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Colorectal cancer (CRC) is a frequently lethal disease with heterogeneous outcomes and drug responses. To resolve inconsistencies among the reported gene expression–based CRC classifications and facilitate clinical translation, we formed an international consortium dedicated to large-scale data sharing and analytics across expert groups. We show marked interconnectivity between six independent classification systems coalescing into four consensus molecular subtypes (CMS) with distinguishing features: CMS1 (MSI Immune, 14%), hypermutated, microsatellite unstable, strong immune activation; CMS2 (Canonical, 37%), epithelial, chromosomally unstable, marked WNT and MYC signaling activation; CMS3 (Metabolic, 13%), epithelial, evident metabolic dysregulation; and CMS4 (Mesenchymal, 23%), prominent transforming growth factor β activation, stromal invasion, and angiogenesis. Samples with mixed features (13%) possibly represent a transition phenotype or intra-tumoral heterogeneity. We consider the CMS groups the most robust classification system currently available for CRC – with clear biological interpretability – and the basis for future clinical stratification and subtype–based targeted interventions.

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Mammalian genetic approaches to study gene function have been hampered by the lack of tools to generate stable loss-of-function phenotypes efficiently. We report here a new vector system, named pSUPER, which directs the synthesis of small interfering RNAs (siRNAs) in mammalian cells. We show that siRNA expression mediated by this vector causes efficient and specific down-regulation of gene expression, resulting in functional inactivation of the targeted genes. Stable expression of siRNAs using this vector mediates persistent suppression of gene expression, allowing the analysis of loss-of-function phenotypes that develop over longer periods of time. Therefore, the pSUPER vector constitutes a new and powerful system to analyze gene function in a variety of mammalian cell types.

This is an author version of the article published on:Questa è la versione dell'autore dell'articolo: Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR.Prahallad A, Sun C, Huang S, Di Nicolantonio F, Salazar R, Zecchin D, Beijersbergen RL, Bardelli A, Bernards R. Nature. 2012 Jan 26;483(7387):100-3. doi: 10.1038/nature10868. The final version is available at: La versione definitiva è disponibile alla URL:http://www.nature.com/nature/journal/v483/n7387/full/nature10868.html . We therefore set out to screen a short hairpin RNA (shRNA) library representing the full complement of 518 human kinases 12 (the "kinome") and 17 additional kinase-related genes (Table S1) for genes whose inhibition confers sensitivity to PLX4032 in BRAF V600E mutant CRC. WiDr cells were infected with the lentiviral kinome shRNA collection and cultured in the absence or presence of PLX4032 for 10 and 18 days, respectively. After this, the relative abundance of shRNA vectors was determined by next generation sequencing of the bar code identifiers present in each shRNA vector (Fig. 1C, see methods). We arbitrarily considered only shRNA vectors that had been sequenced at least 300 times and which were depleted at least five-fold by the drug treatment. Fig. 1D shows that only very few of the 3388 shRNA vectors in the library met this stringent selection criterion, among which were three independent shRNA vectors targeting the Epidermal Growth FactorReceptor (EGFR, see Table S2 for all selected shRNAs). This suggested that suppression of EGFR synergizes with BRAF inhibition in these CRC cells. To validate this finding, we infected WiDr cells with each of these three EGFR shRNA vectors (all of which reduced EGFR levels (Fig. 1F)) and cultured these cells with or without PLX4032 for two weeks. . We therefore began by investigating a potential role of CDC25C in the activation of EGFR. We suppressed CDC25C in WiDr cells by shRNA and monitored levels of p-EGFR.We found that two independent shCDC25C vectors caused an increase in p-EGFR (Fig. 2E).Moreover, treatment of WiDr cells with PLX4032 inhibited phosphorylation of CDC25C at Thr48 (Fig. 2F), which has been shown to be required for its phosphatase activity 15 .Together, these data are consistent with a model in which BRAF inhibition leads to inhibition of MEK and ERK kinases, which in turn leads to a reduced activation of CDC25C. Inhibition of CDC25C in turn causes an increase in p-EGFR due to decreased dephosphorylation (Fig. 2E). Our data do not exclude that the related CDC25A and B or other phosphatases are also involved in this feedback regulation of EGFR.The EGFR is expressed primarily in epithelial cancers 17. Since melanomas are derived from the neural crest, we reasoned that the favourable response of melanomas to vemurafenib might result from the paucity of EGF receptors on these tumours and hence the 6 absence of the feedback activation of EGFR by BRAF inhibition. We compared EGFR expression in a panel of BRAF V600E mutant melanoma, colo...

Posttranslational modification of proteins by the small molecule ubiquitin is a key regulatory event, and the enzymes catalyzing these modifications have been the focus of many studies. Deubiquitinating enzymes, which mediate the removal and processing of ubiquitin, may be functionally as important but are less well understood. Here, we present an inventory of the deubiquitinating enzymes encoded in the human genome. In addition, we review the literature concerning these enzymes, with particular emphasis on their function, specificity, and the regulation of their activity.

BACKGROUNDThe 70-gene signature test (MammaPrint) has been shown to improve prediction of clinical outcome in women with early-stage breast cancer. We sought to provide prospective evidence of the clinical utility of the addition of the 70-gene signature to standard clinical-pathological criteria in selecting patients for adjuvant chemotherapy. METHODSIn this randomized, phase 3 study, we enrolled 6693 women with early-stage breast cancer and determined their genomic risk (using the 70-gene signature) and their clinical risk (using a modified version of Adjuvant! Online). Women at low clinical and genomic risk did not receive chemotherapy, whereas those at high clinical and genomic risk did receive such therapy. In patients with discordant risk results, either the genomic risk or the clinical risk was used to determine the use of chemotherapy. The primary goal was to assess whether, among patients with high-risk clinical features and a low-risk gene-expression profile who did not receive chemotherapy, the lower boundary of the 95% confidence interval for the rate of 5-year survival without distant metastasis would be 92% (i.e., the noninferiority boundary) or higher. RESULTSA total of 1550 patients (23.2%) were deemed to be at high clinical risk and low genomic risk. At 5 years, the rate of survival without distant metastasis in this group was 94.7% (95% confidence interval, 92.5 to 96.2) among those not receiving chemotherapy. The absolute difference in this survival rate between these patients and those who received chemother apy was 1.5 percentage points, with the rate being lower without chemotherapy. Similar rates of survival without distant metastasis were reported in the subgroup of patients who had estrogen-receptor-positive, human epidermal growth factor receptor 2-negative, and either node-negative or node-positive disease. CONCLUSIONSAmong women with early-stage breast cancer who were at high clinical risk and low genomic risk for recurrence, the receipt of no chemotherapy on the basis of the 70-gene signature led to a 5-year rate of survival without distant metastasis that was 1.5 percentage points lower than the rate with chemotherapy. Given these findings, approximately 46% of women with breast cancer who are at high clinical risk might not require chemo-

A large-scale RNA interference screen to discover genes involved in trastuzumab resistance in breast cancer identified only PTEN as a modulator of drug sensitivity. Oncogenic mutants of PIK3CA (activator of the same pathway and frequently mutated in breast cancer) also conferred resistance to trastuzumab in cell culture. In a cohort of 55 breast cancer patients, activation of the PI3K pathway, as judged by the presence of oncogenic PIK3CA mutations or low PTEN expression, was associated with poor prognosis after trastuzumab therapy, and the combined analysis of PTEN and PIK3CA identified twice as many patients at increased risk for progression compared to PTEN alone. Thus, assessment of PI3K pathway activation may provide a biomarker to identify patients unlikely to respond to trastuzumab-based therapy.