Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature

Abstract

The transcriptional activation and repression during NK cell ontology are poorly understood. Here, using single-cell RNA-sequencing, we reveal a novel role for T-bet in suppressing the immature gene signature during murine NK cell development. Based on transcriptome, we identified five distinct NK cell clusters and define their relative developmental maturity in the bone marrow. Transcriptome-based machine-learning classifiers revealed that half of the mTORC2-deficient NK cells belongs to the least mature NK cluster. Mechanistically, loss of mTORC2 results in an increased expression of signature genes representing immature NK cells. Since mTORC2 regulates the expression of T-bet through AktS473-FoxO1 axis, we further characterized the T-bet-deficient NK cells and found an augmented immature transcriptomic signature. Moreover, deletion of Foxo1 restores the expression of T-bet and corrects the abnormal expression of immature NK genes. Collectively, our study reveals a novel role for mTORC2-AktS473-FoxO1-T-bet axis in suppressing the transcriptional signature of immature NK cells.

Transcriptional Regulation of NK Cell Development by mTOR Complexes

“…Single-cell RNA-sequencing technology has provided us an unprecedented insight into the transcriptomic profiles of NK cell heterogeneity and development (Crinier et al, 2018;Yang et al, 2019;Dogra et al, 2020). Using this approach, the transcriptional regulations mediated by mTORC1 and mTORC2 were recently determined (Yang et al, 2020).…”

“…Distribution of each NK clusters along the pseudotime trajectory. Data presented are adapted from Yang et al, 2020. and maturation (Townsend et al, 2004;Intlekofer et al, 2005;Gordon et al, 2012). Both contain highly conserved DNA-binding domains, indicating they bind to the same transcription factor-binding motifs.…”

“…The precise molecular mechanism by which mTORC2 regulates NK cell development and functions and the interplay between mTORC1 and mTORC2 in NK cells are under active investigations. Recent studies have established the requirement of mTORC2 function in NK cell development ( Marcais and Walzer, 2014 ; Marcais et al, 2014 , 2017 ; Yang et al, 2018 , 2020 ). Under homeostatic conditions, both mTORC1 and mTORC2 are activated at relatively higher levels in iNK cells compared to mature NK cells ( Marcais et al, 2017 ).…”

“…The evolving transcriptome of developing mouse and human NK cells has recently deciphered ( Crinier et al, 2018 ; Yang et al, 2018 , 2019 , 2020 ). These studies provide the opportunity to identify the transcriptional activation or repression during NK cell ontology.…”

Enhanced Efficacy of Simultaneous PD-1 and PD-L1 Immune Checkpoint Blockade in High-Grade Serous Ovarian Cancer

“…CDK9 is, in part, recruited to immune genomic loci by TBX21 as part of the PTef-b complex(44), and CDK9 inhibition allows global reactivation of epigenetically silenced genes leading to increased IFN activity and sensitivity to ICB agents in tumor cells(45). In addition, BAY-299 reduces chromatin accessibility of EMB (Figure 7C top), another TBX21 regulated gene recently identified as a marker of immature NK cells and as part of an immature NK cell signature(46). Taken together, these findings suggest that a possible BRD1 inhibitor mechanism of action is altering chromatin accessibility for major NK cell regulatory transcription factors at key immune modulatory genes to allow for a mature (EMB) active and cytotoxic (CDK9) state.Research.on November 24, 2020.…”