Transcriptome and chromatin landscape of iNKT cells are shaped by subset differentiation and antigen exposure

Mallory Paynich Murray,James P Scott-Browne,Sara Herrera-De La Mata,Goo-Young Seo,Mitchell Kronenberg,Jason Greenbaum,Isaac Engel,Sandy Lucette Rosales,Ashu Sethi,Pandurangan Vijayanand,Grégory Seumois,Ashmitaa Logandha Ramamoorthy Premlal

doi:10.1038/s41467-021-21574-w

Abstract

Invariant natural killer T cells (iNKT cells) differentiate into thymic and peripheral NKT1, NKT2 and NKT17 subsets. Here we use RNA-seq and ATAC-seq analyses and show iNKT subsets are similar, regardless of tissue location. Lung iNKT cell subsets possess the most distinct location-specific features, shared with other innate lymphocytes in the lung, possibly consistent with increased activation. Following antigenic stimulation, iNKT cells undergo chromatin and transcriptional changes delineating two populations: one similar to follicular helper T cells and the other NK or effector like. Phenotypic analysis indicates these changes are 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 additional subsets.

Highlights

Invariant natural killer T cells differentiate into thymic and peripheral NKT1, NKT2 and NKT17 subsets
Because the epigenetic landscape of a cell population is more stable than the transcriptome, we analyzed the epigenetic landscape of thymic Invariant natural killer T (iNKT) cell subsets more broadly with the assay for transposase-accessible chromatin using sequencing (ATAC-seq)[13]
We used a different RNA-seq technology allowing for greater sequencing depth[19], we found exceedingly similar gene expression profiles in thymic NKT1, NKT2, and NKT17 thymocytes compared to the previous study[8] (Supplementary Fig. 2)

Summary

Introduction

Invariant natural killer T cells (iNKT cells) differentiate into thymic and peripheral NKT1, NKT2 and NKT17 subsets. INKT cells differentiate into three effector cell subsets, NKT1, NKT2, and NKT17, without exposure to exogenous antigen Their effector functions and cytokine profiles resemble TH1, TH2, and TH17 CD4+ T cells and subsets of other lymphocytes, including ILC, mucosal-associated invariant T (MAIT) cells, and γδ T cells[3,4,5]. We and others have defined the molecular details of iNKT cell subset differentiation using genome-wide analyses of gene expression and chromatin accessibility[7,8,11,12] These data identified the induction and divergence of transcriptional programs between thymic iNKT cell subsets, but the impact of tissue localization on these programs remains incompletely understood. Our genome-wide analysis of the transcriptome and epigenome of iNKT cell subsets provides insights into the stability and plasticity of the chromatin landscapes that are initiated in the thymus and perhaps initiated peripherally as well

Methods

Results

Conclusion