Differential regulation of LRRC37A2 in gastric cancer by DNA methylation

Abstract

Gastric cancer (GC) is one of the leading types of fatal cancer worldwide. Epigenetic manipulation of cancer cells is a useful tool to better understand gene expression regulatory mechanisms and contributes to the discovery of novel biomarkers. Our research group recently reported a list of 83 genes that are potentially modulated by DNA methylation in GC cell lines. Herein, we further explored the regulation of one of these genes, LRRC37A2, in clinical samples. LRRC37A2 expression was evaluated by RT-qPCR, and DNA methylation was studied using next-generation bisulphite sequencing in 36 GC and paired adjacent nonneoplastic tissue samples. We showed that both reduced LRRC37A2 mRNA levels and increased LRRC37A2 exon methylation were associated with undifferentiated and poorly differentiated tumours. Moreover, LRRC37A2 gene expression and methylation levels were inversely correlated at the +45 exon CpG site. We suggest that DNA hypermethylation may contribute to reducing LRRC37A2 expression in undifferentiated and poorly differentiated GC. Therefore, our results show how some genes may be useful to stratify patients who are more likely to benefit from epigenetic therapy.Abbreviations: AR: androgen receptor; 5-AZAdC: 5-aza-2'-deoxycytidine; B2M: beta-2-microglobulin; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GC: gastric cancer; GLM: general linear model; LRRC37A2: leucine-rich repeat containing 37 member A2; SD: standard deviation; TFII-I: general transcription factor II-I; TSS: transcription start site; XBP1: X-box binding protein 1.

Keywords: DNA methylation; LRRC37A2; cancer therapy; gene expression.

Figure 1.

LRRC37A2 mRNA and methylation levels in GC. a: schematic diagram of CpG dinucleotide density across the LRRC37A2 locus and the location of the investigated CpG dinucleotides. b: reduced LRRC37A2 mRNA in GC compared with paired adjacent nonneoplastic tissue samples. c: reduced LRRC37A2 mRNA levels associated with undifferentiated and poorly differentiated GC. In this subset of tumours, significantly reduced LRRC37A2 mRNA levels were also observed compared with paired adjacent nonneoplastic tissue samples. d: significant differences in LRRC37A2 methylation levels across CpG sites between GC and the corresponding adjacent nonneoplastic tissue samples. e: increased LRRC37A2 CpG island methylation associated with undifferentiated and poorly differentiated tumours. f: increased LRRC37A2 exon methylation associated with undifferentiated and poorly differentiated tumours. In this subset of tumours, significantly increased LRRC37A2 mRNA levels were also observed compared with paired adjacent nonneoplastic tissue samples. g: increased methylation at the +45 CpG exon site in undifferentiated and poorly differentiated tumours and the corresponding adjacent nonneoplastic samples compared with well and moderately differentiated tumours and adjacent nonneoplastic samples. h: correlation analysis between LRRC37A2 gene expression and methylation levels.