Tracking global gene expression responses in T cell differentiation

Oriane Simeoni, Vincent Piras, Masaru Tomita, Kumar Selvarajoo

Research output: Contribution to journalArticlepeer-review

11 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)259-266
Number of pages8
JournalGene
Volume569
Issue number2
DOIs
Publication statusPublished - 2015 Sep 15

Keywords

  • Correlation analysis
  • Entropy
  • Gene Ontology
  • Gene expression
  • Principal component analysis
  • RNA-seq
  • T-cell differentiation
  • Transcriptomics

ASJC Scopus subject areas

  • Genetics

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