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Using microarray data, a genome wide analysis of hepatic gene-silencing in four hepatoma variant cell lines was carried out. The purpose of this analysis was to identify candidate genes that may be able to restore liver function in non-functional cell variants, ultimately giving insight into the mechanisms behind global hepatic gene expression. Based on a selection scheme allowing only for genes activated or repressed at least 5 fold in 2 out of the 4 variant cell lines, 225 genes were found to be repressed while a total of 76 genes were found to be activated. Of the repressed genes identified, fourteen candidate genes were chosen based on known function as transcription factors or involvement in signal transduction pathways. One gene of particular interest, ONECUT1 (or HNF6), was analyzed for the capability to restore liver function in one of the cell variant lines. This was done by stable transfection of ONECUT1 into the H11-variant cell line, followed by qPCR to monitor liver gene reactivation. Measurement for liver reactivation was assessed by comparing gene expression values of known liver-specific genes (such as albumin) of parental hepatoma cells to those of variant cell lines. Data indicates that ONECUT1 is not able to directly restore liver function in the variant cell lines. However, the thorough analysis of hepatic gene silencing paves the way for genetic rescue experiments designed to identify genes involved with hepatic function and the genetic programs responsible for establishing and maintaining liver specific gene expression.
Kurkewich, Jeffrey L., "Genome Wide Analysis of Hepatic Gene Silencing in Mammalian Cell Variants" (2012). Undergraduate Honors Theses. 16.