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.

By means of in vivo selection, transcriptomic analysis, functional verification and clinical validation, here we identify a set of genes that marks and mediates breast cancer metastasis to the lungs. Some of these genes serve dual functions, providing growth advantages both in the primary tumour and in the lung microenvironment. Others contribute to aggressive growth selectively in the lung. Many encode extracellular proteins and are of previously unknown relevance to cancer metastasis.Metastasis is frequently a final and fatal step in the progression of solid malignancies. Tumour cell intravasation, survival in circulation, extravasation into a distant organ, angiogenesis and uninhibited growth constitute the metastatic process 1 . The molecular requirements for some of these steps may be tissue specific. Indeed, the proclivity that tumours have for specific organs, such as breast carcinomas for bone and lung, was noted more than a century ago 2 .The identity and time of onset of the changes that endow tumour cells with these metastatic functions are largely unknown and are a subject of debate. It is believed that genomic instability generates large-scale cellular heterogeneity within tumour populations, from which rare cellular variants with augmented metastatic abilities evolve through a darwinian selection process 2,3 . Work on experimental metastasis with tumour cell lines has demonstrated that reinjection of metastatic cell populations can lead to enrichment in the metastatic phenotype 4-6 . Recently, however, the existence of genes expressed by rare cellular variants that specifically mediate metastasis has been challenged 7 . Transcriptomic profiling of primary human carcinomas has identified gene expression patterns that, when present in the bulk primary tumour population, predict a poor prognosis for patients 8-10 . The existence of such signatures has been interpreted to mean that genetic lesions acquired early in tumor-igenesis are sufficient for the metastatic process, and that consequently no metastasis-specific genes exist. However, it is unclear whether these genes predicting metastatic recurrence are also functional mediators.The lungs and bones are frequent sites of breast cancer metastasis, and metastases to these sites differ in terms of their evolution, treatment, morbidity and mortality 11 . Reasoning that each organ places different demands on circulating cancer cells for the establishment of metastases, Selection of cells metastatic to the lungsThe cell line MDA-MB-231 was derived from the pleural effusion of a breast cancer patient suffering from widespread metastasis years after removal of her primary tumour 12 . Individual MDA-MB-231 cells grown and tested as single-cell-derived progenies (SCPs) have distinct metastatic abilities and tissue tropisms 13 despite having similar expression levels of genes constituting a validated Rosetta-type poor prognosis signature 9 ( Supplementary Fig. S1). These different meta-static behaviours, including different tropisms to bone and lung, ...

DNA sequence copy number is the number of copies of DNA at a region of a genome. Cancer progression often involves alterations in DNA copy number. Newly developed microarray technologies enable simultaneous measurement of copy number at thousands of sites in a genome. We have developed a modification of binary segmentation, which we call circular binary segmentation, to translate noisy intensity measurements into regions of equal copy number. The method is evaluated by simulation and is demonstrated on cell line data with known copy number alterations and on a breast cancer cell line data set.

No abstract

Tumor recurrence is a leading cause of cancer mortality. Therapies for recurrent disease may fail, at least in part, because the genomic alterations driving the growth of recurrences are distinct from those in the initial tumor. To explore this hypothesis, we sequenced the exomes of 23 initial low-grade gliomas and recurrent tumors resected from the same patients. In 43% of cases, at least half of the mutations in the initial tumor were undetected at recurrence, including driver mutations in TP53, ATRX, SMARCA4, and BRAF, suggesting recurrent tumors are often seeded by cells derived from the initial tumor at a very early stage of their evolution. Notably, tumors from 6 of 10 patients treated with the chemotherapeutic drug temozolomide (TMZ) followed an alternative evolutionary path to high-grade glioma. At recurrence, these tumors were hypermutated and harbored driver mutations in the RB and AKT-mTOR pathways that bore the signature of TMZ-induced mutagenesis.