Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells

Cody T Mowery; Jacob W Freimer; Zeyu Chen; Salvador Casaní-Galdón; Jennifer M Umhoefer; Maya M Arce; Ketrin Gjoni; Bence Daniel; Katalin Sandor; Benjamin G Gowen; Vinh Nguyen; Dimitre R Simeonov; Christian M Garrido; Gemma L Curie; Ralf Schmidt; Zachary Steinhart; Ansuman T Satpathy; Katherine S Pollard; Jacob E Corn; Bradley E Bernstein; Chun Jimmie Ye; Alexander Marson

doi:10.1038/s41588-024-01743-5

Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells

Nat Genet. 2024 Jun;56(6):1156-1167. doi: 10.1038/s41588-024-01743-5. Epub 2024 May 29.

Authors

Cody T Mowery^{1

2

3

4

5}, Jacob W Freimer^{3

4

5

6}, Zeyu Chen^{7

8

9}, Salvador Casaní-Galdón^{7

8

9}, Jennifer M Umhoefer^{2

3

4

5}, Maya M Arce^{2

3

4}, Ketrin Gjoni^{10

11}, Bence Daniel^{3

12

13

14}, Katalin Sandor^{3

12}, Benjamin G Gowen^{15

16}, Vinh Nguyen^{3

4

5

17

18

19}, Dimitre R Simeonov^{2

4

5}, Christian M Garrido^{3

4

5}, Gemma L Curie^{15

16}, Ralf Schmidt^{3

4

5

20}, Zachary Steinhart^{3

4

5}, Ansuman T Satpathy^{3

12

21

22}, Katherine S Pollard^{10

11

23}, Jacob E Corn^{15

16

24}, Bradley E Bernstein^{7

8

9}, Chun Jimmie Ye^{25

26

27

28

29

30

31}, Alexander Marson^{32

33

34

35

36

37

38}

Affiliations

¹ Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA.
² Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
³ Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
⁴ Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
⁵ Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
⁶ Department of Genetics, Stanford University, Stanford, CA, USA.
⁷ Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
⁸ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁹ Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA.
¹⁰ Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
¹¹ Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
¹² Department of Pathology, Stanford University, Stanford, CA, USA.
¹³ Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
¹⁴ Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA, USA.
¹⁵ Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
¹⁶ Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
¹⁷ Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
¹⁸ Department of Surgery, University of California, San Francisco, San Francisco, CA, USA.
¹⁹ UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA.
²⁰ Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.
²¹ Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
²² Program in Immunology, Stanford University, Stanford, CA, USA.
²³ Chan Zuckerberg Biohub SF, San Francisco, CA, USA.
²⁴ Department of Biology, ETH Zürich, Zürich, Switzerland.
²⁵ Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. [email protected].
²⁶ Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA. [email protected].
²⁷ Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. [email protected].
²⁸ Chan Zuckerberg Biohub SF, San Francisco, CA, USA. [email protected].
²⁹ Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, CA, USA. [email protected].
³⁰ Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA. [email protected].
³¹ Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA. [email protected].
³² Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. [email protected].
³³ Department of Medicine, University of California, San Francisco, San Francisco, CA, USA. [email protected].
³⁴ Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA. [email protected].
³⁵ Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA. [email protected].
³⁶ Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. [email protected].
³⁷ Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA. [email protected].
³⁸ UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA. [email protected].

Abstract

Cis-regulatory elements (CREs) interact with trans regulators to orchestrate gene expression, but how transcriptional regulation is coordinated in multi-gene loci has not been experimentally defined. We sought to characterize the CREs controlling dynamic expression of the adjacent costimulatory genes CD28, CTLA4 and ICOS, encoding regulators of T cell-mediated immunity. Tiling CRISPR interference (CRISPRi) screens in primary human T cells, both conventional and regulatory subsets, uncovered gene-, cell subset- and stimulation-specific CREs. Integration with CRISPR knockout screens and assay for transposase-accessible chromatin with sequencing (ATAC-seq) profiling identified trans regulators influencing chromatin states at specific CRISPRi-responsive elements to control costimulatory gene expression. We then discovered a critical CCCTC-binding factor (CTCF) boundary that reinforces CRE interaction with CTLA4 while also preventing promiscuous activation of CD28. By systematically mapping CREs and associated trans regulators directly in primary human T cell subsets, this work overcomes longstanding experimental limitations to decode context-dependent gene regulatory programs in a complex, multi-gene locus critical to immune homeostasis.

MeSH terms

CCCTC-Binding Factor / genetics
CCCTC-Binding Factor / metabolism
CD28 Antigens* / genetics
CRISPR-Cas Systems
CTLA-4 Antigen* / genetics
Chromatin* / genetics
Chromatin* / metabolism
Gene Expression Regulation*
Humans
Inducible T-Cell Co-Stimulator Protein / genetics
Inducible T-Cell Co-Stimulator Protein / metabolism
T-Lymphocytes / immunology
T-Lymphocytes / metabolism

Substances

CTLA-4 Antigen
CD28 Antigens
CTLA4 protein, human
Chromatin
Inducible T-Cell Co-Stimulator Protein
CCCTC-Binding Factor
ICOS protein, human

Abstract

MeSH terms

Substances

Grants and funding