Genome-wide identification of OTP gene as a novel methylation marker of breast cancer

Abstract

Abstract. Aberrant DNA methylation occurs early and frequently in tumorigenesis. Identification of DNA methylation biomarkers is a field that provides potential for improving the clinical process of breast cancer diagnosis. We utilized a genome-wide technique, methylated DNA isolation assay (MeDIA), in combination with high-resolution CpG microarray analysis to identify hypermethylated genes in breast cancer. Among differentially methylated genes between tumor and adjacent normal tissues, 3 candidate genes (LHX2, WT1 and OTP) were finally selected through a step-wise filtering process and examined for methylation status in normal tissues, primary tumor, and paired adjacent normal-appearing tissues from 39 breast cancer patients. Based on the calculated cut-off values, all genes showed significantly higher frequencies of aberrant hypermethylation in primary tumors (43.6% for LHX2, 89.7% for WT1 and 100% for OTP, P<0.05) while frequencies were intermediate in paired adjacent normal tissues and absent in normal tissues. On further analysis, the methylation level in primary tumors was not significantly correlated with clinicopathological features. Interestingly, DNA methylation of a novel gene OTP was detected in adjacent normal tissues even 6 cm away from primary tumors, suggesting that OTP methylation may qualify as a biomarker for the early detection of breast cancer. In conclusion, we successfully identified a novel gene OTP frequently methylated in breast cancer by genomewide screening. Our results suggest that the OTP gene may play a crucial role in breast carcinogenesis, although further clinical validation will be needed to evaluate the potential application of OTP in the early detection of breast cancer.

Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer

“…McGregor et al has previously reported that WT1 expression was up-regulated in BC cells ( McGregor et al, 2018 ), which was consistent with our findings. Furthermore, we found that WT1 exhibited hypermethylation in BC tissues, which was consistent with the results reported by Kim et al (2012) . Compared to Kim’s research which was performed on BC cells and a single subtype of BC, our study additionally showed that WT1 was highly expressed and hypermethylation in all the four subtypes of BC.…”

Exploring DNA methylation changes in promoter, intragenic, and intergenic regions as early and late events in breast cancer formation

“…We chose a diverse set of genes and two DNA repeats (Table 1 ) to assay for DNA methylation in cancer, adjacent and control mammoplasty tissues. Eight of the 23 examined DNA regions overlapped or were near regions previously reported to be hypermethylated in breast cancer vs. non-cancerous breast tissue, namely, EGFR [ 20 ], GSTP1 [ 21 ], LHX2 [ 22 ], PITX2 [ 23 ], RASSF1A [ 24 ], RUNX3 [ 25 ], APC [ 26 ] and BRCA1 [ 27 , 28 ] or hypomethylated in breast cancer vs. normal breast, namely, TFF1 [ 29 ], satellite 2 and LINE-1, DNA repeats [ 30 , 31 ]. In addition, the first six of the above-mentioned gene regions displayed hypermethylation in one or two breast cancer cell lines (MCF-7 and T-47D) relative to a human breast epithelial cell culture derived from normal breast tissue (human mammary epithelial cells, HMEC) and compared with most normal tissues, including breast tissue as seen in whole-genome DNA methylation data (reduced representation bisulfite sequencing, RRBS) from the ENCODE project [ 5 , 13 , 19 ].…”

Common gene pathways and families altered by DNA methylation in breast and prostate cancers

“…Additional studies have also compared tumor to nonmalignant tissue and the number of genes identified that discriminates the two depends on the filtering or analyses utilized. For example, Kim et al (2012) used several filtering processes to identify six genes, whereas Faryna et al (2012) identified 214 CpG islands but only one CpG island (TAC1) was methylated in all ten cancer samples. The identification of thousands of loci with altered DNA methylation between non-malignant and tumor tissue using genome wide methylation analyses raises several (Li et al 2010, Dedeurwaerder et al 2011, Fang et al 2011, Hill et al 2011, Sun et al 2011, although a study by Van der Auwera et al (2010) did not find any association between hormone receptor status and DNA methylation profile (Table 1).…”