Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis
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Abstract
Abstract Background Traditionally, the transcriptomic and proteomic characterisation of CD4 + T cells at the single-cell level has been performed by two largely exclusive types of technologies: single-cell RNA sequencing (scRNA-seq) and antibody-based cytometry. Here, we present a multi-omics approach allowing the simultaneous targeted quantification of mRNA and protein expression in single cells and investigate its performance to dissect the heterogeneity of human immune cell populations. Methods We have quantified the single-cell expression of 397 genes at the mRNA level and up to 68 proteins using oligo-conjugated antibodies (AbSeq) in 43,656 primary CD4 + T cells isolated from the blood and 31,907 CD45 + cells isolated from the blood and matched duodenal biopsies. We explored the sensitivity of this targeted scRNA-seq approach to dissect the heterogeneity of human immune cell populations and identify trajectories of functional T cell differentiation. Results We provide a high-resolution map of human primary CD4 + T cells and identify precise trajectories of Th1, Th17 and regulatory T cell (Treg) differentiation in the blood and tissue. The sensitivity provided by this multi-omics approach identified the expression of the B7 molecules CD80 and CD86 on the surface of CD4 + Tregs, and we further demonstrated that B7 expression has the potential to identify recently activated T cells in circulation. Moreover, we identified a rare subset of CCR9 + T cells in the blood with tissue-homing properties and expression of several immune checkpoint molecules, suggestive of a regulatory function. Conclusions The transcriptomic and proteomic hybrid technology described in this study provides a cost-effective solution to dissect the heterogeneity of immune cell populations at extremely high resolution. Unexpectedly, CD80 and CD86, normally expressed on antigen-presenting cells, were detected on a subset of activated Tregs, indicating a role for these co-stimulatory molecules in regulating the dynamics of CD4 + T cell responses.
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Trzupek et al.'s data indicated a low correlation between RNA and protein levels.
“Moreover, their data indicated a low correlation between RNA and protein levels [127].”
From Single-cell sequencing to multi-omics: technologies and applications (2024) · cites this paper as [127]
Trzupek et al. discovered a novel subset of T regulatory cells with significantly upregulated CD80 and CD86, as revealed by antibodies-based sequencing.
“Trzupek et al. discovered a novel subset of T regulatory cells (Tregs) with significantly upregulated CD80 and CD86, as revealed by antibodies-based sequencing.”
From Single-cell sequencing to multi-omics: technologies and applications (2024) · cites this paper as [127]
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- Authors
- Trzupek, D., Dunstan, M., Cutler, A. J., Lee, M., Godfrey, L., Jarvis, L., Rainbow, D. B., Aschenbrenner, D., Jones, J. L., Uhlig, H. H., Wicker, L. S., Todd, J. A., & Ferreira, R. C.
- Affiliations
- Centre for Human Genetics (GB)
- University of Cambridge (GB)
- John Radcliffe Hospital (GB)
- Corresponding author
- Todd, John A.
- Ferreira, Ricardo C.
- ORCID
- Venue
- Genome Medicine
- Published
- 2020-06-24
- Volume
- 12
- Issue
- 1
- Pages
- 55-55
- ISSN
- 1756-994X (ISSN-L)
- PMC
- PMC7315544
- OpenAlex
- W3035987524
- Cited by
- 105
- References
- 64
- Citations by year
- 2026: 9 · 2025: 19 · 2024: 20 · 2023: 20 · 2022: 15 · 2021: 16 · 2020: 5 · 2019: 1
- FWCI
- 4.90
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome Medicine (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Apollo
- Funders
- Wellcome Trust (107212/A/15/Z)
- Juvenile Diabetes Research Foundation United States of America (1-SRA-2019-657-A-N, 4-SRA-2017-473-A-A, 4-2007-1003)
- Topics
- Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Health Sciences › Medicine › Oncology › Cancer Immunotherapy and Biomarkers
- Keywords
- CD80, CD86, regulatory T cells, B7 costimulatory molecules, T cell activation, CD4+ T cells, Th1 differentiation, Th17 cell differentiation, T cell differentiation trajectory, immune checkpoint molecules, duodenal biopsy, immune cell heterogeneity
- MeSH terms
- RNA-Seq, Adolescent, Adult, Female, Humans, Male, RNA, B7-1 Antigen, Proteome, T-Lymphocytes, Regulatory, Forkhead Transcription Factors, B7-2 Antigen, Single-Cell Analysis, Transcriptome
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