Damaris Bausch-Fluck


Last Name

Bausch-Fluck

First Name

Damaris

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0000-0002-7593-2262

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2007 - 200912010 - 20199
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Publications 1 - 10 of 10
  • Mass spectrometry-based identification of VHL-regulated cellular membrane proteins in renal cell carcinoma
    Item type: Other Journal Item
    Boysen, Gunther; Wollscheid, Bernd; Bausch-Fluck, Damaris; et al. (2007)
    Pathology, Research and Practice
  • A Mass Spectrometric-Derived Cell Surface Protein Atlas
    Item type: Journal Article
    Bausch-Fluck, Damaris; Hofmann, Andreas; Bock, Thomas; et al. (2015)
    PLoS ONE
    Cell surface proteins are major targets of biomedical research due to their utility as cellular markers and their extracellular accessibility for pharmacological intervention. However, information about the cell surface protein repertoire (the surfaceome) of individual cells is only sparsely available. Here, we applied the Cell Surface Capture (CSC) technology to 41 human and 31 mouse cell types to generate a mass-spectrometry derived Cell Surface Protein Atlas (CSPA) providing cellular surfaceome snapshots at high resolution. The CSPA is presented in form of an easy-to-navigate interactive database, a downloadable data matrix and with tools for targeted surfaceome rediscovery (http://wlab.ethz.ch/cspa). The cellular surfaceome snapshots of different cell types, including cancer cells, resulted in a combined dataset of 1492 human and 1296 mouse cell surface glycoproteins, providing experimental evidence for their cell surface expression on different cell types, including 136 G-protein coupled receptors and 75 membrane receptor tyrosine-protein kinases. Integrated analysis of the CSPA reveals that the concerted biological function of individual cell types is mainly guided by quantitative rather than qualitative surfaceome differences. The CSPA will be useful for the evaluation of drug targets, for the improved classification of cell types and for a better understanding of the surfaceome and its concerted biological functions in complex signaling microenvironments.
  • Identification and Functional Characterization of pVHL-Dependent Cell Surface Proteins in Renal Cell Carcinoma
    Item type: Journal Article
    Boysen, Gunther; Bausch-Fluck, Damaris; Thoma, Claudio R.; et al. (2012)
    Neoplasia
    The identification of cell surface accessible biomarkers enabling diagnosis, disease monitoring, and treatment of renalcell carcinoma (RCC) is as challenging as the biology and progression of RCC is unpredictable. A hallmark of most RCCis the loss-of-function of the von Hippel–Lindau (pVHL) protein by mutation of its gene (VHL). Using the cell surfacecapturing (CSC) technology, we screened and identified cell surface N-glycoproteins in pVHL-negative and positive786-O cells. One hundred six cell surface N-glycoproteins were identified. Stable isotope labeling with amino acidsin cell culture–based quantification of the CSC screen revealed 23 N-glycoproteins whose abundance seemed tochange in a pVHL-dependent manner. Targeted validation experiments using transcriptional profiling of primary RCCsamples revealed that nine glycoproteins, including CD10 and AXL, could be directly linked to pVHL-mediated transcrip-tional regulation. Subsequent human tumor tissue analysis of these cell surface candidate markers showed a correla-tion between epithelial AXL expression and aggressive tumor phenotype, indicating that pVHL-dependent regulation ofglycoproteins may influence the biologic behavior of RCC. Functional characterization of the metalloprotease CD10 incell invasion assays demonstrated a diminished penetrating behavior of pVHL-negative 786-O cells on treatment withthe CD10-specific inhibitor thiorphan. Our proteomic surfaceome screening approach in combination with transcrip-tional profiling and functional validation suggests pVHL-dependent cell surface glycoproteins as potential diagnosticmarkers for therapeutic targeting and RCC patient monitoring.
  • CD proteome and beyond - technologies for targeting the immune cell surfaceome
    Item type: Review Article
    Bock, Thomas; Bausch-Fluck, Damaris; Hofmann, Andreas; et al. (2012)
    Frontiers in Bioscience
    Communication between cells of the immune system and the organism is dependent on information processing mediated by proteins of the cell surface. The cell surface proteome consists of a group of functionally diverse proteins, which not only enables but also limits the interaction capacities of cells within their particular microenvironment. Although these proteins represent a highly important proteome for immunological research, most routinely used technologies for their detection only allow for a fragmented view of the ensemble of cell surface located proteins. A major bottleneck is the limited availability of high quality antibodies against cell surface protein targets that altogether impedes a Systems Biology view on the cell surface proteome (surfaceome) and its concerted functions during signal processing. Recent developments in mass spectrometry-based technologies enable now complementary approaches for the qualitative and quantitative analysis of the surfaceome. Here, we highlight recent progress in the field towards the identification and quantification of the surfaceome as an important subproteome forming the information gateway of the cell.
  • Surfaceome nanoscale organization and extracellular interaction networks
    Item type: Review Article
    Bausch-Fluck, Damaris; Milani, Emanuela S.; Wollscheid, Bernd (2019)
    Current Opinion in Chemical Biology
  • The in silico human surfaceome
    Item type: Journal Article
    Bausch-Fluck, Damaris; Goldmann, Ulrich; Müller, Sebastian; et al. (2018)
    Proceedings of the National Academy of Sciences of the United States of America
    Cell-surface proteins are of great biomedical importance, as demonstrated by the fact that 66% of approved human drugs listed in the DrugBank database target a cell-surface protein. Despite this biomedical relevance, there has been no comprehensive assessment of the human surfaceome, and only a fraction of the predicted 5,000 human transmembrane proteins have been shown to be located at the plasma membrane. To enable analysis of the human surfaceome, we developed the surfaceome predictor SURFY, based on machine learning. As a training set, we used experimentally verified high-confidence cell-surface proteins from the Cell Surface Protein Atlas (CSPA) and trained a random forest classifier on 131 features per protein and, specifically, per topological domain. SURFY was used to predict a human surfaceome of 2,886 proteins with an accuracy of 93.5%, which shows excellent overlap with known cell-surface protein classes (i.e., receptors). In deposited mRNA data, we found that between 543 and 1,100 surfaceome genes were expressed in cancer cell lines and maximally 1,700 surfaceome genes were expressed in embryonic stem cells and derivative lines. Thus, the surfaceome diversity depends on cell type and appears to be more dynamic than the nonsurface proteome. To make the predicted surfaceome readily accessible to the research community, we provide visualization tools for intuitive interrogation (wlab.ethz.ch/surfaceome). The in silico surfaceome enables the filtering of data generated by multiomics screens and supports the elucidation of the surfaceome nanoscale organization.
  • Identification of a seven glycopeptide signature for malignant pleural mesothelioma in human serum by selected reaction monitoring
    Item type: Journal Article
    Cerciello, Ferdinando; Choi, Meena; Nicastri, Annalisa; et al. (2013)
    Clinical Proteomics
    Background Serum biomarkers can improve diagnosis and treatment of malignant pleural mesothelioma (MPM). However, the evaluation of potential new serum biomarker candidates is hampered by a lack of assay technologies for their clinical evaluation. Here we followed a hypothesis-driven targeted proteomics strategy for the identification and clinical evaluation of MPM candidate biomarkers in serum of patient cohorts. Results Based on the hypothesis that cell surface exposed glycoproteins are prone to be released from tumor-cells to the circulatory system, we screened the surfaceome of model cell lines for potential MPM candidate biomarkers. Selected Reaction Monitoring (SRM) assay technology allowed for the direct evaluation of the newly identified candidates in serum. Our evaluation of 51 candidate biomarkers in the context of a training and an independent validation set revealed a reproducible glycopeptide signature of MPM in serum which complemented the MPM biomarker mesothelin. Conclusions Our study shows that SRM assay technology enables the direct clinical evaluation of protein-derived candidate biomarker panels for which clinically reliable ELISA’s currently do not exist.
  • The Human Surfaceome
    Item type: Doctoral Thesis
    Bausch-Fluck, Damaris (2018)
    Systems biology aims to quantitatively understand a biological system (i.e., a cell) as a whole. The first cornerstone to achieve a system-wide characterization of the cell was the complete sequencing of the human genome, which encodes the basic information for building the whole protein repertoire of a cell. Next, mass spectrometry-based strategies opened the opportunity to determine the transcribed and translated gene repertoire of the cell - the proteotype. The proteotype bridges the gap inbetween genotype and phenotype and is defined as the actual state of the proteome of a cell. However, to decipher the complexity of biological systems, the definition of the individual components is not sufficient to understand cellular function. One needs to appreciate that a cell is more than the sum of its parts and that biological function is encoded in interaction networks. These protein interaction networks ultimately define protein function and a molecular understanding of such interactions thus enables the analysis of context-dependent cellular signaling. This thesis focuses on proteins exposed to the extracellular space, termed surfaceome, which guide communication of a cell with its outside world. Hence, the surfaceome has a crucial function as gatekeeper, enabling but also limiting cellular communication. Extracellular signals are turned into intracellular signaling responses through the surfaceome in form of ligand receptor interactions. To gain a system-wide understanding of the surfaceome, the identity, quantity and interactions thereof need to be defined. However, most of the available surfaceome information was solely built on the detection of cell surface proteins by a limited pool of antibodies since cell surface proteins were inherently difficult to analyze using other technologies. Only limited information was available about the surfaceome protein repertoire of a cell; a systematic assessement of the variability of the surfaceome over different cell types was absent; only semi-quantitative information about cell surface proteins has been obtained and there was no conception and very sparse molecular knowledge about the interconnectivity between surfaceome proteins. Hence, the aim of this thesis was to identify and quantify cellular surfaceomes, to determine the surfaceome members and to develop technologies for enabling the investigation of the interconnectivity of surfaceome residing proteins. First, the possibilities and the motivation to uncover the biomedical potential of the surfaceome interaction network are discussed in detail within the introductory chapter one, which was written in the form of a review article (chapter 1). i To follow the systematical approach to functionally define a system by first identifying and quantifying its components and then determining its interactions, we set out to first define the identity of the surfaceome (chapter 2). This was necessary, because the available surfaceome maps were limited to the ~300 Cluster of Differentiation (CD) antibody panel. Surfacome sets of 41 different human and 31 different mouse cell types, which were previously collected in a collaborative effort by applying the Cell Surface Capture (CSC, Wollscheid et al, 2009), were used to build the Cell Surface Protein Atlas (CSPA, wlab.ethz.ch/cspa). The combination of these surfaceome datasets revealed nearly 1500 human and 1300 mouse cell surface proteins, which is a five-fold gain compared to the CD antibody panel. Integrated analysis of the CSPA showed that the concerted biological function of individual cell types is mainly guided by quantitative rather than qualitative surfaceome differences. The CSPA is a unique and highly appreciated experimental surfaceome resource demonstrated by 800 monthly website views and an increasing number of citations of the resulted publication. Moreover, the CSPA provided a first blueprint of the interaction space of the surfaceome. To further extend and refine our surfaceome definition, a bioinformatic strategy was developed to create an in silico definition of the surfaceome (chapter 3). Availabe bioinformatics predictions all relied on the same gene annotation databases, which were themselves relying on the limited experimental basis for surfaceome identities, as outlined above. With the CSPA, we had an excellent experimentally validated surfaceome at hand to use as positive training set for a machine learning approach in order to learn characteristic properties of extracellular domains from surfaceome proteins. A model, which incorporated five discriminant biochemical features of extracellular domains of surfaceome proteins was described and then used to predict 2886 potential human surfaceome proteins. On a large cell line panel of 610 cancer cell lines, over 2300 surfaceome genes were found to be expressed in total, with an average of 800 surfaceome genes per cell lines. Interestingly, primary stem cells and their derivatives expressed in average more than twice as many surfaceome proteins. This in silico surfaceome is the first comprehensive and most accurate definition of the surfaceome and is the basis for all future surfaceome interrogations. This resource is available under wlab.ethz.ch/surfaceome, which also provides user-based visualisations of surfaceomes. With the CSPA and the in silico surfaceome, the global and cell type specific identity of the surfaceome was defined, accomplishing the first step towards a system-wide understanding of the surfaceome. ii The next step in the systemic assessment of the surfaceome was to investigate the surfaceome interaction network. Since current protein-protein interaction (PPI) technologies were hardly applicable to cell surface proteins, it was necessary to develop and tailor PPI technologies to specifically target the surfaceome. The concept of radical based biotinylation was applied and combined with hydrazide chemistry to first functionalize and than target glycans at the cell surface. The Proximity Radical Tagging (PRT) technology was established in order to reveal lateral surfaceome interactions of specific receptors (chapter 4). Proof-of-concept applications, like the detection of proteins associated with lipid rafts and heterodimer partners from Erbb2 and the toll-like receptors demonstrated that PRT is very sensitive and able to reveal proximity information of surfaceome members (chapter 4). PRT was then used to investigate the nanoscale organization of the surfaceome in a larger scale on different cell lines (chapter 5). Several cell surface proteins were targeted by PRT and evidence was found that certain lateral surfaceome neighbourhoods change between cell types, whereas other interactions are stable. It was further demonstrated that the strength of the interaction and probably also a distance constraint could be revealed by appropriate experimental setup. The PRT technology opens for the first time the possibility to accomplish the last step of a systemic elucidation of the surfaceome. Further interrogations of the surfaceome interaction network will reveal new mechanistic and functional insight into the surfaceome with crucial implications for the development of novel therapeutics, as for example multitarget drugs. In summary, the first experimental and bioinformatic definition of the surfaceome was achieved, outlining the protein repertoire of the surfaceome. Further, a tailored technology for the investigation of the lateral nanoscale organization and the interconnectivity of the surfaceome was developed. The CSPA and the in silico surfaceome are both provided as tools for the community, for the rediscovery of surfaceome proteins. The PRT technology allows for systematic, large-scale surfaceome interaction screens in order to further elucidate the functional consequences of dynamic nanoscale changes at the cell surface.
  • N-Glycoprotein SRMAtlas
    Item type: Journal Article
    Hüttenhain, Ruth; Surinova, Silvia; Ossola, Reto; et al. (2013)
    Molecular & Cellular Proteomics
    Protein biomarkers have the potential to transform medicine as they are clinically used to diagnose diseases, stratify patients, and follow disease states. Even though a large number of potential biomarkers have been proposed over the past few years, almost none of them have been implemented so far in the clinic. One of the reasons for this limited success is the lack of technologies to validate proposed biomarker candidates in larger patient cohorts. This limitation could be alleviated by the use of antibody-independent validation methods such as selected reaction monitoring (SRM). Similar to measurements based on affinity reagents, SRM-based targeted mass spectrometry also requires the generation of definitive assays for each targeted analyte. Here, we present a library of SRM assays for 5568 N-glycosites enabling the multiplexed evaluation of clinically relevant N-glycoproteins as biomarker candidates. We demonstrate that this resource can be utilized to select SRM assay sets for cancer-associated N-glycoproteins for their subsequent multiplexed and consistent quantification in 120 human plasma samples. We show that N-glycoproteins spanning 5 orders of magnitude in abundance can be quantified and that previously reported abundance differences in various cancer types can be recapitulated. Together, the established N-glycoprotein SRMAtlas resource facilitates parallel, efficient, consistent, and sensitive evaluation of proposed biomarker candidates in large clinical sample cohorts.
  • Retracted: Integrin-Mediated Signaling Induced by Simian Virus 40 Leads to Transient Uncoupling of Cortical Actin and the Plasma Membrane
    Item type: Journal Article
    Stergiou, Lilli; Bauer, Manuel; Mair, Waltraud; et al. (2013)
    PLoS ONE
    Simian Virus 40 (SV40) is a paradigm pathogen with multivalent binding sites for the sphingolipid GM1, via which it induces its endocytosis for infection. Here we report that SV40 also utilizes cell surface integrins to activate signaling networks required for infection, even in the absence of the previously implicated glycosphingolipids. We identify ILK, PDK1, the RhoGAP GRAF1 and RhoA as core nodes of the signaling network activated upon SV40 engagement of integrins. We show that integrin-mediated signaling through host SV40 engagement induces the de-phosphorylation of Ezrin leading to uncoupling of the plasma membrane and cortical actin. Our results provide functional evidence for a mechanism by which SV40 activates signal transduction in human epithelial cells via integrins in the context of clathrin-independent endocytosis.
Publications 1 - 10 of 10