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Hierarchal single-cell lineage tracing reveals differential fate commitment of CD8 T-cell clones in response to acute infection.

作者信息

Abdullah Leena, Emiliani Francesco E, Vaidya Chinmay M, Stuart Hannah, Kolling Fred W, Ackerman Margaret E, Song Li, McKenna Aaron, Huang Yina H

机构信息

Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA.

Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA.

出版信息

bioRxiv. 2024 Mar 27:2024.03.21.586160. doi: 10.1101/2024.03.21.586160.


DOI:10.1101/2024.03.21.586160
PMID:38585810
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10996474/
Abstract

Generating balanced populations of CD8 effector and memory T cells is necessary for immediate and durable immunity to infections and cancer. Yet, a definitive understanding of CD8 differentiation remains unclear. We used CARLIN, a processive lineage recording mouse model with single-cell RNA-seq and TCR-seq to track endogenous antigen-specific CD8 T cells during acute viral infection. We identified a diverse repertoire of expanded T-cell clones represented by seven transcriptional states. TCR enrichment analysis revealed differential memory- or effector-fate biases within clonal populations. Shared Vb segments and amino acid motifs were found within biased categories despite high TCR diversity. Using single-cell CARLIN barcode-seq we tracked multi-generational clones and found that unlike unbiased or memory-biased clones, which stably retain their fate profiles, effector-biased clones could adopt memory- or effector-bias within subclones. Collectively, our study demonstrates that a heterogenous T-cell repertoire specific for a shared antigen is composed of clones with distinct TCR-intrinsic fate-biases.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9cde/10996474/c08af62e44df/nihpp-2024.03.21.586160v1-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9cde/10996474/074cdabe29a7/nihpp-2024.03.21.586160v1-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9cde/10996474/10787d073e28/nihpp-2024.03.21.586160v1-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9cde/10996474/6747754a6399/nihpp-2024.03.21.586160v1-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9cde/10996474/7cc2d6b1e4ca/nihpp-2024.03.21.586160v1-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9cde/10996474/c688c031fac8/nihpp-2024.03.21.586160v1-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9cde/10996474/c08af62e44df/nihpp-2024.03.21.586160v1-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9cde/10996474/074cdabe29a7/nihpp-2024.03.21.586160v1-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9cde/10996474/10787d073e28/nihpp-2024.03.21.586160v1-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9cde/10996474/6747754a6399/nihpp-2024.03.21.586160v1-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9cde/10996474/7cc2d6b1e4ca/nihpp-2024.03.21.586160v1-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9cde/10996474/c688c031fac8/nihpp-2024.03.21.586160v1-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9cde/10996474/c08af62e44df/nihpp-2024.03.21.586160v1-f0006.jpg

相似文献

[1]
Hierarchal single-cell lineage tracing reveals differential fate commitment of CD8 T-cell clones in response to acute infection.

bioRxiv. 2024-3-27

[2]
T Cell Receptor Diversity and Lineage Relationship between Virus-Specific CD8 T Cell Subsets during Chronic Lymphocytic Choriomeningitis Virus Infection.

J Virol. 2020-9-29

[3]
Divergent clonal differentiation trajectories establish CD8 memory T cell heterogeneity during acute viral infections in humans.

Cell Rep. 2021-5-25

[4]
Clonal lineage tracing reveals mechanisms skewing CD8+ T cell fate decisions in chronic infection.

J Exp Med. 2023-1-2

[5]
Rapid CD8+ T cell repertoire focusing and selection of high-affinity clones into memory following primary infection with a persistent human virus: human cytomegalovirus.

J Immunol. 2007-9-1

[6]
Clonally Expanded Virus-Specific CD8 T Cells Acquire Diverse Transcriptional Phenotypes During Acute, Chronic, and Latent Infections.

Front Immunol. 2022

[7]
Cheating the Hunger Games; Mechanisms Controlling Clonal Diversity of CD8 Effector and Memory Populations.

Front Immunol. 2018-11-29

[8]
Clonal expansion of resident memory T cells in peripheral blood of patients with non-small cell lung cancer during immune checkpoint inhibitor treatment.

J Immunother Cancer. 2023-2

[9]
Dynamics of the cytotoxic T cell response to a model of acute viral infection.

J Virol. 2015-4

[10]
TCR repertoire, clonal dominance, and pulmonary trafficking of mycobacterium-specific CD4+ and CD8+ T effector cells in immunity against tuberculosis.

J Immunol. 2010-10-1

本文引用的文献

[1]
Recruitment of epitope-specific T cell clones with a low-avidity threshold supports efficacy against mutational escape upon re-infection.

Immunity. 2023-6-13

[2]
Simulation-based inference of differentiation trajectories from RNA velocity fields.

Cell Rep Methods. 2022-12-19

[3]
Clonal lineage tracing reveals mechanisms skewing CD8+ T cell fate decisions in chronic infection.

J Exp Med. 2023-1-2

[4]
Divide and Conquer: Phenotypic and Temporal Heterogeneity Within CD8 T Cell Responses.

Front Immunol. 2022

[5]
Type I interferons and MAVS signaling are necessary for tissue resident memory CD8+ T cell responses to RSV infection.

PLoS Pathog. 2022-2

[6]
Resident memory CD8 T cells in regional lymph nodes mediate immunity to metastatic melanoma.

Immunity. 2021-9-14

[7]
Single-cell lineage tracing of metastatic cancer reveals selection of hybrid EMT states.

Cancer Cell. 2021-8-9

[8]
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data.

Nat Methods. 2021-6

[9]
The architectural design of CD8+ T cell responses in acute and chronic infection: Parallel structures with divergent fates.

J Exp Med. 2021-4-5

[10]
Central memory CD8 T cells derive from stem-like Tcf7 effector cells in the absence of cytotoxic differentiation.

Immunity. 2020-11-17

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