title: Tracking global gene expression responses in T cell differentiation.
abstract: 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 Th1, Th2, Treg and Th17 using Pearson correlation, entropy and principal component analyses, with Th0 as a control. Although the global response of Th0 was quite distinct from Th17, surprisingly, it was highly similar to Th1, Th2 and Treg. Moreover, 8 major temporal groups consisting of 5704 differentially expressed genes were revealed for both Th0 and Th17. Gene functional enrichment analysis showed immune responses and metabolic processes were mainly activated between Th0 and Th17, while genes related to cell cycle and replication were differentially regulated. Moreover, we found the upregulation of several novel genes for Th0 and Th17. Overall, we deduce that Th0 is globally similar to Th1, Th2 and Treg. Our results indicate that Th0 is a differentiated state and, therefore, may not be used as a control cell type.
authors.affiliation: ENSEIRB-MATMECA, Bordeaux Institute of Technology, Talence, France; Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
authors.forename: Oriane
authors.initials: O
authors.lastname: Simeoni
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.
authors.forename: Vincent
authors.initials: V
authors.lastname: Piras
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan. Electronic address: kumar@ttck.keio.ac.jp.
authors.forename: Kumar
authors.initials: K
authors.lastname: Selvarajoo
mesh_terms: D000818:Animals; D051379:Mice; D008810:Mice, Inbred C57BL; D011948:Receptors, Antigen, T-Cell; D013601:T-Lymphocytes / Q000166:cytology* / Q000378:metabolism*; D006377:T-Lymphocytes, Helper-Inducer / Q000145:classification / Q000166:cytology* / Q000378:metabolism
chemical_list: D011948:Receptors, Antigen, T-Cell
keywords: Correlation analysis; Entropy; Gene Ontology; Gene expression; Principal component analysis; RNA-seq; T-cell differentiation; Transcriptomics