Ankara : The Department of Molecular Biology and Genetics and the Graduate School of Engineering and Science of Bilkent Univ., 2013.Thesis (Ph. D.) -- Bilkent University, 2013.Includes bibliographical references leaves 109-130.Development of hepatocellular carcinoma (HCC) is a multi-step progressive process
in which a healthy liver transforms into cancerous tissue. Senescence is a permanent
proliferation arrest in response to cell stress such as DNA damage, serving as a major
barrier against tumor development. Most tumor cells are believed to bypass the
senescence barrier (become “immortal”) by inactivating growth control genes and
reactivating telomerase reverse transcriptase gene. Senescence-to-immortality
transition is accompanied by major phenotypic and biochemical changes mediated by
genome-wide transcriptional modifications. This appears to happen during HCC
development in patients with liver cirrhosis; however, the accompanying
transcriptional changes are virtually unknown. This study describes genome-wide
transcriptional changes related to the senescence-to-immortality switch during
hepatocellular carcinogenesis. Starting with a strong support of the hypothesis that in
vitro senescent HCC clones are alike in vivo cirrhosis cells, and in vitro immortal
HCC cells are alike in vivo HCC hepatocytes using microarray data analysis methods; we determined differentially expressed genes and deregulated biological mechanisms
during senescence escape and immortalization. Gene set enrichment analysis revealed
that cirrhosis/senescence-associated genes were preferentially expressed in non-tumor
tissues, less malignant tumors, and differentiated or senescent cells. In contrast,
HCC/immortality genes were up-regulated in tumor tissues, or more malignant tumors
and progenitor cells. In HCC tumors and immortal cells genes involved in DNA
repair, cell cycle, telomere extension and branched chain amino acid metabolism were
up-regulated, whereas genes involved in cell signaling, as well as in drug, lipid,
retinoid and glycolytic metabolism were down-regulated. Through the analysis of
senescence-related gene expression in different liver tissues we showed that cirrhosis
and HCC display expression patterns compatible with senescent and immortal
phenotypes, respectively; dysplasia being a transitional state. Based on these
distinctive gene expression features we developed a 15-gene hepatocellular
immortality signature test that discriminated HCC from cirrhosis with high accuracy.
Since an epigenetic player gene, ATAD2, came forward as one of the hepatocellular
immortality signature test genes in senescence escape processes, we also investigated
roles of epigenetic regulatory genes in hepatocellular carcinogenesis. Bioinformatics
analyzes on cirrhosis and HCC as well as dysplasia and normal liver samples using a
comprehensive list of epigenetic regulatory genes revealed several transcriptionally
deregulated epigenetic regulatory mechanisms during liver carcinogenesis. However,
we could not detect any mutational differences in N-terminal tail encoding DNA
sequences of histone variants. Our findings demonstrate that senescence bypass plays
a central role in hepatocellular carcinogenesis engendering systematic changes in the
transcription of genes regulating DNA repair, proliferation, differentiation and
metabolism.Yıldız, GökhanPh.D