Transcript-specific differences in m6A modifications in endocrine-sensitive and resistant breast cancer cells II

Acquired resistance to endocrine therapies (ET) remains a clinical problem for breast cancer patients whose initial tumors express estrogen receptor α (ER). Epigenetic changes are among the mechanisms involved in the development of ET resistance. We tested the hypothesis that the epitranscriptomic modification N-6 methyladenosine (m6A) differentially regulates the abundance of mRNA transcripts in ET-sensitive MCF-7 versus LCC9 ET-resistant ER+ human breast cancer cells. Direct mRNA sequencing (dRNA-seq) was performed on five replicates for each cell line +/- treatment with 100 nM 4-hydroxytamoxifen (4-OHT) using Nanopore MinION long read RNA-seq. Parallel short read Illumina RNA-seq was used to quantify differential transcript abundance. Statistical analysis integrated m6Anet, a machine-learning algorithm designed to call m6A modified bases, with a generalized linear model following a binomial distribution analysis to identify significant differential m6A modification ratios (DMR). Our findings reveal distinct m6A modification patterns in ET-resistant LCC9 breast cancer cells and in response to 4-OHT treatment compared to their ET-sensitive parental MCF-7 cells, suggesting a potential role for epitranscriptomic alterations in the development of ET resistance.