Summary The Cancer Genome Atlas (TCGA) project has analyzed mRNA expression, miRNA expression, promoter methylation, and DNA copy number in 489 high-grade serous ovarian adenocarcinomas (HGS-OvCa) and the DNA sequences of exons from coding genes in 316 of these tumors. These results show that HGS-OvCa is characterized by TP53 mutations in almost all tumors (96%); low prevalence but statistically recurrent somatic mutations in 9 additional genes including NF1, BRCA1, BRCA2, RB1, and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three miRNA subtypes, four promoter methylation subtypes, a transcriptional signature associated with survival duration and shed new light on the impact on survival of tumors with BRCA1/2 and CCNE1 aberrations. Pathway analyses suggested that homologous recombination is defective in about half of tumors, and that Notch and FOXM1 signaling are involved in serous ovarian cancer pathophysiology.

Some stimulatory receptors of the innate immune system, such as the NKG2D receptor expressed by NK cells and activated CD8 + T cells, recognize self-molecules that are upregulated in diseased cells by poorly understood mechanisms 1 . Here we show that mouse and human NKG2D ligands are upregulated in non-tumor cell lines by genotoxic stress and stalled DNA replication, conditions known to activate a major DNA damage checkpoint pathway initiated by ATM (Ataxia telangiectasia, mutated) or ATR (ATM-and Rad3-related) protein kinases 2 . Ligand upregulation was prevented by pharmacological or genetic inhibition of ATR, ATM or Chk1, the latter a downstream transducer kinase in the pathway. Furthermore, constitutive ligand expression by a tumor cell line was inhibited by ATM siRNA, suggesting that ligand expression in established tumor cells, which often harbor genomic irregularities, may be due to chronic activation of the DNA damage response pathway. Thus, the DNA damage response, previously shown to arrest the cell cycle and enhance DNA repair functions or to trigger apoptosis, may also participate in alerting the immune system to the presence potentially dangerous cells.To investigate mechanisms leading to NKG2D ligand upregulation, we examined two transformed ovarian epithelial cell lines from p53 −/− mice 3 . The C1 cell line had been transduced with K-ras and c-myc, whereas the C2 cell line had been transduced with AKT and c-myc (Fig. 1A). Both transformed cell lines grew well in cell culture but did not express appreciable levels of mouse NKG2D ligands as detected by staining with a tetrameric NKG2D reagent that binds to all mouse NKG2D ligands (Rae1, MULT1 and H60 1 ) (Fig. 1B). Ligand upregulation failed to occur when C1 and C2 cells were transfected or super-transduced with numerous other oncogenes, including E6, E7, E1A, or Ras V12 (data not shown), some of which interfere with expression of the retinoblastoma tumor suppressor gene. When injected into the ovaries of nude mice, both cell lines generated ovarian epithelial tumors, which were established as cell lines T1 and T2 3 . Both T1 and T2 exhibited significant upregulation of NKG2D ligands (Fig. 1B) including Rae1 (see below). These findings suggested that ligand upregulation was not associated with transformation per se.Ligand expression by C1 or C2 cells was not upregulated by numerous cell stress conditions, including heat shock, hyperoxia, hypoxia, inhibition of the cell cycle (by roscovitine), exposure to inflammatory cytokines such as TNF, interferon or IL-6, or incubation in medium of pH6 or pH8.5 ( Fig. 2A, S1, data not shown). In contrast, NKG2D ligands were upregulated in C1 or C2 cells exposed to high doses of ionizing radiation, inhibitors of DNA replication such as mitomycin C, hydroxyurea (HU), 5-fluorouracil (5-FU) and the DNA polymerase inhibitor aphidicolin, or chromatin modifying treatments such as trichostatin A, chloroquine and

To identify common alleles associated with different histotypes of epithelial ovarian cancer (EOC), we pooled data from multiple genome-wide genotyping projects totaling 25,509 EOC cases and 40,941 controls. We identified nine new susceptibility loci for different EOC histotypes: six for serous EOC histotypes (3q28, 4q32.3, 8q21.11, 10q24.33, 18q11.2 and 22q12.1), two for mucinous EOC (3q22.3, 9q31.1) and one for endometrioid EOC (5q12.3). We then meta-analysed the results for high-grade serous ovarian cancer with the results from analysis of 31,448 BRCA1 and BRCA2 mutation carriers, including 3,887 mutation carriers with EOC. This identified an additional three loci at 2q13, 8q24.1 and 12q24.31. Integrated analyses of genes and regulatory biofeatures at each locus predicted candidate susceptibility genes, including OBFC1, a novel susceptibility gene for low grade/borderline serous EOC.