In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8+ T cell fate decisions

Hongling Huang; Peipei Zhou; Jun Wei; Lingyun Long; Hao Shi; Yogesh Dhungana; Nicole M. Chapman; Guotong Fu; Jordy Saravia; Jana L. Raynor; Shaofeng Liu; Gustavo Palacios; Yong Dong Wang; Chenxi Qian; Jiyang Yu; Hongbo Chi

doi:10.1016/j.cell.2021.02.021

In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8⁺ T cell fate decisions

Hongling Huang, Peipei Zhou, Jun Wei, Lingyun Long, Hao Shi, Yogesh Dhungana, Nicole M. Chapman, Guotong Fu, Jordy Saravia, Jana L. Raynor, Shaofeng Liu, Gustavo Palacios, Yong Dong Wang, Chenxi Qian, Jiyang Yu, Hongbo Chi

Research output: Contribution to journal › Article › peer-review

50 Scopus citations

Abstract

How early events in effector T cell (T_EFF) subsets tune memory T cell (T_MEM) responses remains incompletely understood. Here, we systematically investigated metabolic factors in fate determination of T_EFF and T_MEM cells using in vivo pooled CRISPR screening, focusing on negative regulators of T_MEM responses. We found that amino acid transporters Slc7a1 and Slc38a2 dampened the magnitude of T_MEM differentiation, in part through modulating mTORC1 signaling. By integrating genetic and systems approaches, we identified cellular and metabolic heterogeneity among T_EFF cells, with terminal effector differentiation associated with establishment of metabolic quiescence and exit from the cell cycle. Importantly, Pofut1 (protein-O-fucosyltransferase-1) linked GDP-fucose availability to downstream Notch-Rbpj signaling, and perturbation of this nutrient signaling axis blocked terminal effector differentiation but drove context-dependent T_EFF proliferation and T_MEM development. Our study establishes that nutrient uptake and signaling are key determinants of T cell fate and shape the quantity and quality of T_MEM responses. Metabolic changes associated with amino acid transport and nutrient signaling regulate the fate of effector T cell populations and the generation of memory T cell responses.

Original language	English
Pages (from-to)	1245-1261.e21
Journal	Cell
Volume	184
Issue number	5
DOIs	https://doi.org/10.1016/j.cell.2021.02.021
State	Published - 4 Mar 2021
Externally published	Yes

Keywords

GDP-fucose
Notch
T cell memory
cell cycle exit
immunometabolism
in vivo pooled CRISPR screening
metabolic heterogeneity
nutrient signaling
systems immunology
terminal effector cell

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10.1016/j.cell.2021.02.021

Cite this

@article{1993ef2ed7c340a4b939a3312867fade,

title = "In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8+ T cell fate decisions",

abstract = "How early events in effector T cell (TEFF) subsets tune memory T cell (TMEM) responses remains incompletely understood. Here, we systematically investigated metabolic factors in fate determination of TEFF and TMEM cells using in vivo pooled CRISPR screening, focusing on negative regulators of TMEM responses. We found that amino acid transporters Slc7a1 and Slc38a2 dampened the magnitude of TMEM differentiation, in part through modulating mTORC1 signaling. By integrating genetic and systems approaches, we identified cellular and metabolic heterogeneity among TEFF cells, with terminal effector differentiation associated with establishment of metabolic quiescence and exit from the cell cycle. Importantly, Pofut1 (protein-O-fucosyltransferase-1) linked GDP-fucose availability to downstream Notch-Rbpj signaling, and perturbation of this nutrient signaling axis blocked terminal effector differentiation but drove context-dependent TEFF proliferation and TMEM development. Our study establishes that nutrient uptake and signaling are key determinants of T cell fate and shape the quantity and quality of TMEM responses. Metabolic changes associated with amino acid transport and nutrient signaling regulate the fate of effector T cell populations and the generation of memory T cell responses.",

keywords = "GDP-fucose, Notch, T cell memory, cell cycle exit, immunometabolism, in vivo pooled CRISPR screening, metabolic heterogeneity, nutrient signaling, systems immunology, terminal effector cell",

author = "Hongling Huang and Peipei Zhou and Jun Wei and Lingyun Long and Hao Shi and Yogesh Dhungana and Chapman, {Nicole M.} and Guotong Fu and Jordy Saravia and Raynor, {Jana L.} and Shaofeng Liu and Gustavo Palacios and Wang, {Yong Dong} and Chenxi Qian and Jiyang Yu and Hongbo Chi",

note = "Funding Information: The authors acknowledge B.A. Youngblood for P14 mice; D.A. Vignali for B16-OVA cell line; Y.C. Liu for Plat-E cells; E.J. Wherry and Z. Chen for scientific discussions; Y. Wang for editing the manuscript; M. Hendren, A. KC, and S. Rankin for animal management; St. Jude Immunology flow cytometry core facility for cell sorting; The Hartwell Center for microarray, ATAC-seq, and scRNA-seq analyses; Center for Advanced Genome Engineering for targeted sequencing; and Veterinary Pathology Core for histology examination. This work was supported by the National Institutes of Health ( NIH AI105887 , AI131703 , AI140761 , AI150241 , AI150514 , CA250533 , and CA221290 to H.C.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. Publisher Copyright: {\textcopyright} 2021 Elsevier Inc.",

year = "2021",

month = mar,

day = "4",

doi = "10.1016/j.cell.2021.02.021",

language = "English",

volume = "184",

pages = "1245--1261.e21",

journal = "Cell",

issn = "0092-8674",

publisher = "Cell Press",

number = "5",

}

TY - JOUR

T1 - In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8+ T cell fate decisions

AU - Huang, Hongling

AU - Zhou, Peipei

AU - Wei, Jun

AU - Long, Lingyun

AU - Shi, Hao

AU - Dhungana, Yogesh

AU - Chapman, Nicole M.

AU - Fu, Guotong

AU - Saravia, Jordy

AU - Raynor, Jana L.

AU - Liu, Shaofeng

AU - Palacios, Gustavo

AU - Wang, Yong Dong

AU - Qian, Chenxi

AU - Yu, Jiyang

AU - Chi, Hongbo

N1 - Funding Information: The authors acknowledge B.A. Youngblood for P14 mice; D.A. Vignali for B16-OVA cell line; Y.C. Liu for Plat-E cells; E.J. Wherry and Z. Chen for scientific discussions; Y. Wang for editing the manuscript; M. Hendren, A. KC, and S. Rankin for animal management; St. Jude Immunology flow cytometry core facility for cell sorting; The Hartwell Center for microarray, ATAC-seq, and scRNA-seq analyses; Center for Advanced Genome Engineering for targeted sequencing; and Veterinary Pathology Core for histology examination. This work was supported by the National Institutes of Health ( NIH AI105887 , AI131703 , AI140761 , AI150241 , AI150514 , CA250533 , and CA221290 to H.C.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. Publisher Copyright: © 2021 Elsevier Inc.

PY - 2021/3/4

Y1 - 2021/3/4

N2 - How early events in effector T cell (TEFF) subsets tune memory T cell (TMEM) responses remains incompletely understood. Here, we systematically investigated metabolic factors in fate determination of TEFF and TMEM cells using in vivo pooled CRISPR screening, focusing on negative regulators of TMEM responses. We found that amino acid transporters Slc7a1 and Slc38a2 dampened the magnitude of TMEM differentiation, in part through modulating mTORC1 signaling. By integrating genetic and systems approaches, we identified cellular and metabolic heterogeneity among TEFF cells, with terminal effector differentiation associated with establishment of metabolic quiescence and exit from the cell cycle. Importantly, Pofut1 (protein-O-fucosyltransferase-1) linked GDP-fucose availability to downstream Notch-Rbpj signaling, and perturbation of this nutrient signaling axis blocked terminal effector differentiation but drove context-dependent TEFF proliferation and TMEM development. Our study establishes that nutrient uptake and signaling are key determinants of T cell fate and shape the quantity and quality of TMEM responses. Metabolic changes associated with amino acid transport and nutrient signaling regulate the fate of effector T cell populations and the generation of memory T cell responses.

AB - How early events in effector T cell (TEFF) subsets tune memory T cell (TMEM) responses remains incompletely understood. Here, we systematically investigated metabolic factors in fate determination of TEFF and TMEM cells using in vivo pooled CRISPR screening, focusing on negative regulators of TMEM responses. We found that amino acid transporters Slc7a1 and Slc38a2 dampened the magnitude of TMEM differentiation, in part through modulating mTORC1 signaling. By integrating genetic and systems approaches, we identified cellular and metabolic heterogeneity among TEFF cells, with terminal effector differentiation associated with establishment of metabolic quiescence and exit from the cell cycle. Importantly, Pofut1 (protein-O-fucosyltransferase-1) linked GDP-fucose availability to downstream Notch-Rbpj signaling, and perturbation of this nutrient signaling axis blocked terminal effector differentiation but drove context-dependent TEFF proliferation and TMEM development. Our study establishes that nutrient uptake and signaling are key determinants of T cell fate and shape the quantity and quality of TMEM responses. Metabolic changes associated with amino acid transport and nutrient signaling regulate the fate of effector T cell populations and the generation of memory T cell responses.

KW - GDP-fucose

KW - Notch

KW - T cell memory

KW - cell cycle exit

KW - immunometabolism

KW - in vivo pooled CRISPR screening

KW - metabolic heterogeneity

KW - nutrient signaling

KW - systems immunology

KW - terminal effector cell

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U2 - 10.1016/j.cell.2021.02.021

DO - 10.1016/j.cell.2021.02.021

M3 - Article

C2 - 33636132

AN - SCOPUS:85101771524

SN - 0092-8674

VL - 184

SP - 1245-1261.e21

JO - Cell

JF - Cell

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