SRA

Autoimmune disease is caused by environmental and genetic factors. Genetic factors associated with increased susceptibility to multiple sclerosis (MS), an autoimmune disease of the central nervous system, have been identified, but their mechanisms of action are incompletely understood.(Briggs, 2019) We previously established that the association between MS risk and the interleukin-7 receptor-a gene (IL7R) is mediated by alternative splicing of IL7R transcripts.(Gregory et al., 2007) This splicing is regulated by the RNA helicase DEAD Box Polypeptide 39B (DDX39B), which shows genetic and functional epistasis with IL7R in enhancing MS risk (Galarza-Munoz et al., 2017). Here we discover that DDX39B, which is also known by immunologists as BAT1 (Spies et al., 1989), impacts the expression of many genes likely to play roles in autoimmunity.(Allcock et al., 2001; Degli-Esposti et al., 1992) We show that DDX39B controls expression of Forkhead Box P3 (FOXP3), a master regulator of the development, maintenance and function of CD4+/CD25+ T regulatory cells(Georgiev et al., 2019; Josefowicz et al., 2012) and repressor of autoimmunity (Bennett et al., 2001; Brunkow et al., 2001; Chatila et al., 2000; Wildin et al., 2001). Splicing of FOXP3 introns, which belong to a new subclass of introns with C-rich polypyrimidine tracts, was exquisitely sensitive to DDX39B levels, making FOXP3 expression highly sensitive to the levels of this RNA helicase. Low DDX39B levels in primary human T regulatory cells lead to loss of regulatory gene expression and cytokine signatures and gain of effector ones. Given the importance of FOXP3 in autoimmunity, this work cements DDX39B as a critically important guardian of immune tolerance that can reduce autoimmune disease risk by regulating IL7R splicing and upregulating FOXP3. Overall design: Primary human CD4 positive T cells from two donors were activated with anti-CD3 and anti-CD28. After two days the cells were transduced with with lentiviruses coding non-targeting control or DDX39B (Sh3 or Sh5) shRNAs for 3 days. After 4 more days of selection with puromycin and one day without drug, RNA was isolated for analysis.