Genetic and epigenetic targets in liver cancer

Ankara : The Department of Molecular Biology and Genetics and the Institute of Engineering and Science of Bilkent University, 2010.Thesis (Ph. D.) -- Bilkent University, 2010.Includes bibliographical references leaves 132-143.Hepatocellular carcinoma (HCC) kills nearly 600.000 people each year and the only effective therapy for this cancer is liver transplantation or tumor ablation only when the tumor is small enough. These tumors are surprisingly resistant to conventional therapies such as chemotherapy and radiotherapy. Moreover, as HCC is almost always associated with cirrhosis, the treatment with cytotoxic agents is dangerous as they will also affect hepatic functions of the diseased liver. Therefore, there is urgent need to find novel therapeutic approaches against HCC in order to diminish death toll. Our overall goal is to discover “druggable target genes” in HCC. In other words, we wish to identify novel genes and novel mechanisms involved in these cancers in order to use them as potential therapeutic targets. During my thesis work, I developed different approaches to find new mechanisms and novel targets: 1- Deciphering the role of canonical Wnt signaling in HCC: We classified human HCC cell lines into "well-differentiated" and "poorly differentiated" subtypes, based on the expression of hepatocyte lineage, epithelial and mesenchymal markers. Poorly differentiated cell lines lost epithelial and hepatocyte lineage markers, and overexpressed mesenchymal markers. Also, they were highly motile and invasive. We compared the expression of 45 Wnt pathway genes between two subtypes. Likewise, six Frizzled receptors, and canonical Wnt3 ligand were expressed in both subtypes. In contrast, canonical ligand Wnt8b and noncanonical ligands Wnt4, Wnt5a, Wnt5b and Wnt7b were expressed selectively in well- and poorly differentiated cell lines, respectively. Canonical Wnt signaling activity, as tested by a TCF reporter assay was detected in 80% of welldifferentiated, contrary to 14% of poorly differentiated cell lines. TCF activity generated by ectopic mutant β-catenin was weak in poorly differentiated SNU449 cell line, suggesting a repressive mechanism. We tested Wnt5a as a candidate antagonist. It strongly inhibited canonical Wnt signaling that is activated by mutant β-catenin in HCC cell lines. 2. Systematic screening of protein kinases and phosphatases as potential therapeutic targets: There is evidence of aberrant activation of several signaling cascades in HCC, and a multikinase inhibitor, sorafenib, has shown survival benefits in patients with advanced HCC. We used siRNAs to screen a large number of kinases and phosphatases to identify related genes involved in HCC cell survival. A total of 7 kinases and 5 phosphatases were identified as strong candidate targets. 3-Screening of a set of selected epigenetic regulators as potential therapeutic targets: Recent studies have indicated that senescence arrest or senescence escape could be regulated by epigenetic changes on chromatin. We wanted to identify key histone methylation and acetylation changes associated with senescence or senescence escape, and select key histone modifying enzymes, as potential targets for “pro-senescence” interventions (therapeutic interventions that allow senescence induction in cancer cells). We identified ATAD2 as an epigenetic target, and found ATAD2 gene overexpressed in HCC compared to normal liver. We also found a stepwise increase of ATAD2 protein expression in late stages with respect to pre-neoplastic and early stage during hepatocellular carcinogenesis. ATAD2 knockdown using siRNAs in cancer cells leads to increase in global histone acetylation and inhibit cell proliferation and induce caspase-3 dependent apoptosis in HCC and induce senescence in MRC5 cells. Its potentiator role (coactivator role with estrogen, androgen and myc targets) indicates ATAD2 as a potential therepeutic target for HCC.Yüzügüllü, HalukPh.D