Transcriptome and Chromatin Landscape of iNKT cells are Shaped by Subset Differentiation and Antigen Exposure [ATAC-seq]

Invariant natural killer T cells (iNKT cells) differentiate into thymic NKT1, NKT2 and NKT17 subsets that are also peripheral. We determined if the gene programs associated with these thymic subsets were maintained in peripheral sites, the influence of tissue location, and if there were large-scale changes after antigen exposure. RNA-seq and ATAC-seq analyses showed that iNKT cells in any subset were similar, regardless of tissue location. Lung iNKT cell subsets shared the most distinct location-specific features, shared with other innate lymphocytes in the lung, possibly consistent with increased activation. After antigenic stimulation, iNKT cells underwent chromatin and transcription changes leading to two populations: one similar to follicular helper T cells and the other like NK cells. Phenotypic analysis indicated these changes were observed long-term, suggesting that iNKT cells gene programs are not fixed, but they are capable of chromatin remodeling after antigen to give rise to several new subsets. Overall design: Transcriptome and epigenome analysis of NKT cell subsets isolated from thymus, spleen, lung and liver from unchallenged C57Bl/6J mice, as well as splenic NKT cells isolated from mice 6d post-challenge with the strong NKT agonist alpha-galactosyl-ceramide.