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 8

Loss of T-box TFs in NK cells results in ILC-3–biased ILC progenitor cell phenotype.

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Loss of T-box TFs in NK cells results in ILC-3–biased ILC progenitor cel...
(A) Heatmap of differentially expressed ILCP-associated marker genes expressed by in vitro CD56bright KO versus control clusters. (B) UMAP of in vitro CD56bright NK cells only. (C) UMAP overlaid with density of cells originating from control samples and T+E edited samples. (D) Violin plot of ILCP-related markers within clusters identified in B. (E) Expression of indicated ILCP-related markers overlaid on UMAP space. DEGs were determined using Wilcoxon’s rank-sum test and adjusted P value of less than 0.05. (F) Protein expression of CD117. NKp80, CD94, and NKG2D of in vitro–maintained TRAC-edited (control) and gated T-BET/EOMES–DKO cells 8 days after CRISPR electroporation quantified by flow cytometry. n = 4 donors, 2 independent experiments. Data were compared with ratio paired t test. *P < 0.05, **P < 0.01.