title: Identification of T cell-restricted genes, and signatures for different T cell responses, using a comprehensive collection of microarray datasets.
abstract: We used a comprehensive collection of Affymetrix microarray datasets to ascertain which genes or molecules distinguish the known major subsets of human T cells. Our strategy allowed us to identify the genes expressed in most T cell subsets: TCR alphabeta+ and gammadelta+, three effector subsets (Th1, Th2, and T follicular helper cells), T central memory, T effector memory, activated T cells, and others. Our genechip dataset also allowed for identification of genes preferentially or exclusively expressed by T cells, compared with numerous non-T cell leukocyte subsets profiled. Cross-comparisons between microarray datasets revealed important features of certain subsets. For instance, blood gammadelta T cells expressed no unique gene transcripts, but did differ from alphabeta T cells in numerous genes that were down-regulated. Hierarchical clustering of all the genes differentially expressed between T cell subsets enabled the identification of precise signatures. Moreover, the different T cell subsets could be distinguished at the level of gene expression by a smaller subset of predictor genes, most of which have not previously been associated directly with any of the individual subsets. T cell activation had the greatest influence on gene regulation, whereas central and effector memory T cells displayed surprisingly similar gene expression profiles. Knowledge of the patterns of gene expression that underlie fundamental T cell activities, such as activation, various effector functions, and immunological memory, provide the basis for a better understanding of T cells and their role in immune defense.
authors.affiliation: Garvan Institute of Medical Research, Darlinghurst, Australia.
authors.forename: Tatyana
authors.initials: T
authors.lastname: Chtanova
authors.forename: Rebecca
authors.initials: R
authors.lastname: Newton
authors.forename: Sue M
authors.initials: SM
authors.lastname: Liu
authors.forename: Lilach
authors.initials: L
authors.lastname: Weininger
authors.forename: Timothy R
authors.initials: TR
authors.lastname: Young
authors.forename: Diego G
authors.initials: DG
authors.lastname: Silva
authors.forename: Francesco
authors.initials: F
authors.lastname: Bertoni
authors.forename: Andrea
authors.initials: A
authors.lastname: Rinaldi
authors.forename: Stephane
authors.initials: S
authors.lastname: Chappaz
authors.forename: Federica
authors.initials: F
authors.lastname: Sallusto
authors.forename: Michael S
authors.initials: MS
authors.lastname: Rolph
authors.forename: Charles R
authors.initials: CR
authors.lastname: Mackay
mesh_terms: D016000:Cluster Analysis; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000276:immunology; D006801:Humans; D007156:Immunologic Memory / Q000235:genetics; D008213:Lymphocyte Activation / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000032:analysis; D016176:T-Lymphocyte Subsets / Q000276:immunology / Q000502:physiology
chemical_list: D012333:RNA, Messenger