Mutation and methylation analysis of the chromodomain-helicase-DNA binding 5 gene in ovarian cancer

Neoplasia. 2008 Nov;10(11):1253-8. doi: 10.1593/neo.08718.

Abstract

Chromodomain, helicase, DNA binding 5 (CHD5) is a member of a subclass of the chromatin remodeling Swi/Snf proteins and has recently been proposed as a tumor suppressor in a diverse range of human cancers. We analyzed all 41 coding exons of CHD5 for somatic mutations in 123 primary ovarian cancers as well as 60 primary breast cancers using high-resolution melt analysis. We also examined methylation of the CHD5 promoter in 48 ovarian cancer samples by methylation-specific single-stranded conformation polymorphism and bisulfite sequencing. In contrast to previous studies, no mutations were identified in the breast cancers, but somatic heterozygous missense mutations were identified in 3 of 123 ovarian cancers. We identified promoter methylation in 3 of 45 samples with normal CHD5 and in 2 of 3 samples with CHD5 mutation, suggesting these tumors may have biallelic inactivation of CHD5. Hemizygous copy number loss at CHD5 occurred in 6 of 85 samples as assessed by single nucleotide polymorphism array. Tumors with CHD5 mutation or methylation were more likely to have mutation of KRAS or BRAF (P = .04). The aggregate frequency of CHD5 haploinsufficiency or inactivation is 16.2% in ovarian cancer. Thus, CHD5 may play a role as a tumor suppressor gene in ovarian cancer; however, it is likely that there is another target of the frequent copy number neutral loss of heterozygosity observed at 1p36.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CpG Islands
  • DNA Helicases / genetics*
  • DNA Methylation*
  • DNA Mutational Analysis
  • Female
  • Gene Dosage
  • Genes, Tumor Suppressor
  • Humans
  • Mutation*
  • Nerve Tissue Proteins / genetics*
  • Oligonucleotide Array Sequence Analysis
  • Ovarian Neoplasms / genetics*
  • Ovarian Neoplasms / metabolism
  • Polymorphism, Genetic
  • Polymorphism, Single-Stranded Conformational
  • Promoter Regions, Genetic
  • Proto-Oncogene Proteins / genetics
  • Proto-Oncogene Proteins / metabolism
  • Proto-Oncogene Proteins B-raf / genetics
  • Proto-Oncogene Proteins p21(ras)
  • Reverse Transcriptase Polymerase Chain Reaction
  • ras Proteins / genetics
  • ras Proteins / metabolism

Substances

  • KRAS protein, human
  • Nerve Tissue Proteins
  • Proto-Oncogene Proteins
  • BRAF protein, human
  • Proto-Oncogene Proteins B-raf
  • DNA Helicases
  • CHD5 protein, human
  • Proto-Oncogene Proteins p21(ras)
  • ras Proteins