Identification of novel growth promoters of ovarian cancer

© 2011 Dr. Manasa RamakrishnaOvarian cancer is a heterogeneous, genomically unstable and highly lethal disease in women. Despite nearly half a century of research in ovarian cancer, few early detection markers, disease drivers or chemoresistance conferring genes have been discovered. The recent and rapid advances in microarray and sequencing technologies have provided new tools with which a thorough search can be performed to discover novel ovarian cancer associated genes. This thesis describes the use of two high resolution microarray platforms to identify novel growth promoters of ovarian cancer. This study investigated a cohort of 72 ovarian tumours using the Affymetrix Genome-Wide Human SNP Array 6.0 (SNP6) to assess copy number, and the Affymetrix GeneChip® Whole Transcript (WT) Sense Target Array 1.0 to study gene expression. The high quality copy number data generated using the SNP6 platform was used to define frequently gained regions of the ovarian cancer genome. Gene expression data was integrated with the copy number data using novel informatics approaches to identify genes whose expression was directly affected by copy number gain. Further integrative analyses and a search of current literature yielded seven candidate drivers of ovarian cancer - PRKCI, RAB2A, PUF60 (SIAHBP1), MYNN, PTK2, PLEC1 and TPX2. These seven candidate ovarian cancer driver genes were tested for functional effects using immortalised ovarian cancer cell lines. Nine cell lines were chosen in such a way that each of the seven candidate genes were represented by at least two cell lines that showed copy number gain and two cell lines that were copy number neutral at the candidate gene locus. Small-interfering RNAs were used to knockdown the expression of candidate genes in the selected ovarian cancer cell lines. Changes in cell proliferation upon gene knockdown were recorded for all cell lines and all genes. TPX2 and RAB2A, showed a significant decrease in proliferation following siRNA knockdown in some cell lines. The changes in proliferation for TPX2 were copy number independent while for RAB2A, changes were strongly driven by copy number. The functional assays validated the power of the analysis methods in identifying novel ovarian cancer drivers