scRNAseq of CNS-infiltrating T cells from EAE-affected wt C57BL6 mice or littermate controls heterozygous or homozygous for a gene variant orthologous for the human polymorphism HDAC7 R166H

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. wt, HDAC7 ki/wt or HDAC7 ki/ki littermate controls were immunized with MOG35-55 to induce experimental autoimmune encephalomyelitis (EAE). After 14 days, mice were sacrificed and brains and spinal cords were harvested. CNS-infiltrating T cells were FACS-sorted and used for t single-cell transcriptomic analysis.