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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.

Type Journal
ISBN 0022-1767 (Print)
Authors Chtanova, T.;Newton, R.;Liu, S. M.;Weininger, L.;Young, T. R.;Silva, D. G.;Bertoni, F.;Rinaldi, A.;Chappaz, S.;Sallusto, F.;Rolph, M. S.;Mackay, C. R. :
Publisher Name J IMMUNOL
Published Date 2005-01-01 00:00:00
Published Volume 175
Published Issue 12
Published Pages 7837-47
URL http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16339519
Status Published In-print