Title: Integrating 5hmC and gene expression data to infer regulatory mechanisms.

Authors: Mitrea, Cristina; Wijesinghe, Priyanga; Dyson, Greg; Kruger, Adéle; Ruden, Douglas M; Draghici, Sorin; Bollig-Fischer, Aliccia

Published In Bioinformatics, (2018 05 01)

Abstract: Motivation: Epigenetic mechanisms are known to play a major role in breast cancer. However, the role of 5-hydroxymethylcytosine (5hmC) remains understudied. We hypothesize that 5hmC mediates redox regulation of gene expression in an aggressive subtype known as triple negative breast cancer (TNBC). To address this, our objective was to highlight genes that may be the target of this process by identifying redox-regulated, antioxidant-sensitive, gene-localized 5hmC changes associated with mRNA changes in TNBC cells. Results: We proceeded to develop an approach to integrate novel Pvu-sequencing and RNA-sequencing data. The result of our approach to merge genome-wide, high-throughput TNBC cell line datasets to identify significant, concordant 5hmC and mRNA changes in response to antioxidant treatment produced a gene set with relevance to cancer stem cell function. Moreover, we have established a method that will be useful for continued research of 5hmC in TNBC cells and tissue samples. Availability and implementation: Data are available at Gene Expression Omnibus (GEO) under accession number GSE103850. Contact: bollig@karmanos.org.

PubMed ID: 29220513

MeSH Terms: 5-Methylcytosine/analogs & derivatives*; Cell Line, Tumor; Computational Biology; Epigenesis, Genetic*; Female; Gene Expression Profiling; Gene Expression Regulation, Neoplastic*; Humans; Sequence Analysis, DNA; Sequence Analysis, RNA; Triple Negative Breast Neoplasms/genetics*