iNKT cells differentiate into three effector cell subsets in the thymus, NKT1, NKT2, and NKT17, which closely resemble subsets of Th1, Th2, and Th17 CD4⁺ T cells, as well as ILC1, ILC2, and ILC3 innate lymphoid cells, respectively. Recent work from our lab and others recently determined that thymic iNKT cell subsets have a highly divergent epigenetic landscape and gene program.  Following egress from the thymus, iNKT cells localize to tissues throughout the body and many do not recirculate.  Although the phenotype and localization of iNKT cells in the periphery has been established, how tissue localization impacts the epigenetic landscape of each subset is not known.  Here, we assess global chromatin accessibility in iNKT cell subsets in peripheral tissues including the spleen, lymph nodes, and liver, as well as the lung, where they provide vital immunity to bacterial infections.  To do this, we utilized an assay for transposase-accessible chromatin using sequencing (ATAC-seq).  With ATAC-seq, we are identifying regions of open chromatin and nucleosome-bound and nucleosome-free positions in regulatory regions.  Future experiments will determine the impact of tissue localization on the gene regulatory landscape of iNKT cell subsets, and the degree to which regulatory elements established in the thymus carry over into tissues. Further, we will determine if the tissue microenvironment contributes to priming or activation of these cells.

Supported by NIH R01 AI71922 and T32 AI 125179