Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors

Luis G. Acevedo, Mark Bieda, Roland Green, Peggy J. Farnham

Research output: Contribution to journalArticle

37 Scopus citations

Abstract

There is widespread interest in efficient characterization of differences between tumor and normal samples. Here, we show an effective methodology for genome-scale characterization of tumors. Using matched normal and tumor samples from liver cancer patients, as well as non-cancer-related normal liver tissue, we first determined changes in gene expression as monitored on RNA expression arrays. We identified several hundred mRNAs that were consistently changed in the tumor samples. To characterize the mechanisms responsible for creation of the tumor-specific transcriptome, we performed chromatin immunoprecipitation on microarray experiments to assay binding of RNA polymerase II, H3me3K27, and H3me3K9 and DNA methylation in 25,000 promoter regions. These experiments identified changes in active and silenced regions of the genome in the tumor cells. Finally, we used a "virtual comparative genomic hybridization" method to identify copy number alterations in the tumor samples. Through comparison of RNA polymerase II binding, chromatin structure, DNA methylation, and copy number changes, we suggest that the major contributor to creation of the liver tumor transcriptome was changes in gene copy number.

Original languageEnglish (US)
Pages (from-to)2641-2651
Number of pages11
JournalCancer Research
Volume68
Issue number8
DOIs
StatePublished - Apr 15 2008

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ASJC Scopus subject areas

  • Cancer Research
  • Oncology

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