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.

We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, and miRNA expression levels and reverse-phase protein arrays, of which all, except for aneuploidy, revealed clustering primarily organized by histology, tissue type, or anatomic origin. The influence of cell type was evident in DNA-methylation-based clustering, even after excluding sites with known preexisting tissue-type-specific methylation. Integrative clustering further emphasized the dominant role of cell-of-origin patterns. Molecular similarities among histologically or anatomically related cancer types provide a basis for focused pan-cancer analyses, such as pan-gastrointestinal, pan-gynecological, pan-kidney, and pan-squamous cancers, and those related by stemness features, which in turn may inform strategies for future therapeutic development.

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SUMMARY Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival.

Background On August 14, 2014, the United States Food and Drug Administration approved the anti-angiogenesis drug, bevacizumab, for women with advanced cervical cancer based on a 2012 interim analysis of 271 deaths on GOG protocol 240. We now report the planned protocol-specified final analysis of the primary objective, overall survival (OS). Methods A phase III randomized trial using a 2×2 factorial design was conducted to determine whether intravenous chemotherapy [(cisplatin 50 mg/m2 plus paclitaxel 135 or 175 mg/m2) or (topotecan 0.75 mg/m2 days 1–3 plus paclitaxel 175 mg/m2)] with or without bevacizumab (15 mg/kg) improves OS in recurrent/persistent/metastatic cervical cancer. Patients were prospectively stratified by performance status, prior radiosensitizing platinum, and disease status. We estimated enrolling 450 patients with 346 deaths at final analysis to provide 90% power to detect a 30% reduction in risk of death. Findings On March 7, 2014, 348 deaths occurred among 452 patients. Regimens administering bevacizumab continued to demonstrate significant improvement in OS: 16.8 vs 13.3 mos (HR 0.77;95% CI 0.62–0.95;p=0.0068). Updated progression-free survival also favored bevacizumab (HR 0.68;95% CI 0.56–0.84;p=0.0002). Final OS among 20% (n=91) not treated with prior pelvic radiotherapy was 24.5 (bevacizumab) vs 16.8 mos (without bevacizumab). Fistula (any grade) occurred in 14.5% (n=32) receiving bevacizumab (all previously irradiated). Grade 3+ fistula developed in 5.9% (n=13) and did not result in surgical emergency, sepsis and/or death. Post-progression OS was not significantly different among those who did and did not receive bevacizumab (median 8.4 vs 7.1 mos: HR 0.32;95% CI 0.66–1.05;p=0.06). Interpretation The benefit conferred by incorporation of bevacizumab is sustained with extended follow-up as evidenced by the survival curves remaining separated. Following progression on bevacizumab, a negative rebound effect was not observed. This represents proof-of-concept of the efficacy and tolerability of anti-angiogenesis therapy in advanced cervical cancer. Funding National Cancer Institute (USA).

SUMMARY Hotspot mutations in splicing factor genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of RNA splicing in cancer. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome Atlas (TCGA), and we identified 119 splicing factor genes with significant non-silent mutation patterns, including mutation over-representation, recurrent loss of function (tumor suppressor-like), or hotspot mutation profile (oncogene-like). Furthermore, RNA sequencing analysis revealed altered splicing events associated with selected splicing factor mutations. In addition, we were able to identify common gene pathway profiles associated with the presence of these mutations. Our analysis suggests that somatic alteration of genes involved in the RNA-splicing process is common in cancer and may represent an underappreciated hallmark of tumorigenesis.