Selection of Primer Location for qMSP Analysis of Alu Methylation Level in Vietnamese Patients with Breast Cancer

Abstract

In the mammalian genome, DNA methylation occurs at the cytosine in CpG complexes. Changes in genomic DNA methylation status, reflected by the CpG methylation status of the retrotransposon Alu elements, are closely related to the initiation and development of cancer. Abnormalities in Alu methylation have been documented in many early-stage tumors where the Alu methylation level correlates with cellular malignancy. Therefore, the assessment of Alu methylation level as a biomarker for early diagnosis and prognosis has been of interest in many types of cancer. Our study aims to investigate the nucleotide positions on the CpG-rich sequence of Alu for the design of primers used for quantitative methylation-specific PCR reaction (qMSP). Using two primer pairs designed from the 5' Alu region for analysis of the Alu methylation level in 25 pairs of cancer/adjacent tissue samples of Vietnamese patients with breast cancer, we find out the primer pair that significantly distinguished the Alu methylation status between cancer and adjacent tissue samples. Selecting the right qMSP primer pair will facilitate the profiling of Alu methylation levels in breast cancer samples when compared with non-cancerous samples, thereby determining its potential in becoming an epigenetic marker for early diagnosis, prognosis as well as in supporting breast cancer treatment to be more effective in Vietnam.

Keywords: Alu methylation, breast cancer, primers of qMSP.