In silico identification and in vitro expression analysis of breast cancer-related m⁶A-SNPs

Research on m⁶A-associated SNPs (m⁶A-SNPs) has emerged recently due to their possible critical roles in many key biological processes. In this sense, several investigations have identified m⁶A-SNPs in different diseases. In order to gain a more complete understanding of the role that m⁶A-SNPs can play in breast cancer, we performed an in silico analysis to identify the m⁶A-SNPs associated with breast cancer and to evaluate their possible effects. For this purpose, we downloaded SNPs related to breast cancer and a list of m⁶A-SNPs from public databases in order to identify which ones appear in both. Subsequently, we assessed the identified m⁶A-SNPs in silico by expression quantitative trait loci (eQTL) analysis and differential gene expression analysis. We genotyped the m⁶A-SNPs found in the in silico analysis in 35 patients with breast cancer, and we carried out a gene expression analysis experimentally on those that showed differences. Our results identified 981 m⁶A-SNPs related to breast cancer. Four m⁶A-SNPs showed an eQTL effect and only three were in genes that presented an altered gene expression. When the three m⁶A-SNPs were evaluated in the tissue sample of our breast cancer patients, only the m⁶A-SNP rs76563149 located in ZNF354A gene presented differences in allele frequencies and a low gene expression in breast cancer tissues, especially in luminal B HER2+ subtype. Future investigations of these m⁶A-SNPs should expand the study in different ethnic groups and increase the sample sizes to test their association with breast cancer and elucidate their molecular function.