Dissecting the dynamic Q2 Q1 transcriptional landscape of early T helper cell differentiation into Th1, Th2, and Th1/2 hybrid cells

CD4+ T cell differentiation is a key element of the adaptive immune system driving appropriate immune responses by selective differentiation into specialized subsets such as Th1 and Th2 cells. Besides those canonical Th cell lineages, hybrid phenotypes such as Th1/2 cells have been identified in vivo, and their generation could be reproduced in vitro. While master transcription factors like T-bet and GATA-3 regulate and maintain differentiation into the canonical lineages, the transcriptional architecture of hybrid phenotypes is less well understood. In particular, it remains unclear whether a hybrid phenotype implies a mixture of the effects of several canonical lineages for each gene, or rather a bimodal behavior across genes. Th cell differentiation is a dynamic process in which the regulatory factors are modulated over time, but longitudinal studies of Th cell differentiation are sparse. Here, we present a dynamic transcriptome analysis following Th cell differentiation into Th1, Th2 and Th1/2 hybrid cells. We found that only a minority of ~20% of Th cell specific genes clearly shows mixed effects from both Th1 and Th2 cells on Th1/2 hybrid cells. While most genes follow either Th1 or Th2 cell gene expression, another fraction of ~20% of genes follows a Th1 and Th2 cell independent transcriptional program under control of the transcription factors STAT1 and STAT4. Overall, our results emphasize the key role of high-resolution longitudinal data for the characterization of cellular phenotypes. Time course microarray data for Th1, Th2 and hybrid Th12 differentiation, including Th0 control