Project Z04

Advanced Proteomics

Project leader: Jeroen Krijgsveld

Abstract

The proteomics platform provides access to proteomic methodologies and high-end mass-spectrometry, covering the whole range from sample preparation to mass spectrometry and data analysis. In addition it includes a set of biochemical tools for global quantitative proteomics, nascent proteomics, secretome analysis, and analysis of protein interactions that are amenable to capture various aspects of cell signaling.

Over the past years we have developed a range of proteomic techniques for global quantitative proteome profiling of cells and tissues. This includes an ultra-sensitive application for sample preparation based on magnetic bead technology implemented on a robotic system, allowing standardized proteome analysis across multiple samples, opening up opportunities for many applications where sample amounts are scarce. We have introduced methods for the analysis of specific sub-proteomes that play crucial roles in cell regulation, especially secreted and chromatin-bound proteins. In addition, we combine pulsed-SILAC labeling and clickchemistry with mass spectrometry for nascent proteome analysis, as a powerful means to understand the proteome response of distinct signaling events.

In this project, we will use these methodologies to gain a better mechanistic understanding of various aspects of Wnt signaling. We will support the consortium in its endeavors to identify protein interactions and processing of Wnt signals. In more elaborate projects, we will use SILAC-TMT-based proteomics to understand Wnt/STOP signaling, and to investigate how distinct Wnt/FZD receptor combinations elicit different downstream responses in canonical and non-canonical Wnt signaling. Furthermore, we will exploit our low-input proteomic workflow to establish spatial proteomics, generating deep proteomic profiles across organs (liver) and organisms (Hydra) to understand function and dynamics of Wnt signaling in a tissue context.

Project-related publications

  • Bunina D, Abazova N, Diaz N, Noh K-M*, Krijgsveld J*, Zaugg JB*. 2020. Genomic rewiring of SOX2 chromatin interaction network during differentiation of ESCs to postmitotic neurons. *Joint senior authors. Cell Syst. 10(6):480-494.e8. PMID: 32553182
  • Rafiee MR, Sigismondo G, Kalxdorf M, Förster L, Brügger B, Béthune J, Krijgsveld J. 2020. Protease-resistant streptavidin for interaction proteomics. Mol Syst Biol. 16(5):e9370. PMID: 32400114
  • Müller T, Kalxdorf M, Longuespée R, Kazdal DN, Stenzinger A, Krijgsveld J. 2020. Automated sample preparation with SP3 for low-input clinical proteomics. Mol Syst Biol. 16(1):e9111. PMID: 32129943.
  • Kuhn TC, Knobel J, Burkert-Rettenmaier S, Li X, Meyer IS, Jungmann A, Sicklinger F, Backs J, Lasitschka F, Müller OJ, Katus HA, Krijgsveld J*, Leuschner F*. 2020. Secretome analysis of cardiomyocytes identifies PCSK6 as a novel player in cardiac remodeling after myocardial infarction. *Joint senior authors. Circulation. 141:1628–1644. PMID: 32100557.
  • Carnesecchi J, Sigismondo G, Domsch K, Baader CEP, Rafiee MR, Krijgsveld J and Lohmann I. 2020. Multilevel and lineage-specific interactome of the Hox transcription factor Ubx contributes to its functional specificity. Nature Communications. 11(1): 1388. PMID: 32170121
  • Trendel J, Schwarzl T, Horos R, Prakash A, Bateman A, Hentze MW, Krijgsveld J. 2019. The human RNAbinding proteome and its dynamics during arsenite-induced translational arrest. Cell. 176(1-2):391-
    403. PMID: 30528433
  • Hughes, C., S. Moggridge, T. Müller, P. Sorensen, G. Morin, and J. Krijgsveld. 2019. Single-pot, solid-phase-enhanced sample preparation for proteomics experiments. Nature Protocols. 14(1):68-85. PMID: 30464214
  • Buczak, K., A. Ori, J.M. Kirkpatrick, K. Holzer, D. Dauch, S. Roessler, V. Endris, F. Lasitschka, L. Parca, A. Schmidt, L. Zender, P. Schirmacher, J. Krijgsveld, S. Singer, and M. Beck. 2018. Spatial Tissue Proteomics Quantifies Inter- and Intratumor Heterogeneity in Hepatocellular Carcinoma (HCC). Mol. Cell. Proteomics. 17:810–825. PMID: 29363612
  • Rafiee, M.-R., C. Girardot, G. Sigismondo, J. Krijgsveld. 2016. Expanding the circuitry of pluripotency by selective isolation of chromatin-associated proteins. Mol Cell. 64(3):624-635. PMID: 27773674
  • Eichelbaum, K., M. Winter, M. Berriel Diaz, S. Herzig, and J. Krijgsveld. 2012. Selective enrichment of newly synthesized proteins for quantitative secretome analysis. Nature Biotechnology. 30:984-990. PMID: 23000932