T-BET and EOMES sustain mature human NK cell identity and antitumor function
Pamela Wong, … , Melissa M. Berrien-Elliott, Todd A. Fehniger
Pamela Wong, … , Melissa M. Berrien-Elliott, Todd A. Fehniger
Published June 6, 2023
Citation Information: J Clin Invest. 2023;133(13):e162530. https://doi.org/10.1172/JCI162530.
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Research Article Immunology

T-BET and EOMES sustain mature human NK cell identity and antitumor function

Abstract

Since the T-box transcription factors (TFs) T-BET and EOMES are necessary for initiation of NK cell development, their ongoing requirement for mature NK cell homeostasis, function, and molecular programming remains unclear. To address this, T-BET and EOMES were deleted in unexpanded primary human NK cells using CRISPR/Cas9. Deleting these TFs compromised in vivo antitumor response of human NK cells. Mechanistically, T-BET and EOMES were required for normal NK cell proliferation and persistence in vivo. NK cells lacking T-BET and EOMES also exhibited defective responses to cytokine stimulation. Single-cell RNA-Seq revealed a specific T-box transcriptional program in human NK cells, which was rapidly lost following T-BET and EOMES deletion. Further, T-BET– and EOMES-deleted CD56bright NK cells acquired an innate lymphoid cell precursor–like (ILCP-like) profile with increased expression of the ILC-3–associated TFs RORC and AHR, revealing a role for T-box TFs in maintaining mature NK cell phenotypes and an unexpected role of suppressing alternative ILC lineages. Our study reveals the critical importance of sustained EOMES and T-BET expression to orchestrate mature NK cell function and identity.

Authors

Pamela Wong, Jennifer A. Foltz, Lily Chang, Carly C. Neal, Tony Yao, Celia C. Cubitt, Jennifer Tran, Samantha Kersting-Schadek, Sathvik Palakurty, Natalia Jaeger, David A. Russler-Germain, Nancy D. Marin, Margery Gang, Julia A. Wagner, Alice Y. Zhou, Miriam T. Jacobs, Mark Foster, Timothy Schappe, Lynne Marsala, Ethan McClain, Patrick Pence, Michelle Becker-Hapak, Bryan Fisk, Allegra A. Petti, Obi L. Griffith, Malachi Griffith, Melissa M. Berrien-Elliott, Todd A. Fehniger

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Figure 9

EOMES and T-BET maintain NK cell chromatin accessibility.

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EOMES and T-BET maintain NK cell chromatin accessibility. (A) Differenti...
(A) Differentially accessible regions (DARs) identified by DESeq2 (blue, FDR > 0.05; pink, FDR ≤ 0.05). (B) HOMER de novo motif enrichment analysis on all DARs using findMotifsGenome.pl with automatically generated background by HOMER. (C) Square pie chart of genomic region distribution of all DARs annotated using Chipseeker annotatePeak function. (D) Venn diagram of overlapping genes annotated as downregulated DARs in ATAC-seq and genes identified as downregulated DEGs in CD56bright or CD56dim KO clusters in scRNA-Seq. (E) Genomic region distribution of DARs (100 regions total, annotated to 82 unique genes) that are annotated to be in or near DEGs. (F) Representative peaks in PRF1, S1PR5, and GZMM, regions showing loss of accessibility in T+E edited NK cells. n = 2 donors, 2 independent experiments.