DNA methylation in multiple myeloma is weakly associated with gene transcription

PLoS One. 2012;7(12):e52626. doi: 10.1371/journal.pone.0052626. Epub 2012 Dec 20.

Abstract

Previous studies have now demonstrated that both genic and global hypomethylation characterizes the multiple myeloma (MM) epigenome. Whether these methylation changes are associated with global and corresponding increases (or decreases) in transcriptional activity are poorly understood. The purpose of our current study was to correlate DNA methylation levels in MM to gene expression. We analyzed matching datasets generated by the GoldenGate methylation BeadArray and Affymetrix gene expression platforms in 193 MM samples. We subsequently utilized two independent statistical approaches to identify methylation-expression correlations. In the first approach, we used a linear correlation parameter by computing a Pearson correlation coefficient. In the second approach, we discretized samples into low and high methylation groups and then compared the gene expression differences between the groups. Only methylation of 2.1% and 25.3% of CpG sites on the methylation array correlated to gene expression by Pearson correlation or the discretization method, respectively. Among the genes with methylation-expression correlations were IGF1R, DLC1, p16, and IL17RB. In conclusion, DNA methylation may directly regulate relatively few genes and suggests that additional studies are needed to determine the effects of genome-wide methylation changes in MM.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Aberrations
  • Computational Biology / methods
  • CpG Islands
  • DNA Methylation*
  • Epigenesis, Genetic
  • Epigenomics
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic*
  • Humans
  • Multiple Myeloma / genetics*
  • Reproducibility of Results
  • Transcription, Genetic*

Grants and funding

This research was supported in part by the Multiple Myeloma Research Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. No additional external funding received for this study.