Tumor Liver vs Normal Liver: ChIP-chip and RNA expression

There is widespread interest in efficient characterization of differences between tumor and normal samples. Here, we demonstrate 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 ChIP-chip experiments to assay binding of RNA polymerase II, H3me3K27, and H3me3K9 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” (vCGH) method to identify copy number alterations in the tumor samples. Through comparison of RNA Polymerase II binding, chromatin structure, and copy number changes, we suggest that the major contributor to creation of the liver tumor transcriptome was changes in gene copy number. Keywords: ChIP-chip, gene expression, CGH Source material: Liver samples from human liver cancer patients, normal human liver samples, liver cell lines and normal human hepatocytes. Experiments: ChIP-chip with abs against POLII, H3me3K27, and H3me3K9, and DNA methylation using NimbleGen 5 kb promoter arrays. RNA expression from the listed sources using Illumina Bead system. Compare normal liver to tumor liver and normal cell lines to tumor cell lines.