Integrative scATAC-seq and scRNA-seq analyses map thymic iNKT cell development and identify Cbfβ for its commitment

Authors

Jie Wang, Henry Ford HealthFollow
Indra Adrianto, Henry Ford HealthFollow
Kalpana Subedi, Henry Ford HealthFollow
Tingting Liu, Henry Ford HealthFollow
Xiaojun Wu, Henry Ford HealthFollow
Qijun Yi, Henry Ford HealthFollow
Ian Loveless, Henry Ford HealthFollow
Congcong Yin, Henry Ford HealthFollow
Indrani Datta, Henry Ford HealthFollow
Derek B. Sant'Angelo
Mitchell Kronenberg
Li Zhou, Henry Ford HealthFollow
Qing-Sheng Mi, Henry Ford HealthFollow

Recommended Citation

Wang J, Adrianto I, Subedi K, Liu T, Wu X, Yi Q, Loveless I, Yin C, Datta I, Sant'Angelo DB, Kronenberg M, Zhou L, and Mi QS. Integrative scATAC-seq and scRNA-seq analyses map thymic iNKT cell development and identify Cbfβ for its commitment. Cell Discov 2023; 9(1):61.

Document Type

Article

Publication Date

6-20-2023

Publication Title

Cell Discov

Abstract

Unlike conventional αβT cells, invariant natural killer T (iNKT) cells complete their terminal differentiation to functional iNKT1/2/17 cells in the thymus. However, underlying molecular programs that guide iNKT subset differentiation remain unclear. Here, we profiled the transcriptomes of over 17,000 iNKT cells and the chromatin accessibility states of over 39,000 iNKT cells across four thymic iNKT developmental stages using single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) to define their developmental trajectories. Our study discovered novel features for iNKT precursors and different iNKT subsets and indicated that iNKT2 and iNKT17 lineage commitment may occur as early as stage 0 (ST0) by two distinct programs, while iNKT1 commitments may occur post ST0. Both iNKT1 and iNKT2 cells exhibit extensive phenotypic and functional heterogeneity, while iNKT17 cells are relatively homogenous. Furthermore, we identified that a novel transcription factor, Cbfβ, was highly expressed in iNKT progenitor commitment checkpoint, which showed a similar expression trajectory with other known transcription factors for iNKT cells development, Zbtb16 and Egr2, and could direct iNKT cells fate and drive their effector phenotype differentiation. Conditional deletion of Cbfβ blocked early iNKT cell development and led to severe impairment of iNKT1/2/17 cell differentiation. Overall, our findings uncovered distinct iNKT developmental programs as well as their cellular heterogeneity, and identified a novel transcription factor Cbfβ as a key regulator for early iNKT cell commitment.

PubMed ID

37336875

Volume

9

Issue

1

First Page

61

Last Page

61