Single-cell multiomic analysis of thymocyte development reveals drivers of CD4+ T cell and CD8+ T cell lineage commitment

Zoë Steier; Dominik A Aylard; Laura L McIntyre; Isabel Baldwin; Esther Jeong Yoon Kim; Lydia K Lutes; Can Ergen; Tse-Shun Huang; Ellen A Robey; Nir Yosef; Aaron Streets

doi:10.1038/s41590-023-01584-0

Single-cell multiomic analysis of thymocyte development reveals drivers of CD4⁺ T cell and CD8⁺ T cell lineage commitment

Nat Immunol. 2023 Sep;24(9):1579-1590. doi: 10.1038/s41590-023-01584-0. Epub 2023 Aug 14.

Authors

Zoë Steier^#^{1

2

3

4

5

6}, Dominik A Aylard^#⁷, Laura L McIntyre⁷, Isabel Baldwin⁷, Esther Jeong Yoon Kim⁷, Lydia K Lutes⁷, Can Ergen^{3

8}, Tse-Shun Huang⁹, Ellen A Robey¹⁰, Nir Yosef^{11

12

13}, Aaron Streets^{14

15

16

17}

Affiliations

¹ University of California, Berkeley, Department of Bioengineering, Berkeley, CA, USA.
² UC Berkeley - UCSF Graduate Program in Bioengineering, Berkeley and San Francisco, CA, USA.
³ University of California, Berkeley, Center for Computational Biology, Berkeley, CA, USA.
⁴ Massachusetts Institute of Technology, Institute for Medical Engineering and Science, Cambridge, MA, USA.
⁵ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁶ Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
⁷ University of California, Berkeley, Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, Berkeley, CA, USA.
⁸ University of California, Berkeley, Department of Electrical Engineering and Computer Sciences, Berkeley, CA, USA.
⁹ BioLegend, Inc., San Diego, CA, USA.
¹⁰ University of California, Berkeley, Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, Berkeley, CA, USA. erobey@berkeley.edu.
¹¹ University of California, Berkeley, Center for Computational Biology, Berkeley, CA, USA. nir.yosef@weizmann.ac.il.
¹² University of California, Berkeley, Department of Electrical Engineering and Computer Sciences, Berkeley, CA, USA. nir.yosef@weizmann.ac.il.
¹³ Weizmann Institute of Science, Department of Systems Immunology, Rehovot, Israel. nir.yosef@weizmann.ac.il.
¹⁴ University of California, Berkeley, Department of Bioengineering, Berkeley, CA, USA. astreets@berkeley.edu.
¹⁵ UC Berkeley - UCSF Graduate Program in Bioengineering, Berkeley and San Francisco, CA, USA. astreets@berkeley.edu.
¹⁶ University of California, Berkeley, Center for Computational Biology, Berkeley, CA, USA. astreets@berkeley.edu.
¹⁷ Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA. astreets@berkeley.edu.

^# Contributed equally.

Abstract

The development of CD4⁺ T cells and CD8⁺ T cells in the thymus is critical to adaptive immunity and is widely studied as a model of lineage commitment. Recognition of self-peptide major histocompatibility complex (MHC) class I or II by the T cell antigen receptor (TCR) determines the CD8⁺ or CD4⁺ T cell lineage choice, respectively, but how distinct TCR signals drive transcriptional programs of lineage commitment remains largely unknown. Here we applied CITE-seq to measure RNA and surface proteins in thymocytes from wild-type and T cell lineage-restricted mice to generate a comprehensive timeline of cell states for each T cell lineage. These analyses identified a sequential process whereby all thymocytes initiate CD4⁺ T cell lineage differentiation during a first wave of TCR signaling, followed by a second TCR signaling wave that coincides with CD8⁺ T cell lineage specification. CITE-seq and pharmaceutical inhibition experiments implicated a TCR-calcineurin-NFAT-GATA3 axis in driving the CD4⁺ T cell fate. Our data provide a resource for understanding cell fate decisions and implicate a sequential selection process in guiding lineage choice.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
CD4 Antigens
CD4-Positive T-Lymphocytes*
CD8-Positive T-Lymphocytes*
Cell Differentiation
Cell Lineage
Histocompatibility Antigens Class I
Mice
Mice, Transgenic
Multiomics
Receptors, Antigen, T-Cell / metabolism
Thymocytes
Thymus Gland

Substances

Receptors, Antigen, T-Cell
Histocompatibility Antigens Class I
CD4 Antigens

Abstract

Publication types

MeSH terms

Substances

Grants and funding