SFB granted in 2016 – endeavour of the integrative data analysis going far beyond the current state-of-the-art for JAK-STAT signalling analyses published in 2024

CEMM  |  VETMEDUNI | MPL 

DOI: 10.1038/s41590-024-01804-1

The integrative efforts of all SFB members have produced the following deliverables and often surprising insights into JAK-STAT biology:

  • Transcriptome and epigenome variability in homeostasis of T cells and macrophages isolated from large cohorts of C57BL/6 mice.
  • Tissue context deprivation of immune cells leads to loss of gene signatures driven by JAK-STAT in situ and single cytokine treatment restores multiple JAK-STAT pathways, including those not directly activated by the cytokine’s receptor.
  • STAT1 was previously considered to be the key player in signal transduction of all IFNs, while STAT2 and IRF9 were only seen as constituents of the ISGF3 complex together with STAT1. Our discovery of the dominant role of STAT2 and IRF9 in homeostatic gene expression necessitates a complete revision of this basic tenet of JAK-STAT biology as it cannot be reconciled the previous model of tonic IFN-I receptor signalling.
  • The literature places STAT3 and STAT5, but not other STATs, in the category of ‘master regulator’ TFs with a major impact on the development of cell types. However, we find that STAT2 has a greater impact than STAT3 and STAT5 on homeostatic gene expression. Surprisingly, however, ISGs are among the genes under the homeostatic control of STAT3 and STAT5.
  • Homeostatic gene expression differs significantly between wildtype (WT) cells and cells expressing only the STAT1a isoform. In the presence of only the Stat1b isoform, homeostatic gene expression differs from that of both STAT1a and STAT1 KO cells. Thus, the two isoforms are non-redundant in the maintenance of homeostatic gene expression. These data refute two prevailing concepts: (i) that STAT isoforms are redundant as components of the ISGF3 complex and (ii) that the loss of homeostatic gene expression reflects the loss of a tonic IFN-I receptor signal.
  • All STATs influence tonic gene expression in splenic macrophages and CD8+ T cells. However, none of the STATs except STAT5, not even the master regulator STAT3, have a major impact on chromatin accessibility under cell homeostasis. STAT5 has the expected clear effect in CD8+ T cells, which diminishes in B cells and macrophages. In contrast, myeloid and lymphoid cells expressing the activated STAT5N642H display a clear increase in accessible chromatin, in keeping with the transforming ability of this mutant.
  • Hyperactivated STAT5 activates chromatin regions and genes that are not affected in STAT5-deficient cells. The de novo STAT5 targets might contribute to the leukemic progression observed in vivo.

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Joint last authors (from left to right) Thomas Decker (SFB deputy speaker), Mathias Müller (SFB speaker), Christoph Bock