SUMMARY Annotation of prostate cancer genomes provides a foundation for discoveries that can impact disease understanding and treatment. Concordant assessment of DNA copy number, mRNA expression, and focused exon resequencing in 218 prostate cancer tumors identified the nuclear receptor coactivator NCOA2 as an oncogene in ~11 percent of tumors. Additionally, the androgen-driven TMPRSS2-ERG fusion was associated with a previously unrecognized, prostate-specific deletion at chromosome 3p14 that implicates FOXP1, RYBP and SHQ1 as potential cooperative tumor suppressors. DNA copy-number data from primary tumors revealed that copy-number alterations robustly define clusters of low- and high-risk disease beyond that achieved by Gleason score. The genomic and clinical outcome data from these patients is now made available as a public resource.

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, ...

Cellular senescence has been theorized to oppose neoplastic transformation triggered by activation of oncogenic pathways in vitro 1-3 , but the relevance of senescence in vivo has not been established. The PTEN and p53 tumour suppressors are among the most commonly inactivated or mutated genes in human cancer including prostate cancer 4,5 . Although they are functionally distinct, reciprocal cooperation has been proposed, as PTEN is thought to regulate p53 stability, and p53 to enhance PTEN transcription 6-10 . Here we show that conditional inactivation of Trp53 in the mouse prostate fails to produce a tumour phenotype, whereas complete Pten inactivation in the prostate triggers nonlethal invasive prostate cancer after long latency. Strikingly, combined inactivation of Pten and Trp53 elicits invasive prostate cancer as early as 2 weeks after puberty and is invariably lethal by 7 months of age. Importantly, acute Pten inactivation induces growth arrest through the p53-dependent cellular senescence pathway both in vitro and in vivo, which can be fully rescued by combined loss of Trp53. Furthermore, we detected evidence of cellular senescence in specimens from early-stage human prostate cancer. Our results demonstrate the relevance of cellular senescence in restricting tumorigenesis in vivo and support a model for cooperative tumour suppression in which p53 is an essential failsafe protein of Pten-deficient tumours.'Cellular senescence' describes a permanent form of cell cycle arrest in primary cultured cells, which can be triggered by DNA damage or activated oncogenes 1-3 . Although it has been implicated in mediating the response to anti-tumour treatments 11 , there is still no evidence that senescence opposes tumorigenesis.Up to 70% of primary prostate tumours lose one PTEN allele and retain the other copy 12-15 . Similarly, p53 is found completely lost or mutated almost exclusively in advanced prostate cancer 16,17 . Because complete loss of Pten in the mouse seems to be crucial for the development of invasive prostate tumours 18,19 , why human invasive prostate cancer wouldCorrespondence and requests for materials should be addressed to P.P.P. (p-pandolfi@ski.mskcc.org). Author Information Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.Supplementary Information is linked to the online version of the paper at www.nature.com/nature. (Supplementary Fig. S1). As expected, in the presence of Pb-Cre4, recombination of Pten and Trp53 was restricted to the three prostatic lobes, namely the anterior prostate (AP), ventral prostate (VP) and dorsolateral prostate (DLP), with minor recombination occurring in seminal vesicles ( Supplementary Fig. S2a). NIH Public AccessTo study early effects of Pten and/or Trp53 inactivation in the prostate, mice were killed at 9 weeks of age and histopathological analysis was performed. Wild-type (WT) mice displayed normal prostate histology, whereas age-matched Pten pc−/− littermate...

The molecular basis for breast cancer metastasis to the brain is largely unknown 1,2 . Brain relapse typically occurs years after the removal of a breast tumour [2][3][4] , suggesting that disseminated cancer cells must acquire specialized functions to overtake this organ. Here we show that breast cancer metastasis to the brain involves mediators of extravasation through non-fenestrated capillaries, complemented by specific enhancers of blood-brain barrier crossing and brain colonization. We isolated cells that preferentially infiltrate the brain from patients with advanced disease. Gene expression analysis of these cells and of clinical samples, coupled with functional analysis, identified the cyclooxygenase COX2 (also known as PTGS2), the epidermal growth factor receptor (EGFR) ligand HBEGF, and the α2,6-sialyltransferase ST6GALNAC5 as mediators of cancer cell passage through the blood-brain barrier. EGFR ligands and COX2 were previously linked to breast cancer infiltration of the lungs, but not the bones or liver 5,6 , suggesting a sharing of these mediators in cerebral and pulmonary metastases. In contrast, ST6GALNAC5 specifically mediates brain metastasis. Normally restricted to the brain 7 , the expression of ST6GALNAC5 in breast cancer cells enhances their adhesion to brain endothelial cells and their passage through the blood-brain barrier. This co-option of a brain sialyltransferase highlights the role of cell-surface glycosylation in organspecific metastatic interactions.Brain metastasis affects an estimated 10% of cancer patients with disseminated disease 2,8,9 . Even small lesions can cause neurological disability, and the median survival time of patientsCorrespondence and requests for materials should be addressed to J.M. (E-mail: j-massague@ski.mskcc.org). † Present addresses: Institut de Malalties Hemato-Oncològiques, Hospital Clínic, 08036 Barcelona, Spain (C.N.); Oncology Programme, Institute for Research in Biomedicine, 08028 Barcelona, Spain (R.R.G.). Author InformationThe clinical microarray data on the brain metastatic cell lines have been deposited in NCBI's Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo) under the GEO series accession number GSE12237.Supplementary Information is linked to the online version of the paper at www.nature.com/nature. Full Methods and any associated references are available in the online version of the paper at www.nature.com/nature. 11 and also by tight junctions and astrocyte foot processes in the blood-brain barrier (BBB) 2,8 , whereas the capillaries in the bone marrow and the liver are fenestrated 11,12 . The composition of the parenchyma also varies extensively between these organs. The protracted progression of disseminated cancer cells in different environments may give rise to metastatic speciation, as suggested by the coexistence of malignant cells with different organ tropisms in fluids from patients with advanced disease 5,13 . Analysis of such malignant cell populations has revealed genes that selectively mediate breast cance...

A search for general regulators of cancer metastasis has yielded a set of microRNAs for which expression is specifically lost as human breast cancer cells develop metastatic potential. Here we show that restoring the expression of these microRNAs in malignant cells suppresses lung and bone metastasis by human cancer cells in vivo. Of these microRNAs, miR-126 restoration reduces overall tumour growth and proliferation, whereas miR-335 inhibits metastatic cell invasion. miR-335 regulates a set of genes whose collective expression in a large cohort of human tumours is associated with risk of distal metastasis. miR-335 suppresses metastasis and migration through targeting of the progenitor cell transcription factor SOX4 and extracellular matrix component tenascin C. Expression of miR-126 and miR-335 is lost in the majority of primary breast tumours from patients who relapse, and the loss of expression of either microRNA is associated with poor distal metastasis-free survival. miR-335 and miR-126 are thus identified as metastasis suppressor microRNAs in human breast cancer.Although metastasis is the overwhelming cause of mortality in patients with solid tumours, our understanding of its molecular and cellular determinants is limited 1-3 . Transcriptional profiling has revealed sets of genes, or `signatures', for which expression in primary tumours correlates with metastatic relapse or poor survival 4 . Some of these genes endow cancer cells with a more invasive phenotype, enhanced angiogenic and intravasation activity, the ability to exit from the circulation, or an ability to modify the metastasis microenvironment 5,6 . Such gene sets are thus providing numerous candidate mediators of metastasis to be validated through functional and clinical studies. Much less insight, however, has been gained into the

In human lung adenocarcinomas harboring EGFR mutations, a second-site point mutation that substitutes methionine for threonine at position 790 (T790M) is associated with approximately half of cases of acquired resistance to the EGFR kinase inhibitors, gefitinib and erlotinib. To identify other potential mechanisms that contribute to disease progression, we used array-based comparative genomic hybridization (aCGH) to compare genomic profiles of EGFR mutant tumors from untreated patients with those from patients with acquired resistance. Among three loci demonstrating recurrent copy number alterations (CNAs) specific to the acquired resistance set, one contained the MET proto-oncogene. Collectively, analysis of tumor samples from multiple independent patient cohorts revealed that MET was amplified in tumors from 9 of 43 (21%) patients with acquired resistance but in only two tumors from 62 untreated patients (3%) (P ‫؍‬ 0.007, Fisher's Exact test). Among 10 resistant tumors from the nine patients with MET amplification, 4 also harbored the EGFR T790M mutation. We also found that an existing EGFR mutant lung adenocarcinoma cell line, NCI-H820, harbors MET amplification in addition to a drug-sensitive EGFR mutation and the T790M change. Growth inhibition studies demonstrate that these cells are resistant to both erlotinib and an irreversible EGFR inhibitor (CL-387,785) but sensitive to a multikinase inhibitor (XL880) with potent activity against MET. Taken together, these data suggest that MET amplification occurs independently of EGFR T790M mutations and that MET may be a clinically relevant therapeutic target for some patients with acquired resistance to gefitinib or erlotinib.lung adenocarcinoma ͉ XL880

The optimal treatment of patients with cancer depends on establishing accurate diagnoses by using a complex combination of clinical and histopathological data. In some instances, this task is difficult or impossible because of atypical clinical presentation or histopathology. To determine whether the diagnosis of multiple common adult malignancies could be achieved purely by molecular classification, we subjected 218 tumor samples, spanning 14 common tumor types, and 90 normal tissue samples to oligonucleotide microarray gene expression analysis. The expression levels of 16,063 genes and expressed sequence tags were used to evaluate the accuracy of a multiclass classifier based on a support vector machine algorithm. Overall classification accuracy was 78%, far exceeding the accuracy of random classification (9%). Poorly differentiated cancers resulted in low-confidence predictions and could not be accurately classified according to their tissue of origin, indicating that they are molecularly distinct entities with dramatically different gene expression patterns compared with their well differentiated counterparts. Taken together, these results demonstrate the feasibility of accurate, multiclass molecular cancer classification and suggest a strategy for future clinical implementation of molecular cancer diagnostics.

who had undergone a lobectomy with mediastinal lymph node dissection were retrospectively reviewed. Comprehensive histological subtyping was used to estimate the percentage of each histological subtype and to identify the predominant subtype. Tumors were classified according to the proposed new IASLC/ATS/ERS adenocarcinoma classification. Statistical analyses were made including Kaplan-Meier and Cox regression analyses. There were 323 females (63%) and 191 males (37%) with a median age of 69 years (33-89 years) and 298 stage IA and 216 stage IB patients. Three overall prognostic groups were identified: low grade: adenocarcinoma in situ (n ¼ 1) and minimally invasive adenocarcinoma (n ¼ 8) had 100% 5-year disease-free survival; intermediate grade: non-mucinous lepidic predominant (n ¼ 29), papillary predominant (n ¼ 143) and acinar predominant (n ¼ 232) with 90, 83 and 84% 5-year disease-free survival, respectively; and high grade: invasive mucinous adenocarcinoma (n ¼ 13), colloid predominant (n ¼ 9), solid predominant (n ¼ 67) and micropapillary predominant (n ¼ 12), with 75, 7170 and 67%, 5-year disease-free survival, respectively (Po0.001). Among the clinicopathological factors, stage 1B versus 1A (Po0.001), male sex (Po0.008), high histological grade (Po0.001), vascular invasion (P ¼ 0.002) and necrosis (Po0.001) were poorer prognostic factors on univariate analysis. Both gross tumor size (P ¼ 0.04) and invasive tumor size adjusted by the percentage of lepidic growth (Po0.001) were significantly associated with disease-free survival with a slightly stronger association for the latter. Multivariate analysis showed the prognostic groups of the IASLC/ATS/ERS histological classification (P ¼ 0.038), male gender (P ¼ 0.007), tumor invasive size (P ¼ 0.026) and necrosis (P ¼ 0.002) were significant poor prognostic factors. In summary, the proposed IASLC/ATS/ERS classification of lung adenocarcinoma identifies histological categories with prognostic differences that may be helpful in