improve the prognosis and therapeutic treatment for patients with OSCC.

Highlights

Oral squamous cell carcinoma (OSCC) is a genetic and epigenetic disease
Identification of aberrantly hypermethylated tumor suppressor candidates in oral squamous cell carcinoma (OSCC) In this study, we investigated transcriptional silencing by the promoter hypermethylation of 14 well-known tumor suppressor candidate genes (MGMT, sFRP2, sFRP1, HIC1, sFRP4, Timp3, sFRP5, Tissue factor pathway inhibitor-2 (TFPI2), p16, SOX17, GATA4, GATA5, FBN2, and TCERG1L) in OSCC cell lines
The results for transcriptional expression and promoter hypermethylation by the reverse transcriptase polymerase chain reaction (RT-PCR) and methylation-specific PCR (MSP) analyses of tumor suppressor genes (TSGs) are summarized in Fig. 1a (Additional file 1: Figure S1) with the following three categories: (1) genes are silenced by promoter hypermethylation with re-expression by 5-aza-dC treatment, (2) genes are silenced by promoter hypermethylation without re-expression by 5-aza-dC treatment, and (3) gene expression is not correlated with promoter methylation

Summary

Introduction

Oral squamous cell carcinoma (OSCC) is a genetic and epigenetic disease. There is growing evidence to suggest that environmental factors due to epigenetic changes can be involved in the OSCC pathogenesis. Tumor suppressor genes (TSGs) are commonly inactivated by promoter hypermethylation in human cancers, the epigenetic changes and the mechanism of TSGs in human OSCC remain unclear. We assessed the methylation status of the TSGs, which are associated with epigenetic silencing in human cancers, OSCC cell lines, primary tumors, and normal oral mucosa. Epigenetic modification, including DNA methylation and many types of histone modifications, is responsible for the altered gene expression patterns that allow for specific phenotypes [1]. DNA methylation is the primary and most studied epigenetic modification [1] and plays an important role in normal mammalian development, but aberrant methylation patterns are correlated with several differentiation-related diseases, including many types of human cancers. High-throughput genome-wide methylation studies offer a sophisticated strategy to understand the significance of DNA methylation and its impact on gene regulation [3, 5]

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Conclusion