CELL BIOLOGY PROTEOMICS
Our research focuses on the development and application of quantitative mass spectrometry and microscopy-based proteomics to advance the understanding of human cell biology. Currently, we study centrosomes, cilia, autophagosomes, mitochondria, and structures in the nucleus. The main objectives are to determine the protein composition and dynamic properties of these cell organelles, the function of selected groups of proteins, and how they contribute to the biological processes and diseases associated with these organelles. We are also studying cell signalling mediated by post translation modifications, currently within the DNA damage response and the autophagy and immune systems.
PhD Fellow Signe Krogh Ohlsen
Centrosomes in animal cells are dynamic organelles with a proteinaceous matrix of pericentriolar material assembled around a pair of centrioles. They organize the microtubule cytoskeleton, the mitotic spindle apparatus, and are essential for biogenesis of the primary cilium that mediates key signaling events. Mutations affecting genes essential for cilia/centrosome formation or function can lead to a number of severe human diseases and developmental defects, now known as the "ciliopathies". We study the protein composition and dynamics of the centrosome using the SILAC-based quantitative proteomics and the subcellular localization using antibodies in collaboration with the Human Protein Atlas project and transgenomics in collaboration with the Hyman lab. We explore the function of individual proteins by protein-protein interaction analysis and by RNAi knockdown in combination with cell assays.
Databases and resources
MSQuant is a tool for quantitative proteomics/mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.
Mortensen, P., Gouw, J. W., Olsen, J. V., Ong, S. E., Rigbolt, K. T., Bunkenborg, J., Cox, J., Foster, L. J., Heck, A. J., Blagoev, B., Andersen, J. S., and Mann, M. (2009) MSQuant, an Open Source Platform for Mass Spectrometry-Based Quantitative Proteomics. Journal of proteome research, 1, 393-403
Schandorff, S., Olsen, J.V., Bunkenborg, J., Blagoev, B., Zhang, Y., Andersen, J.S., and Mann, M. (2007). A mass spectrometry-friendly database for cSNP identification. Nature methods 4, 465-466.
LTQ-Orbitrap XL, Thermo Fisher
LTQ-Orbitrap Velos ETD, Thermo Fisher
LTQ-FT-ICR Ultra, Thermo Fisher
CellObserver microscope, Zeiss
LSM-510 Confocal laser scanning microscope, Zeiss
Ultra centrifuges, Sorvall
Angus Lamond, University of Dundee
Matthias Mann , MPI, Munich
Laura Trinkle-Mulcahy, University of Ottawa, Ottawa
Torben Heick Jensen, AArhus University
Jiri Lukas, Jiri Bartek and Marja Jäättelä, Danich Cancer Society
Guido Kroemer, INSERM, Institut Gustave Roussy, University of Paris
Jörn Dengjel, Albert-Ludwigs University of Freiburg
Moustapha Kassem, University of Southern Denmark/Odense University Hospital
Jeppe Vinther, University of Copenhagen
Emma Lundberg and Mathias Uhlen , Karolinska, Stockholm
Anthony Hyman and Ina Poser, MPI, Dresden
Erich Nigg, University of Basel, Basel
Friedhelm Hildebrandt, University of Michigan, Ann Arbor
Monika Gad and Simon Skøde Jensen, Bioneer A/S
National and international networks
European Commission FP7 large integrative consortium
Proteomics is a major new field in biomedical research, which deals with the large-scale identification and characterization of large groups of proteins, or proteomes. These can either be the components of a subcellular organelle or compartment, or even the entire protein repertoire of whole cells and tissues. Proteomics is essential in future attempts to build a quantitative, systems-based description of cell biology. Current first generation proteomics approaches largely measure protein complexes and proteomes as homogeneous and static entities with little or no quantitative annotation. The PROSPECTS (PROteomics SPECification in Time and Space) project was initiated by world leaders in this young discipline to make a major advance in the field both by developing much more powerful instrumentation and by applying novel proteomics methods. The goal is to annotate quantitatively the human proteome with respect to protein localization and dynamics. Complementary technologies, including mass spectrometry, cryoelectron microscopy and cell imaging will be applied in innovative ways to capture transient protein complexes and the spatial and temporal dimensions of entire proteomes. These new proteomics technologies will be developed in a generic fashion to maximize their utility to the wider biomedical community. Comprehensive data sets generated in PROSPECTS will foster many downstream functional studies. Unique insights into the molecular basis of multiple forms of human disease, specifically neurodegeneration and other diseases related to folding stress, can be expected. The multidimensional data sets generated in PROSPECTS will be integrated using advanced data aggregation and machine learning. The data will be available to the scientific community via annotated online public databases, and used as a basis for a systems biological modelling of the human proteome with spatial and temporal resolution within the cell.
European Commision FP7 large integrative consortium
The APO-SYS consortium aims at obtaining major progress in comprehension of apoptosis (and more generally cell death) in human diseases, by combining a series of systems biology approaches, in silico, in vitro (in organello and in cellula), in vivo and by integrating experimental results with large data sets acquired on tissue samples from patients suffering from diseases that are caused by deregulated apoptosis, in particular cancer and AIDS. The consortium will address the striking complexity of human cell death pathways using an integrated method involving high-throughput screening, and ”omics” approaches applied to biological systems and computational modeling leading to accurate and disease relevant in silico models of apoptotic signaling triggered along the two principal pathways, the extrinsic pathways (stimulated by ligation of death receptors) and the intrinsic pathways (stimulated by intracellular stress causing mitochondrial membrane permeabilization). Furthermore, the consortium will comparatively asses the system biology of apoptotic and non-apoptotic cell death (necrosis, autophagy and mitotic catastrophe) in order to understand the extent of overlap in the mechanism leading to different phenotypic manifestation of cell death as well as the molecular ”switches” that decide whether cells remain alive or die through one or the other cell death pathway.
Nordic Cilia and Centrosome Network
Research conducted during the past decade has greatly improved our understanding of basic cilia and centrosome biology as well as our appreciation of the importance of these organelles for human health and development. However, much still remains to be learned about these physiologically important organelles. For example, while proteomics, transcriptomics and comparative genomics studies have revealed the identity of most of the components of cilia and centrosomes, we still do not know how many of these components interact and function at the molecular, cellular, and organismal level. Second, diagnosis of ciliopathies is complicated by the fact that these disorders are very pleiotropic in nature and often result from mutations in multiple genes. Third, we still do not know how to efficiently treat ciliopathies, and it is predicted that many cilia-related diseases have not even been discovered yet. To address these issues concerted efforts and improved collaborations between basic and clinical scientists (including human geneticists) are essential. A Nordic cilia/centrosome network has been established to strengthen collaborations between Nordic cilia/centrosome labs, including collaborations between basic and clinical scientists; to improve education and training of students within the field of cilia and centrosome biology; and to generate an official platform for promoting cilia/centrosome research in the Nordic countries.
Treg Center: Regulatory T- cells as a new treatment paradigm for immune disorders
Innovation consortium, The Danish Research Council
The overall aim of the TREG Center is to build a strong Danish expertise and a broad technology platform within immune tolerance in order for Danish companies and the Danish society to develop radically new therapies of Treg cell-related disorders.
Andersen, J.S., Wilkinson, C.J., Mayor, T., Mortensen, P., Nigg, E.A., and Mann, M. (2003). Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426, 570-574.
Andersen, J. S., Lam, Y. W., Leung, A. K., Ong, S. E., Lyon, C. E., Lamond, A. I., and Mann, M. (2005) Nucleolar proteome dynamics. Nature 433, 77-83.
Andersen, J. S., and Mann, M. (2006) Organellar proteomics: turning inventories into insights. EMBO Rep 7, 874-879.
Lam, Y. W., Lamond, A. I., Mann, M., and Andersen, J. S. (2007) Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins. Curr Biol 17, 749-760.
Dengjel, J., Akimov, V., Olsen, J. V., Bunkenborg, J., Mann, M., Blagoev, B., and Andersen, J. S. (2007) Quantitative proteomic assessment of very early cellular signaling events. Nat Biotechnol 25, 566-568.
Bennetzen, M. V., Larsen, D. H., Bunkenborg, J., Bartek, J., Lukas, J., and Andersen, J. S. (2010) Site-specific phosphorylation dynamics of the nuclear proteome during the DNA damage response. Mol Cell Proteomics 6, 1314-23.