Identification of T cell-restricted genes, and signatures for different T cell responses, using a comprehensive collection of microarray datasets

T Chtanova, R Newton, SM Liu, L Weininger… - The Journal of …, 2005 - journals.aai.org
T Chtanova, R Newton, SM Liu, L Weininger, TR Young, DG Silva, F Bertoni, A Rinaldi…
The Journal of Immunology, 2005journals.aai.org
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 αβ+ and γδ+, 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 …
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 αβ+ and γδ+, 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 γδ T cells expressed no unique gene transcripts, but did differ from αβ 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.
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