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Precursors of human CD4 cytotoxic T lymphocytes identified by single-cell transcriptome analysis

Precursors of human CD4 cytotoxic T lymphocytes identified by single-cell transcriptome analysis
Precursors of human CD4 cytotoxic T lymphocytes identified by single-cell transcriptome analysis

CD4+ cytotoxic T lymphocytes (CD4-CTLs) have been reported to play a protective role in several viral infections. However, little is known in humans about the biology of CD4-CTL generation, their functional properties, and heterogeneity, especially in relation to other well-described CD4+ memory T cell subsets. We performed single-cell RNA sequencing in more than 9000 cells to unravel CD4-CTL heterogeneity, transcriptional profile, and clonality in humans. Single-cell differential gene expression analysis revealed a spectrum of known transcripts, including several linked to cytotoxic and costimulatory function that are expressed at higher levels in the TEMRA (effector memory T cells expressing CD45RA) subset, which is highly enriched for CD4-CTLs, compared with CD4+ T cells in the central memory (TCM) and effector memory (TEM) subsets. Simultaneous T cell antigen receptor (TCR) analysis in single cells and bulk subsets revealed that CD4-TEMRA cells show marked clonal expansion compared with TCM and TEM cells and that most of CD4-TEMRA were dengue virus (DENV)-specific in donors with previous DENV infection. The profile of CD4-TEMRA was highly heterogeneous across donors, with four distinct clusters identified by the single-cell analysis. We identified distinct clusters of CD4-CTL effector and precursor cells in the TEMRA subset; the precursor cells shared TCR clonotypes with CD4-CTL effectors and were distinguished by high expression of the interleukin-7 receptor. Our identification of a CD4-CTL precursor population may allow further investigation of how CD4-CTLs arise in humans and, thus, could provide insights into the mechanisms that may be used to generate durable and effective CD4-CTL immunity.

Journal Article
2470-9468
Patil, Veena S.
c049d38f-b882-4dd5-9992-1cfeb8a101f8
Madrigal, Ariel
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Schmiedel, Benjamin J.
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Clarke, James
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O'Rourke, Patrick
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de Silva, Aruna D.
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Harris, Eva
e49e73fa-2cfa-41db-b4d1-25b99cb0b0f8
Peters, Bjoern
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Seumois, Gregory
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Weiskopf, Daniela
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Sette, Alessandro
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Vijayanand, Pandurangan
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Patil, Veena S.
c049d38f-b882-4dd5-9992-1cfeb8a101f8
Madrigal, Ariel
a9e9a737-f068-4040-aff8-1b9b1763adf1
Schmiedel, Benjamin J.
ba8ead04-6642-48b4-b4a6-b96910e17fab
Clarke, James
867dce7c-1a12-42f2-acc3-63c440ff0024
O'Rourke, Patrick
5697ca9d-4728-4dab-8cb7-2bbc16e9cad2
de Silva, Aruna D.
408fe904-2994-49c8-bbcd-5091551924c4
Harris, Eva
e49e73fa-2cfa-41db-b4d1-25b99cb0b0f8
Peters, Bjoern
c49863c8-d2c6-4db4-9d2c-72a7c0cbe117
Seumois, Gregory
0be7d3d6-5526-458c-aa5c-cce52410a2ed
Weiskopf, Daniela
0baaee36-7c36-49e1-a97e-9251d8d34904
Sette, Alessandro
240988b3-3c05-4041-a39b-8be8e145803c
Vijayanand, Pandurangan
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Patil, Veena S., Madrigal, Ariel, Schmiedel, Benjamin J., Clarke, James, O'Rourke, Patrick, de Silva, Aruna D., Harris, Eva, Peters, Bjoern, Seumois, Gregory, Weiskopf, Daniela, Sette, Alessandro and Vijayanand, Pandurangan (2018) Precursors of human CD4 cytotoxic T lymphocytes identified by single-cell transcriptome analysis. Science immunology, 3 (19). (doi:10.1126/sciimmunol.aan8664).

Record type: Article

Abstract

CD4+ cytotoxic T lymphocytes (CD4-CTLs) have been reported to play a protective role in several viral infections. However, little is known in humans about the biology of CD4-CTL generation, their functional properties, and heterogeneity, especially in relation to other well-described CD4+ memory T cell subsets. We performed single-cell RNA sequencing in more than 9000 cells to unravel CD4-CTL heterogeneity, transcriptional profile, and clonality in humans. Single-cell differential gene expression analysis revealed a spectrum of known transcripts, including several linked to cytotoxic and costimulatory function that are expressed at higher levels in the TEMRA (effector memory T cells expressing CD45RA) subset, which is highly enriched for CD4-CTLs, compared with CD4+ T cells in the central memory (TCM) and effector memory (TEM) subsets. Simultaneous T cell antigen receptor (TCR) analysis in single cells and bulk subsets revealed that CD4-TEMRA cells show marked clonal expansion compared with TCM and TEM cells and that most of CD4-TEMRA were dengue virus (DENV)-specific in donors with previous DENV infection. The profile of CD4-TEMRA was highly heterogeneous across donors, with four distinct clusters identified by the single-cell analysis. We identified distinct clusters of CD4-CTL effector and precursor cells in the TEMRA subset; the precursor cells shared TCR clonotypes with CD4-CTL effectors and were distinguished by high expression of the interleukin-7 receptor. Our identification of a CD4-CTL precursor population may allow further investigation of how CD4-CTLs arise in humans and, thus, could provide insights into the mechanisms that may be used to generate durable and effective CD4-CTL immunity.

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Patil et al_Science Immunology_Authors accepted manuscript - Accepted Manuscript
Restricted to Repository staff only until 19 July 2018.
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Accepted/In Press date: 30 November 2017
e-pub ahead of print date: 19 January 2018
Published date: 19 January 2018
Additional Information: Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
Keywords: Journal Article

Identifiers

Local EPrints ID: 422442
URI: https://eprints.soton.ac.uk/id/eprint/422442
ISSN: 2470-9468
PURE UUID: a93ffec8-0ee7-4d15-9fcb-977c152cfa16

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Date deposited: 24 Jul 2018 16:30
Last modified: 17 Jul 2019 17:10

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Contributors

Author: Veena S. Patil
Author: Ariel Madrigal
Author: Benjamin J. Schmiedel
Author: James Clarke
Author: Patrick O'Rourke
Author: Aruna D. de Silva
Author: Eva Harris
Author: Bjoern Peters
Author: Gregory Seumois
Author: Daniela Weiskopf
Author: Alessandro Sette
Author: Pandurangan Vijayanand

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