Systems immunology approaches to study T cells in health and disease

doi:10.1038/s41540-024-00446-1

Review

. 2024 Oct 9;10(1):117.

doi: 10.1038/s41540-024-00446-1.

Systems immunology approaches to study T cells in health and disease

Aaron Yang¹, Amanda C Poholek^{2

3}

Affiliations

¹ Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
² Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. poholeka@pitt.edu.
³ Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. poholeka@pitt.edu.

PMID: 39384819
PMCID: PMC11464710
DOI: 10.1038/s41540-024-00446-1

Review

Systems immunology approaches to study T cells in health and disease

Aaron Yang et al. NPJ Syst Biol Appl. 2024.

. 2024 Oct 9;10(1):117.

doi: 10.1038/s41540-024-00446-1.

Authors

Aaron Yang¹, Amanda C Poholek^{2

3}

Affiliations

¹ Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
² Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. poholeka@pitt.edu.
³ Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. poholeka@pitt.edu.

PMID: 39384819
PMCID: PMC11464710
DOI: 10.1038/s41540-024-00446-1

Abstract

T cells are dynamically regulated immune cells that are implicated in a variety of diseases ranging from infection, cancer and autoimmunity. Recent advancements in sequencing methods have provided valuable insights in the transcriptional and epigenetic regulation of T cells in various disease settings. In this review, we identify the key sequencing-based methods that have been applied to understand the transcriptomic and epigenomic regulation of T cells in diseases.

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Conflict of interest statement

The authors declare no competing interests.

Figures

**Fig. 1. Overview of sequencing methods for investigation of T cell regulation and function.**
We identify cellular limitations, type of genomic output, and uses for each method. Made with Biorender.

See this image and copyright information in PMC

References

1. Mardis, E. R. A decade’s perspective on DNA sequencing technology. Nature470, 198–203 (2011). - PubMed
1. Sun, L., Su, Y., Jiao, A., Wang, X. & Zhang, B. T cells in health and disease. Signal Transduct. Target Ther.8, 1–50 (2023). - PMC - PubMed
1. Kaech, S. M., Wherry, E. J. & Ahmed, R. Effector and memory T-cell differentiation: implications for vaccine development. Nat. Rev. Immunol.2, 251–262 (2002). - PubMed
1. Papale, M. A Review of Proteomics Strategies to Study T-Cell Activation and Function in Cancer Disease. in Cytotoxic T-Cells: Methods and Protocols (eds. Gigante, M. & Ranieri, E.) (Springer, 2021). - PubMed
1. Lim, S. A., Su, W., Chapman, N. M. & Chi, H. Lipid metabolism in T cell signaling and function. Nat. Chem. Biol.18, 470–481 (2022). - PMC - PubMed

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[1] Mardis, E. R. A decade’s perspective on DNA sequencing technology. Nature470, 198–203 (2011). - PubMed

[2] Mardis, E. R. A decade’s perspective on DNA sequencing technology. Nature470, 198–203 (2011). - PubMed

[3] Sun, L., Su, Y., Jiao, A., Wang, X. & Zhang, B. T cells in health and disease. Signal Transduct. Target Ther.8, 1–50 (2023). - PMC - PubMed

[4] Sun, L., Su, Y., Jiao, A., Wang, X. & Zhang, B. T cells in health and disease. Signal Transduct. Target Ther.8, 1–50 (2023). - PMC - PubMed

[5] Kaech, S. M., Wherry, E. J. & Ahmed, R. Effector and memory T-cell differentiation: implications for vaccine development. Nat. Rev. Immunol.2, 251–262 (2002). - PubMed

[6] Kaech, S. M., Wherry, E. J. & Ahmed, R. Effector and memory T-cell differentiation: implications for vaccine development. Nat. Rev. Immunol.2, 251–262 (2002). - PubMed

[7] Papale, M. A Review of Proteomics Strategies to Study T-Cell Activation and Function in Cancer Disease. in Cytotoxic T-Cells: Methods and Protocols (eds. Gigante, M. & Ranieri, E.) (Springer, 2021). - PubMed

[8] Papale, M. A Review of Proteomics Strategies to Study T-Cell Activation and Function in Cancer Disease. in Cytotoxic T-Cells: Methods and Protocols (eds. Gigante, M. & Ranieri, E.) (Springer, 2021). - PubMed

[9] Lim, S. A., Su, W., Chapman, N. M. & Chi, H. Lipid metabolism in T cell signaling and function. Nat. Chem. Biol.18, 470–481 (2022). - PMC - PubMed

[10] Lim, S. A., Su, W., Chapman, N. M. & Chi, H. Lipid metabolism in T cell signaling and function. Nat. Chem. Biol.18, 470–481 (2022). - PMC - PubMed

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Systems immunology approaches to study T cells in health and disease

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Systems immunology approaches to study T cells in health and disease

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