Ovarian cancer is the most common cause of death due to gynaecological cancer. Comprehensive genomic analysis by the TCGA consortium of HGSOC (high grade serous ovarian cancer) has not identified mutated genes (except p53 and BRCA) at sufficient frequency. Copy number variations (CNV's) are the most predominant in HGSOC. However, it is challenging to identify cancer driver genes that contribute to tumorigenesis. Using primarily copy number data from TCGA for HGSOC (n=316) we have devised a scoring method to identify new genes involved in the pathogenesis of HGSOC. The data includes frequency of amplification or deletion, size of the amplicon or deleted segment, the number of genes within the amplicon or deletion, level of expression in the tumour compared to normal, presence or absence of mutation, the effect of gene alteration on survival. Each parameter was scored for all genes (maximum 24). We implemented this scoring system to the TCGA data on HGSOC and identified known cancer drivers supporting this approach. The topmost oncogene was CCNE1 (score=14) and the tumour suppressor gene was MAP2K4 (score=11). We validated the function of the topmost previously unidentified genes, RNF144B (score=9), an oncogene and PPP2R2A (score=11), a tumour suppressor. RNF144B is an E3 ubiquitin ligase that recognizes target genes for ubiquitination. RNF144B is amplified and over expressed (RNAseq) in 16% of HGSOCs (n=316, TCGA). RNF144B is expressed as a 35kDA protein in both normal (ovary and fallopian tube) and ovarian cancer cell lines. Over expression of RNF144B in PEO4 and OVCAR3 cells significantly increased cell proliferation (p=0.03 & 0.002), colony formation (p=0.009 & 0.001) and migration of the cells (p=0.04 & 0.01). The expression of RNF144B assessed by immunohistochemistry (IHC) was up regulated (2 or 3+) in 40% of primary tumours (HGSOC) (n=100). PPP2R2A encodes for the regulatory subunit of a serine/threonine phosphatase PP2A. PPP2R2A is homozygously deleted and down regulated in 38% of HGSOCs (n=316, TCGA). It is expressed as a 54kDA in both normal (ovary and fallopian tube) and ovarian cancer cell lines (reduced expression in 4/10). Over expression of PPP2R2A in OVCAR3 & OVCAR5 cells significantly inhibited cell proliferation (p=0.001 & 0.0007), colony formation (p=0.001 & 0.0004) and migration (p=0.001 & 0.05) of the cells. In OVCAR-5 cells that express low levels of PPP2R2A, niraparib a PARP2 inhibitor inhibited cell proliferation compared to control suggesting synthetic lethality. There was no expression of PPP2R2A by IHC in72% of primary tumours (n=100, HGSOC). The above data provide evidence for the role of RNF144B and PPP2R2A in the pathogenesis of ovarian cancer.
Citation Format: Pacharla Manasa, Chirukandath Sidhanth, Syama Krishnapriya, Kanchan Murhekar, Trivadi S. Ganesan. Characterisation of RNF144B and PPP2R2A identified by a novel approach using TCGA data in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB195.