Integrative analysis of the DNA methylome and transcriptome in uterine leiomyoma shows altered regulation of genes involved in metabolism, proliferation, extracellular matrix, and vesicles

Abstract

Uterine leiomyomas (ULs) are the most common benign tumors in women of reproductive age. Despite the high prevalence, tumor pathology remains unclear, which hampers the development of safe and effective treatments. Epigenetic mechanisms appear to be involved in UL development, particularly via DNA methylation that regulates gene expression. We aimed to determine the relationship between DNA methylation and gene expression in UL compared with adjacent myometrium (MM) to identify 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, and a different global transcriptome profile. Integration of DNA methylation and whole‐transcriptome RNA‐sequencing data identified 93 genes regulated by methylation, with 22 hypomethylated/upregulated and 71 hypermethylated/downregulated. Functional enrichment analysis showed dysregulated biological processes and molecular functions involved in metabolism and cell physiology, response to extracellular signals, invasion, and proliferation, as well as pathways related to uterine biology and cancer. Cellular components such 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, RIMS2, TFAP2C) and hypermethylation/downregulation of tumor suppressor genes (EFEMP1, FBLN2, ARHGAP10, HTATIP2), which are related to proliferation, invasion, altered metabolism, deposition of extracellular matrix, and Wnt/β‐catenin pathway dysregulation. This confirms that key processes of UL development are under DNA methylation control. Finally, inhibition of DNA methyltransferases by 5‐aza‐2'‐deoxycitidine increased the expression of hypermethylated/downregulated genes in UL cells in vitro. In conclusion, gene regulation by DNA methylation is implicated in UL pathogenesis, and reversion of this methylation could offer a therapeutic option for UL. © 2022 The Pathological Society of Great Britain and Ireland.

H3K4me3 mediates uterine leiomyoma pathogenesis via neuronal processes, synapsis components, proliferation, and Wnt/β-catenin and TGF-β pathways

“…To identify which DEGs could be implicated in UL pathogenesis, we integrated the transcriptomic data obtained by RNA-seq from two previous studies using independent patient cohorts [ 17 , 19 ]. The gene expression count matrix from the GSE192354 dataset revealed 1837 significant DEGs (FDR-adjusted p -value< 0.01) with a substantial difference in expression between ULs and MM tissue (log2FC > 1 or < − 1), including 1175 upregulated and 662 downregulated genes.…”

“…The role of epigenomic instability, via aberrant DNA methylation, has been recently considered for the onset and maintenance of ULs [ 19 , 34 – 39 ]. Reversing the methylation could potentially restore gene expression and ultimately become a therapeutic alternative for women with ULs [ 19 , 40 ].…”

“…The role of epigenomic instability, via aberrant DNA methylation, has been recently considered for the onset and maintenance of ULs [ 19 , 34 – 39 ]. Reversing the methylation could potentially restore gene expression and ultimately become a therapeutic alternative for women with ULs [ 19 , 40 ]. The methylation in histones 3 (H3) and 4 (H4) is widely accepted to regulate gene transcription [ 13 ] and the profile of some histone modification has been analyzed in UL [ 17 ] The trimethylation of H3K4 is emerging as a key epigenetic modification in several cancers [ 14 – 16 ].…”

PLP1 may serve as a potential diagnostic biomarker of uterine fibroids

“…As one of the well-studied epigenomic processes in mammals ( Bestor, 2000 ), DNA methylation was considered as a potential mechanism in the pathology of UFs. Many aberrantly hypermethylation/hypomethylation genes were detected in by genome-wide DNA methylation assays ( Li et al, 2003 ; Yamagata et al, 2009 ; Navarro et al, 2012 ; Islam et al, 2013 ; Maekawa et al, 2013 ; Carbajo-García et al, 2022 ), and numerous genes were validated to participate in the developmental progress of the UFs in vitro experiments. SATB homeobox 2 and neuregulin 1 were proved to be the upregulated hypermethylated genes involved in the pathogenesis of uterine leiomyoma by activating the WNT/β-catenin and TGF-β pathways ( Sato et al, 2019 ).…”

Deciphering the Role of Histone Modifications in Uterine Leiomyoma: Acetylation of H3K27 Regulates the Expression of Genes Involved in Proliferation, Cell Signaling, Cell Transport, Angiogenesis and Extracellular Matrix Formation

“…Epigenetics include variations in the gene expression profile not caused by changes in the DNA sequence, resulting from processes such as DNA methylation, histone modification, and non-coding RNAs [ 16 ]. Genome-wide DNA methylation studies have revealed subsets of suppressed or overexpressed genes accompanied by aberrant promoter methylation [ 17 , 18 , 19 ], also evaluating DNA methylation in UL focusing on stem cell population [ 20 ] or mutation status [ 21 ]. Furthermore, differential promoter access resulting from altered 3D chromatin structure and histone modifications plays a role in regulating transcription of key genes thought to be involved in leiomyoma etiology [ 22 ].…”