Assessment of the global chromatin landscape and transcriptome of peripheral iNKT cell subsets

Abstract

Abstract Vα14i invariant Natural Killer T (iNKT) cells are important modulators of immune responses. They differentiate into three effector cell subsets in the thymus, NKT1, NKT2, and NKT17, which resemble Th1, Th2, and Th17 CD4 T cells. After exiting the thymus, iNKT cells localize to tissues and do not recirculate, but the impact of tissue localization on the epigenetic landscape and transcriptome of each subset is not known. We assessed global chromatin accessibility and transcriptional activity using ATACseq and RNAseq in iNKT cell subsets isolated from the thymus, spleen, liver, and lung. By comparing iNKT cell subsets within each tissue, we found over 5,000 differentially accessible regions of chromatin. This is consistent with previous analyses showing great differences in the transcriptomes of the thymic iNKT cell subsets. Interestingly, relatively limited differences in the accessible chromatin or transcriptome were observed when comparing the same subset from different sites, e.g., NKT1 cells from different tissues. An exception is the unique set of accessible chromatin regions and transcripts identified in all iNKT cell subsets in the lung. Lung iNKT cells exhibited features of increased AP-1 transcription factor activity, which has been correlated with both activation and tissue residency, found in other lung lymphocyte populations. After antigen challenge, an iNKT cell subset with features similar to T follicular helper cells is abundant; these cells are highly different from the other subsets. Taken together, these data indicate that the epigenome and transcriptome of iNKT cells is highly impacted by subset decision, and much less by tissue localization, although dynamic changes occur after antigen exposure.