Integrated genetic and epigenetic analysis of childhood acute lymphoblastic leukemia. Academic Article uri icon

Overview

abstract

  • Acute lymphoblastic leukemia (ALL) is the commonest childhood malignancy and is characterized by recurring structural genetic alterations. Previous studies of DNA methylation suggest epigenetic alterations may also be important, but an integrated genome-wide analysis of genetic and epigenetic alterations in ALL has not been performed. We analyzed 137 B-lineage and 30 T-lineage childhood ALL cases using microarray analysis of DNA copy number alterations and gene expression, and genome-wide cytosine methylation profiling using the HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) assay. We found that the different genetic subtypes of ALL are characterized by distinct DNA methylation signatures that exhibit significant correlation with gene expression profiles. We also identified an epigenetic signature common to all cases, with correlation to gene expression in 65% of these genes, suggesting that a core set of epigenetically deregulated genes is central to the initiation or maintenance of lymphoid transformation. Finally, we identified aberrant methylation in multiple genes also targeted by recurring DNA copy number alterations in ALL, suggesting that these genes are inactivated far more frequently than suggested by structural genomic analyses alone. Together, these results demonstrate subtype- and disease-specific alterations in cytosine methylation in ALL that influence transcriptional activity, and are likely to exert a key role in leukemogenesis.

publication date

  • June 10, 2013

Research

keywords

  • Epigenesis, Genetic
  • Precursor Cell Lymphoblastic Leukemia-Lymphoma

Identity

PubMed Central ID

  • PMC3696550

Scopus Document Identifier

  • 84879634027

Digital Object Identifier (DOI)

  • 10.1093/nar/30.1.207

PubMed ID

  • 23921123

Additional Document Info

volume

  • 123

issue

  • 7