A Mass Spectrometric-Derived Cell Surface Protein Atlas

Abstract

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.

A Combined Omics Approach to Generate the Surface Atlas of Human Naive CD4+ T Cells during Early T-Cell Receptor Activation

“…However, very recently, Bausch-Fluck et al published a massspectrometry-derived cell surface protein atlas providing a surfaceome snapshot of 78 different human and murine cellular species. Among them a mixed CD4 ϩ /CD25 Ϫ T-cell population is listed, which contains nonactivated, naive as well as memory T cells (40). This population can be clearly distinguished from the pure naive CD4 ϩ /CD45RA ϩ T-cell population, which are investigated in the current manuscript, and has no further focus on the activation process.…”

Mass Spectrometry-Based Identification of Extracellular Domains of Cell Surface N-Glycoproteins: Defining the Accessible Surfaceome for Immunophenotyping Stem Cells and Their Derivatives

“…This work-flow enables comparisons of cell surface N-glycoproteins observed among various experimental conditions (e.g., cell types, organ types, and developmental stages). We maintain an in-house repository of data from three sources: data generated in-house, data from the Cell Surface Protein Atlas (Atlas [24]; downloaded from http://wlab.ethz.ch/cspa/), and data from other publications that may not be contained in the Atlas. While proteins of interest for distinguishing cellular phenotypes can be identified by directly including the desired cell types for comparison within a quantitative CSC-Technology experiment, the Atlas may still add value as a freely available repository populated with data from a variety of cell types.…”

“…Given the power of this approach, CSC-Technology data from over 80 mouse and human cell types (normal and diseased) have now been deposited into a publicly accessible repository, the Cell Surface Protein Atlas (CSPA; http://wlab.ethz.ch/cspa/) [24]. When these data are analyzed comparatively, classification of a particular protein as routinely vs. rarely observed among cell types can be made immediately.…”

“…Although the presence of a protein among disparate cell types may not preclude its utility for a specific context in vitro, this type of analysis can rapidly focus a candidate list from hundreds to tens in cases where a cell type specific marker is desired. In cases where proteins unique to a single cell type are rare, it is expected that panels of surface markers will be necessary for adequate barcoding and sorting well-defined cell populations [24, 25], and in this context the CSPA is also valuable for highlighting potential marker combinations that can be further examined in the next step (Fig. 1).…”

“…We have used this strategy to identify markers and to generate new antibodies for a variety of stem cells and their progeny, including: selecting pluripotent stem cell-derived hepatocytes [28] and cardiomyocytes ([29] and in preparation ); isolating induced pluripotent stem cells reprogrammed from mouse fibroblasts [30]; and identifying proteins in human pluripotent stem cells that can be targeted by small molecules for the purpose of eliminating tumorigenic cells [25]. Although our previous work and this chapter have focused on stem cells, the approach is equally applicable to other mammalian cell types, as demonstrated by others [16, 20, 24, 31–33], and variations of this approach that rely on cysteine or lysine containing peptides have also been described [31]. …”