“…Focusing on the gene expression data, we found that different combinations of the four TFs led to increased expression of several genes involved in the regulation of T cell homeostasis, activation, proliferation, differentiation and function (Figure 4A ), such as IRF family members ( Irf1 , Irf2 , Irf5 , Irf7 and Irf9 (Hammami et al, 2015; Hida et al, 2000; Martinet et al, 2015; Simon et al, 1997; Zhou et al, 2012)), JAK-STAT signaling pathway members ( Jak1 , Jak2 , Stat1 , Stat2 and Stat5a (Seif et al, 2017)), SOCS family members ( Socs1 , Socs2 and Socs4 (Palmer and Restifo, 2009) ), cytokine signaling ( Tgfb1 , Il2rb , Ifngr1 and Il17ra (Curtsinger et al, 2012; Oh and Li, 2013; Ross and Cantrell, 2018; Tosello Boari et al, 2018)) and other factors ( Atf3 , Batf2 , Ets2 , Gadd45a , Klf4 , etc. (Filén et al, 2010; Kayama et al, 2019; Salvador et al, 2005; Yamada et al, 2009; Zaldumbide et al, 2002)). To more systematically evaluate these transcriptional effects, we created a gene signature consisting of genes that are the most differentially expressed (up or down) between untreated fibroblasts and CD8+ T cells (using DESeq2; see Methods ).…”