Bulk RNAseq of human Tregs transduced with a lentivirus encoding a shRNA targeting the HDAC7 gene or a scrambled control

Genome-wide association studies identifying hundreds of susceptibility loci for autoimmune diseases indicate that genes active in immune cells predominantly mediate risk. Identification and functional characterization of causal variants remains challenging. Here, we focused on the immunomodulatory role of a protective variant in HDAC7 (rs148755202, HDAC7.p.R166H), identified in a study of low-frequency coding variation in multiple sclerosis (MS). Through transcriptomic analysis, we demonstrate that HDAC7 regulates genes essential for the function of FoxP3+ regulatory T cells (Tregs), an immunosuppressive subset of CD4 T cells that is dysfunctional in patients with MS. Moreover, Treg cell-specific conditional hemizygous deletion of HDAC7 increases severity of experimental autoimmune encephalitis (EAE), a mouse model of MS. Strikingly, Tregs transduced with the protective HDAC7 R166H variant exhibit higher suppressive capacity in an in vitro functional assay, mirroring functional defects previously observed in patients. In vivo modelling of the human HDAC7 R166H variant, by generation of a knock-in mouse model bearing the orthologous R150H substitution, showed decreased EAE severity linked to transcriptomic alterations of brain infiltrating Tregs as assessed by single cell RNA-seq. Our data suggest that dysregulation of epigenetic modifiers, a novel molecular class associated with disease risk, can influence disease onset. Finally, our approach provides a template for translation of genetic susceptibility loci to detailed functional characterization, using human in vitro and mouse in vivo modelling. CD4+CD25hiCD127lo–neg Tregs are FACS-sorted and stimulated with aCD3/aCD28. On day 1, they are infected with lentiviral pseudoparticles containing HDAC7 or scrambled control shRNAs. After 5 days, GFP+ cells are sorted for transcriptomic analysis