Tracking global gene expression responses in T cell differentiation

Upon receiving antigens from the innate immune cells, CD4(+) T cells differentiate into distinct effector cells. To probe the global responses of distinct effector cells, we analyzed transcriptome-wide expressions of Th-1, Th-2, T-reg and Th-17 using Pearson correlation, entropy and principal component analyses, with Th-0 as a control. Although the global response of Th-0 was quite distinct from Th-17, surprisingly, it was highly similar to Th-1, Th-2 and T-reg. Moreover, 8 major temporal groups consisting of 5704 differentially expressed genes were revealed for both Th-0 and Th-17. Gene functional enrichment analysis showed immune responses and metabolic processes were mainly activated between Th-0 and Th-17, while genes related to cell cycle and replication were differentially regulated. Moreover, we found the upregulation of several novel genes for Th-0 and Th-17. Overall, we deduce that Th-0 is globally similar to Th-1, Th-2 and T-reg. Our results indicate that Th-0 is a differentiated state and, therefore, may not be used as a control cell type. (C) 2015 Elsevier B.V. All rights reserved.