NPC Valorisation Voucher - Netherlands Proteomics Centre

Top publications with NPC contributionIn this NPC HighLights we provide a short list ofpapers that appeared recently in some of the topjournals and to which NPC participants contributed.With the guarantee of being by far notcomprehensive, this overview shows some elegantground-breaking research.Tumour suppressor RNF43 is a stem-cellE3 ligase that induces endocytosis of WntreceptorsKoo, B.K., Spit, M., Jordens, I., Low, T.Y., Stange, D.E.,van de Wetering, M., van Es, J.H., Mohammed, S., Heck, A.J.,Maurice, M.M., Clevers, H.Nature (2012) Aug 30;488(7413):665-9. doi: 10.1038/nature11308.Hubrecht Institute, KNAW and University Medical CenterUtrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.LGR5+ stem cells reside at crypt bottoms, intermingled withPaneth cells that provide Wnt, Notch and epidermal growth32 | NPC factor Highlights signals. Here 16 we | November find that the 2012 related RNF43 and ZNRF3transmembrane E3 ubiquitin ligases are uniquely expressedin LGR5+ stem cells. Simultaneous deletion of the two genesencoding these proteins in the intestinal epithelium of miceinduces rapidly growing adenomas containing high numbersof Paneth and LGR5+ stem cells. In vitro, growth of organoidsderived from these adenomas is arrested when Wnt secretionis inhibited, indicating a dependence of the adenomastem cells on Wnt produced by adenoma Paneth cells. In theHEK293T human cancer cell line, expression of RNF43 blocksWnt responses and targets surface-expressed frizzled receptorsto lysosomes. In the RNF43-mutant colorectal cancercell line HCT116, reconstitution of RNF43 expression removesits response to exogenous Wnt. We conclude that RNF43 andZNRF3 reduce Wnt signals by selectively ubiquitinating frizzledreceptors, thereby targeting these Wnt receptors for degradation.The landscape of cancer genes andmutational processes in breast cancerStephens, P.J. et. AlNature (2012) May 16;486(7403):400-4. doi: 10.1038/nature11017.Cancer Genome Project, Wellcome Trust Sanger Institute,Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.All cancers carry somatic mutations in their genomes. A subset,known as driver mutations, confer clonal selective advantage oncancer cells and are causally implicated in oncogenesis, and theremainder are passenger mutations. The driver mutations andmutational processes operative in breast cancer have not yetbeen comprehensively explored. Here we examine the genomesof 100 tumours for somatic copy number changes and mutationsin the coding exons of protein-coding genes. The number ofsomatic mutations varied markedly between individual tumours.We found strong correlations between mutation number, age atwhich cancer was diagnosed and cancer histological grade, andobserved multiple mutational signatures, including one presentin about ten per cent of tumours characterized by numerousmutations of cytosine at TpC dinucleotides. Driver mutationswere identified in several new cancer genes including AKT2,ARID1B, CASP8, CDKN1B, MAP3K1, MAP3K13, NCOR1, SMARCD1and TBX3. Among the 100 tumours, we found driver mutationsin at least 40 cancer genes and 73 different combinations ofmutated cancer genes. The results highlight the substantialgenetic diversity underlying this common disease.High-sensitivity Orbitrap mass analysis ofintact macromolecular assembliesRose, R.J., Damoc, E., Denisov, E., Makarov, A., Heck, A.J.Nature Methods (2012) Oct 14. doi: 10.1038/nmeth.2208.[Epub ahead of print]Biomolecular Mass Spectrometry and Proteomics, BijvoetCenter for Biomolecular Research and Utrecht Institute ofPharmaceutical Sciences, Utrecht University, Utrecht,The Netherlands. Netherlands Proteomics Center, Utrecht,The Netherlands.The analysis of intact protein assemblies in native-like statesby mass spectrometry offers a wealth of information on theirbiochemical and biophysical properties. Here we show thatthe Orbitrap mass analyzer can be used to measure proteinassemblies of molecular weights approaching one megadaltonwith sensitivity down to the detection of single ions. Minor instrumentalmodifications enabled the measurement of variousprotein assemblies with outstanding mass-spectral resolution.Protease bias in absolute protein quantitationPeng, M., Taouatas, N., Cappadona, S., van Breukelen, B.,Mohammed, S., Scholten, A., Heck, A.J.Nature Methods (2012) May 30;9(6):524-5. doi: 10.1038/nmeth.2031.Trypsin is the most commonly used protease in typical proteomicsexperiments. (Absolute) Quantitation using spectralcounts provides insight into protein abundances. This isdependent on the protease used. In other words, the use ofa single protease, such as trypsin, can introduce biases in theobserved protein abundances.