NPC Valorisation Voucher - Netherlands Proteomics Centre

34 |The Lgr5 intestinal stem cell signature:robust expression of proposed quiescent‘+4’ cell markersMuñoz, J., Stange, D.E., Schepers, A.G., van de Wetering, M.,Koo, B.K., Itzkovitz, S., Volckmann, R., Kung, K.S., Koster, J.,Radulescu, S., Myant, K., Versteeg, R., Sansom, O.J., van Es,J.H., Barker, N., van Oudenaarden, A., Mohammed, S., Heck,A.J., Clevers, H.EMBO J. 2012 Jun 12;31(14):3079-91. doi: 10.1038/emboj.2012.166.Bijvoet Center for Biomolecular Research, Utrecht Institute forPharmaceutical Sciences, University, The Netherlands.Two types of stem cells are currently defined in small intestinalcrypts: cycling crypt base columnar (CBC) cells and quiescent‘+4’ cells. Here, we combine transcriptomics with proteomicsto define a definitive molecular signature for Lgr5(+)CBC cells. Transcriptional profiling of FACS-sorted Lgr5(+)stem cells and their daughters using two microarray platformsrevealed an mRNA stem cell signature of 384 unique genes.Quantitative mass spectrometry on the same cell populationsidentified 278 proteins enriched in intestinal stem cells. ThemRNA and protein data sets showed a high level of correlationand a combined signature of 510 stem cell-enriched genes wasdefined. Spatial expression patterns were further characterizedby mRNA in-situ hybridization, revealing that approximatelyhalf of the genes were expressed in a gradient withhighest levels at the crypt bottom, while the other half wasexpressed uniquely in Lgr5(+)stem cells. Lineage tracing usinga newly established knock-in mouse for one of the signaturegenes, Smoc2, confirmed its stem cell specificity. Using thisresource, we find-and confirm by independent approaches-thatthe proposed quiescent/’+4’ stem cell markers Bmi1, Tert,Hopx and Lrig1 are robustly expressed in CBC cells.Other highlighted publicationsAlbers, H.M., Ovaa, H.Chemical evolution of autotaxin inhibitorsChem Rev. (2012) May 9;112(5):2593-603. Epub 2012 Feb 15.Kruiswijk, F., Yuniati, L., Magliozzi, R., Low, T.Y., Lim, R.,Bolder, R., Mohammed, S., Proud, C.G., Heck, A.J., Pagano,M., Guardavaccaro, D.Coupled activation and degradation of eEF2K regulates proteinsynthesis in response to genotoxic stressSci Signal. 2012 Jun 5;5(227):ra40.Meinema, A.C., Poolman, B., Veenhoff, L.M.The transport of integral membrane proteins across thenuclear pore complexNucleus. (2012) Jul 1;3(4).Ongay S., Boichenko A., Govorukhina N., Bischoff R.Glycopeptide enrichment and separation for proteinglycosylation analysisJ Sep Sci. (2012) Sep;35(18):2341-72. doi: 10.1002/jssc.201200434.Bischoff, R., and Schlüter, H.Amino acids: Chemistry, functionality and selected nonenzymaticpost-translational modificationsJ. Proteomics (2012) 75, 2275-2296Kovanich, D., Aye, T.T., Heck, A.J., Scholten, A.Probing the specificity of protein-protein interactions byquantitative chemical proteomicsMethods Mol Biol. (2012) 803:167-81.Kovanich, D, Cappadona, S., Raijmakers, R., Mohammed, S.,Scholten, A., Heck, A.J.Applications of stable isotope dimethyl labeling in quantitativeproteomicsAnal Bioanal Chem. (2012) Sep;404(4):991-1009.van Geel, R., Pruijn, G.J., van Delft, F.L., Boelens, W.C.Preventing thiol-yne addition improves the specificity ofstrain-promoted azide-alkyne cycloadditionBioconjug Chem. (2012) Mar 21;23(3):392-8. Epub 2012 Mar 8.Krijgsheld, P., Altelaar, A.F., Post, H., Ringrose, J.H., Müller,W.H., Heck, A.J., Wösten, H.A.Spatially Resolving the Secretome within the Mycelium of theCell Factory Aspergillus nigerJournal of Proteome Research (2012) 11 (5), 2807-2818Lindhoud, S., van den Berg, W.A., van den Heuvel, R.H., Heck,A.J., van Mierlo, C.P., van Berkel, W.J.Cofactor Binding Protects Flavodoxin against Oxidative StressPLoS One. 2012;7(7):e41363. (IF: 4.092)Smaczniak, C., Immink, R.G., Angenent, G.C., Kaufmann, K.Developmental and evolutionary diversity of plant MADSdomainfactors: insights from recent studiesDevelopment. (2012) Sep;139(17):3081-98. doi: 10.1242/dev.074674.Eschrich, S., Fulp, W.J., Pawitan, Y., Foekens, J.A., Smid, M.,Martens, J.W., Echevarria, M., Kamath, V., Lee, J.H., Harris,E.E., Bergh, J., Torres-Roca, J.F.Validation of a radiosensitivity molevular signature in breastcancerClin Cancer Res. (2012) Sep 15;18(18):5134-5143. Epub 2012Jul 25.Godinho, M.F., Wulfkuhle, J.D., Look, M.P., Sieuwerts, A.M.,Sleijfer, S., Foekens, J.A., Petricoin, E.F. 3rd, Dorssers, L.C.,van Agthoven, T.BCAR4 induces antiestrogen resistance but sensitizes breastcancer to lapatinibBr J Cancer. (2012) Sep 4;107(6):947-55. doi: 10.1038/bjc.2012.351. Epub 2012 Aug 14.Richau, K.H., Kaschani, F., Verdoes, M., Pansuriya, T.C.,Niessen, S., Stüber, K., Colby, T., Overkleeft, H.S., Bogyo, M.,Van der Hoorn, R.A.Subclassification and biochemical analysis of plant papain-likecysteine proteases displays subfamily-specific characteristics.Plant Physiol. 2012 Apr;158(4):1583-99. Epub 2012 Feb 27.