Genomic profiling maps loss of heterozygosity and defines the timing and stage dependence of epigenetic and genetic events in Wilms' tumors

Eric Yuan, Chi Ming Li, Darrell J. Yamashiro, Jessica Kandel, Harshwardhan Thaker, Vundavalli V. Murty, Benjamin Tycko

Research output: Contribution to journalArticle

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Abstract

To understand genetic and epigenetic pathways in Wilms' tumors, we carried out a genome scan for loss of heterozygosity (LOH) using Affymetrix 1OK single nucleotide polymorphism (SNP) chips and supplemented the data with karyotype information. To score loss of imprinting (LOI) of the IGF2 gene, we assessed DNA methylation of the H19 5′ differentially methylated region (DMR). Few chromosomal regions other than band 11p13 (WT1) were lost in Wilms' tumors from Denys-Drash and Wilms' tumor-aniridia syndromes, whereas sporadic Wilms' tumors showed LOH of several regions, most frequently 11p15 but also 1p, 4q, 7p, 11q, 14q, 16q, and 17p. LOI was common in the sporadic Wilms' tumors but absent in the syndromic cases. The SNP chips identified novel centers of LOH in the sporadic tumors, including a 2.4-Mb minimal region on chromosome 4q24-q25. Losses of chromosomes 1p, 14q, 16q, and 17p were more common in tumors presenting at an advanced stage; 11p15 LOH was seen at all stages, whereas LOI was associated with early-stage presentation. Wilms' tumors with LOI often completely lacked LOH in the genome-wide analysis, and in some tumors with concomitant 16q LOH and LOI, the loss of chromosome 16q was mosaic, whereas the H19 DMR methylation was complete. These findings confirm molecular differences between sporadic and syndromic Wilms' tumors, define regions of recurrent LOH, and indicate that gain of methylation at the H19 DMR is an early event in Wilms' tumorigenesis that is independent of chromosomal losses. The data further suggest a biological difference between sporadic Wilms' tumors with and without LOI.

Original languageEnglish (US)
Pages (from-to)493-502
Number of pages10
JournalMolecular Cancer Research
Volume3
Issue number9
DOIs
StatePublished - Sep 1 2005
Externally publishedYes

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Wilms Tumor
Loss of Heterozygosity
Epigenomics
Chromosomes
Methylation
Single Nucleotide Polymorphism
Aniridia
Genome
Neoplasms
DNA Methylation
Karyotype
Carcinogenesis

ASJC Scopus subject areas

  • Molecular Biology
  • Oncology
  • Cancer Research

Cite this

Genomic profiling maps loss of heterozygosity and defines the timing and stage dependence of epigenetic and genetic events in Wilms' tumors. / Yuan, Eric; Li, Chi Ming; Yamashiro, Darrell J.; Kandel, Jessica; Thaker, Harshwardhan; Murty, Vundavalli V.; Tycko, Benjamin.

In: Molecular Cancer Research, Vol. 3, No. 9, 01.09.2005, p. 493-502.

Research output: Contribution to journalArticle

Yuan, Eric ; Li, Chi Ming ; Yamashiro, Darrell J. ; Kandel, Jessica ; Thaker, Harshwardhan ; Murty, Vundavalli V. ; Tycko, Benjamin. / Genomic profiling maps loss of heterozygosity and defines the timing and stage dependence of epigenetic and genetic events in Wilms' tumors. In: Molecular Cancer Research. 2005 ; Vol. 3, No. 9. pp. 493-502.
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