Comparative Microarray Analysis of Gene Expression During Activation of Human Peripheral Blood T Cells and Leukemic Jurkat T Cells

Abstract

SUMMARY: Activation of T cells involves a complex cascade of signal transduction pathways linking T-cell receptorengagement at the cell membrane to the transcription of multiple genes within the nucleus. The T-cell leukemia-derived cell line Jurkat has generally been used as a model system for the activation of T cells. However, genome-wide comprehensive studies investigating the activation status, and thus the appropriateness, of this cell line for this purpose have not been performed. We sought to compare the transcriptional profiles of phenotypically purified human CD2 ϩ T cells with those of Jurkat T cells during T-cell activation, using cDNA microarrays containing 6912 genes. About 300 genes were up-regulated by more than 2-fold during activation of both peripheral blood (PB) T cells and Jurkat T cells. The number of down-regulated genes was significantly lower than that of up-regulated genes. Only 79 genes in PB T cells and 37 genes in Jurkat T cells were down-regulated by more than 2-fold during activation. Comparison of gene expression during activation of Jurkat and PB T cells revealed a common set of genes that were up-regulated, such as Rho GTPase-activating protein 1, SKP2, CDC25A, T-cell specific transcription factor 7, cytoskeletal proteins, and signaling molecules. Genes that were commonly down-regulated in both PB T cells and Jurkat T cells included CDK inhibitors (p16, p19, p27), proapoptotic caspases, and the transcription factors c-fos and jun-B. After activation, 71 genes in PB T cells and only 3 genes in Jurkat T cells were up-regulated 4-fold or more. Of these up-regulated genes and expressed sequence tags, 44 were constitutively expressed at high levels in nonactivated Jurkat cells. Quantitative real-time RT-PCR analysis confirmed our microarray data. Our findings indicate that although there is significant overlap in the activation-associated transcriptional profiles in PB T cells compared with Jurkat T cells, there is a subset of genes showing differential expression patterns during the activation of the two cell types. (Lab Invest 2003, 83:765-776).

Alternative splicing networks regulated by signaling in human T cells

“…In the present study, of 10,374 genes for which we obtained reliable sequence coverage in either resting or stimulated cells (10 or more reads per 50 bp of gene length), 312 exhibit a change of twofold or greater in mRNA expression between resting and stimulated cells (Supplemental Table S3). As observed in previous studies profiling gene expression in T cells (Lin et al 2003;Ip et al 2007), we observe that a larger number of genes are up-regulated upon stimulation than are repressed (207 vs. 115). Importantly, further consistent with our previous studies (Ip et al 2007), none of the 178 differentially spliced exons are located within this set of 312 transcriptionally regulated genes.…”

Global analysis of alternative splicing during T-cell activation

“…Widespread changes in transcription in response to T-cell activation have long been known to occur and have been extensively studied by others Lin et al 2003;Hess et al 2004). However, surprisingly, our data also reveal extensive regulation of AS upon stimulation of T cells.…”

“…However, there are aspects of gene regulation and cellular function that differ between T-cell-derived lines and primary T cells (Lin et al 2003). For example, Jurkat cells are defective in the expression of two lipid phosphatases, PTEN and SHIP, leading to the constitutive activation of the kinases PI3K and ITK (Abraham and Weiss 2004).…”

“…The probe signals are analyzed by the generative model for the alternative splicing array platform (GenASAP) algorithm, which predicts the percent exclusion level (%ex) for each alternative exon and also provides a rank as a confidence score for each prediction (Pan et al 2004;Shai et al 2006). In order to gain a broader understanding of the immune system, additional probes were included on the microarray to monitor AS events that are associated with genes known to be involved in eliciting an immune response, as well as genes reported to have increased levels of expression during T-cell activation (Teague et al 1999;Raghavan et al 2002;Lin et al 2003;Lynch 2004).…”

“…During the past decade, microarray analyses have detected global transcriptional changes during T-cell activation both in vivo and in vitro Lin et al 2003;Hess et al 2004). These studies identified many genes that are differentially expressed in resting and activated T cells and have greatly enhanced our knowledge of the factors that are essential to elicit an immune response.…”