ePoster Presentation 49th Annual Scientific Meeting of the Australian and New Zealand Society for Immunology 2021

Discovery and functional validation of an autoimmune disease linked super-enhancer that regulates SATB1 (#218)

Katherine A Brown 1 2 , Ying Ying Wong 1 2 , Veronika K Bandara 1 2 , John E Schjenken 3 4 , Stephen Pederson 5 , Jimmy Breen 5 , Marc Beyer 6 , Joachim L. Schultze 7 , Sarah Robertson 4 , Tim Sadlon 1 2 , Simon C Barry 1 2
  1. Molecular Immunology , Robinson Research Institute, The University of Adelaide, North Adelaide, SA, Australia
  2. Department of Paediatrics, Women's and Children's Hospital, North Adelaide, SA, Australia
  3. Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW, Australia
  4. Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
  5. The University of Adelaide, Adelaide, SA, Australia
  6. Molecular Immunology, DZNE, German Center for Neurodegenerative Diseases, Bonn, Germany
  7. Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany

The molecular mechanisms driving autoimmunity (AI) are poorly understood but are thought to involve both genetic and environmental factors. Few AI associated genetic-risk loci are linked to alterations in gene coding, but are found frequently in T cell restricted enhancers. This links AI-associated variation to disruption of normal transcriptional control of the enhancers’ target genes.

SATB1 is a genome organizer that is important in T cell lineage commitment and function. We used Chromatin conformation capture to identify a super-enhancer (SE) -308kb upstream of the SATB1 promoter in human primary CD4+ T cells. The SE resides in a hotspot for AI-associated genetic variation in Crohns/IBD, psoriasis and MS. Together, this indicates that altered enhancer activity and hence inappropriate regulation of SATB1 in T cells may be the mechanism by which these risk regions contribute to AI.

To model the function of this super-enhancer in the physiological context, CRISPR was used to delete the SE region in mice. Analysis of CD4+ T cells revealed reduced SATB1 protein levels and a significant decrease in the ability of naïve CD4+ T cells to polarize toward Th1 and Th17 subsets, but a significant increase in IL-5 production from Th2 polarized cells. RNA-seq and ATAC-seq analysis of SE-/-CD4+ T cells identified changes in the transcriptome and chromatin accessibility at multiple loci, including the SATB1 locus. Using an in vivo CD45RBhiCD4+ T cell transfer model of colitis, we have shown that SE-/- mice do not develop colitis, but instead present with a skin phenotype characterized by increased immune infiltration into the skin.

These data indicate that loss of the super-enhancer, likely through decreasing SATB1 expression, causes widespread changes in the CD4+ cell transcriptome and altered cellular responses, and this may for the first time identify the immunological pathways impacted by the associated AI genetic-risk.