title: A Combined Omics Approach to Generate the Surface Atlas of Human Naive CD4+ T Cells during Early T-Cell Receptor Activation.
abstract: Naive CD4(+) T cells are the common precursors of multiple effector and memory T-cell subsets and possess a high plasticity in terms of differentiation potential. This stem-cell-like character is important for cell therapies aiming at regeneration of specific immunity. Cell surface proteins are crucial for recognition and response to signals mediated by other cells or environmental changes. Knowledge of cell surface proteins of human naive CD4(+) T cells and their changes during the early phase of T-cell activation is urgently needed for a guided differentiation of naive T cells and may support the selection of pluripotent cells for cell therapy. Periodate oxidation and aniline-catalyzed oxime ligation technology was applied with subsequent quantitative liquid chromatography-tandem MS to generate a data set describing the surface proteome of primary human naive CD4(+) T cells and to monitor dynamic changes during the early phase of activation. This led to the identification of 173 N-glycosylated surface proteins. To independently confirm the proteomic data set and to analyze the cell surface by an alternative technique a systematic phenotypic expression analysis of surface antigens via flow cytometry was performed. This screening expanded the previous data set, resulting in 229 surface proteins, which were expressed on naive unstimulated and activated CD4(+) T cells. Furthermore, we generated a surface expression atlas based on transcriptome data, experimental annotation, and predicted subcellular localization, and correlated the proteomics result with this transcriptional data set. This extensive surface atlas provides an overall naive CD4(+) T cell surface resource and will enable future studies aiming at a deeper understanding of mechanisms of T-cell biology allowing the identification of novel immune targets usable for the development of therapeutic treatments.
authors.affiliation: From the ‡Center of Allergy and Environment (ZAUM), Technische Universität und Helmholtz Zentrum München, Munich, Germany;
authors.forename: Anke
authors.initials: A
authors.lastname: Graessel
authors.affiliation: §Research Unit Protein Science, Helmholtz Zentrum München, Neuherberg, Germany;
authors.forename: Stefanie M
authors.initials: SM
authors.lastname: Hauck
authors.affiliation: §Research Unit Protein Science, Helmholtz Zentrum München, Neuherberg, Germany;
authors.forename: Christine
authors.initials: C
authors.lastname: von Toerne
authors.affiliation: ¶Department of Informatics, Bioinformatics & Computational Biology i12, Technische Universität München, Garching/Munich, Germany; ‖New York Consortium on Membrane Protein Structure (NYCOMPS), New York Structural Biology Center, New York, New York 10027;
authors.forename: Edda
authors.initials: E
authors.lastname: Kloppmann
authors.affiliation: ¶Department of Informatics, Bioinformatics & Computational Biology i12, Technische Universität München, Garching/Munich, Germany; **TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Technische Universität München, Munich, Germany;
authors.forename: Tatyana
authors.initials: T
authors.lastname: Goldberg
authors.affiliation: ‡‡Institute of Virology, Helmholtz Zentrum München, Neuherberg, Germany;
authors.forename: Herwig
authors.initials: H
authors.lastname: Koppensteiner
authors.affiliation: ‡‡Institute of Virology, Helmholtz Zentrum München, Neuherberg, Germany; §§Institute of Medical Virology and Epidemiology of Viral Diseases, University Clinic Tübingen, Tübingen, Germany;
authors.forename: Michael
authors.initials: M
authors.lastname: Schindler
authors.affiliation: ¶¶Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany;
authors.forename: Bettina
authors.initials: B
authors.lastname: Knapp
authors.affiliation: ¶¶Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany;
authors.forename: Linda
authors.initials: L
authors.lastname: Krause
authors.affiliation: From the ‡Center of Allergy and Environment (ZAUM), Technische Universität und Helmholtz Zentrum München, Munich, Germany; ‖‖DZL- Member of the German Lung Research Center.
authors.forename: Katharina
authors.initials: K
authors.lastname: Dietz
authors.affiliation: From the ‡Center of Allergy and Environment (ZAUM), Technische Universität und Helmholtz Zentrum München, Munich, Germany; ‖‖DZL- Member of the German Lung Research Center.
authors.forename: Carsten B
authors.initials: CB
authors.lastname: Schmidt-Weber
authors.affiliation: From the ‡Center of Allergy and Environment (ZAUM), Technische Universität und Helmholtz Zentrum München, Munich, Germany; ‖‖DZL- Member of the German Lung Research Center Kathrin.Suttner@lrz.tum.de.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Suttner
mesh_terms: D015496:CD4-Positive T-Lymphocytes / Q000378:metabolism*; D002462:Cell Membrane / Q000378:metabolism; D016000:Cluster Analysis; D003198:Computer Simulation; D005434:Flow Cytometry; D020869:Gene Expression Profiling; D063990:Gene Ontology; D006023:Glycoproteins / Q000378:metabolism; D006801:Humans; D008213:Lymphocyte Activation / Q000276:immunology*; D020543:Proteome / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D011948:Receptors, Antigen, T-Cell / Q000378:metabolism*; D015203:Reproducibility of Results; D059467:Transcriptome / Q000235:genetics
chemical_list: D006023:Glycoproteins; D020543:Proteome; D011948:Receptors, Antigen, T-Cell