Genome-wide DNA methylation analysis reveals a potential mechanism for the pathogenesis and development of uterine leiomyomas

PLoS One. 2013 Jun 20;8(6):e66632. doi: 10.1371/journal.pone.0066632. Print 2013.


Background: The pathogenesis of uterine leiomyomas, the most common benign tumor in women, remains unclear. Since acquired factors such as obesity, hypertension and early menarche place women at greater risk for uterine leiomyomas, uterine leiomyomas may be associated with epigenetic abnormalities that are caused by unfavorable environmental exposures.

Principal findings: Profiles of genome-wide DNA methylation and mRNA expression were investigated in leiomyomas and in myometrium with and without leiomyomas. Profiles of DNA methylation and mRNA expression in the myometrium with and without leiomyomas were quite similar while those in leiomyomas were distinct. We identified 120 genes whose DNA methylation and mRNA expression patterns differed between leiomyomas and the adjacent myometrium. The biological relevance of the aberrantly methylated and expressed genes was cancer process, including IRS1 that is related to transformation, and collagen-related genes such as COL4A1, COL4A2 and COL6A3. We also detected 22 target genes of estrogen receptor (ER) alpha, including apoptosis-related genes, that have aberrant DNA methylation in the promoter, suggesting that the aberrant epigenetic regulation of ER alpha-target genes contributes to the aberrant response to estrogen.

Conclusions: Aberrant DNA methylation and its related transcriptional aberration were associated with cancer processes, which may represent a critical initial mechanism that triggers transformation of a single tumor stem cell that will eventually develop into a monoclonal leiomyoma tumor. The aberrant epigenetic regulation of ER alpha-target genes also may contribute to the aberrant response to estrogen, which is involved in the development of uterine leiomyomas after menarche.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Apoptosis Regulatory Proteins / genetics
  • Chromosomes, Human, X / genetics
  • Collagen Type IV / genetics
  • Collagen Type VI / genetics
  • DNA Methylation*
  • Female
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic
  • Genetic Predisposition to Disease / genetics
  • Genome-Wide Association Study / methods*
  • Humans
  • Insulin Receptor Substrate Proteins / genetics
  • Leiomyoma / genetics*
  • Leiomyoma / pathology
  • Middle Aged
  • Receptors, Estrogen / genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • Uterine Neoplasms / genetics*
  • Uterine Neoplasms / pathology


  • Apoptosis Regulatory Proteins
  • COL4A1 protein, human
  • COL4A2 protein, human
  • Collagen Type IV
  • Collagen Type VI
  • IRS1 protein, human
  • Insulin Receptor Substrate Proteins
  • Receptors, Estrogen

Associated data

  • GEO/GSE45188

Grants and funding

This work was supported in part by Japan Society for the Promotion of Science KAKENHI Grant Number 23791846, 23890140, 24592471, and 24791704 for Scientific Research from the Ministry of Education, Science, and Culture, Japan ( The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.