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

ABSTRACT

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.

KEYWORDS:

• Breast cancer
• epigenetics
• m⁶A methylation
• m⁶A-SNP
• SNP

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data Availability Statement

The data that support the findings of this study are available from the corresponding authors, MMP and FO, upon request.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/15592294.2022.2111137

Additional information

Funding

This work was supported by Basque Government (Grupos Consolidados with Grant No. IT1633-22 and predoctoral fellowship PRE_2019_2_0005 to Tamara Kleinbielen).