GSE192352
Integrative analysis of gene expression and DNA methylation reveals epigenetic regulation of tumor suppressor genes and oncogenes involved in uterine leiomyoma pathogenesis [RNA-seq]
Uterine leiomyomas (UL) are the most common benign tumors in women of reproductive age. Despite the high prevalence, its pathology remains unclear, which hampers the development of safe and effective treatments. Several works have pointed the involvement of epigenetic mechanisms in UL development. Specifically, DNA methylation plays an important role in gene expression regulation. We aim to determine the relationship between DNA methylation and gene expression in UL compared to adjacent myometrium (MM) to describe molecular mechanisms involved in UL formation that are under epigenetic control. Our results showed a different DNA methylation profile between UL and MM, leading to hypermethylation of UL, as well as a different global transcriptome profile. Integration of DNA methylation and transcriptome data resulted in 93 genes regulated by methylation, 22 hypomethylated/upregulated and 71 hypermethylated/downregulated. Functional enrichment analysis showed dysregulated biological processes involved in metabolism and cell physiology, response to extracellular signals, invasion, and proliferation in UL. Cellular components as cell membranes, vesicles, extracellular matrix, and cell junctions were dysregulated in UL. In addition, we found hypomethylation/upregulation of oncogenes (PRL, ATP8B4, CEMIP, ZPMS2-AS1) and hypermethylation/downregulation of tumor suppressor genes (EFEMP1, FBLN2, ARHGAP10, HTATIP2) in UL, which were related to proliferation, invasion, altered metabolism, deposit of extracellular matrix and Wnt/ß-catenin pathway dysregulation. This confirms that key processes of UL development are under DNA methylation control. Finally, 5-aza-CdR treatment increased expression of hypermethylated/downregulated genes in UL cells. In conclusion, DNA methylation gene regulation is implicated in UL pathogenesis, and its reversion could be a potential therapeutic option. Overall design: Prospective study of DNA methylation by methyl-seq and gene expression by RNAseq of uterine leiomyoma (UL) versus adjacent myometrium (MM) tissue. Samples were collected from women aged 27-49 years (n=31). RNAseq and GW-DNAmet results were statistically analyzed (FDR < 0.05) and validated by quantitative real-time PCR and pyrosequencing, respectively.  Participants were recruited between September 2018–September 2020 at Hospital Universitario y Politécnico La Fe.