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Journal of immunology (Baltimore, Md. : 1950)
07 01, 2017;199 (1): 323-335.

Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4 T Cells in Peripheral Blood of Subjects with Type 1 Diabetes.

Karen Cerosaletti, Fariba Barahmand-Pour-Whitman, Junbao Yang, Hannah A DeBerg, Matthew J Dufort, Sara A Murray, Elisabeth Israelsson, Cate Speake, Vivian H Gersuk, James A Eddy, Helena Reijonen, Carla J Greenbaum, William W Kwok, Erik Wambre, Martin Prlic, Raphael Gottardo, Gerald T Nepom, Peter S Linsley
Author Information
  1. Karen Cerosaletti: Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101; plinsley@benaroyaresearch.org kcerosaletti@benaroyaresearch.org.
  2. Fariba Barahmand-Pour-Whitman: Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101.
  3. Junbao Yang: Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101.
  4. Hannah A DeBerg: Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101. ORCID
  5. Matthew J Dufort: Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101. ORCID
  6. Sara A Murray: Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101.
  7. Elisabeth Israelsson: Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101.
  8. Cate Speake: Diabetes Clinical Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101. ORCID
  9. Vivian H Gersuk: Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101.
  10. James A Eddy: Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101. ORCID
  11. Helena Reijonen: Diabetes Clinical Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101.
  12. Carla J Greenbaum: Diabetes Clinical Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101. ORCID
  13. William W Kwok: Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101.
  14. Erik Wambre: Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101.
  15. Martin Prlic: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and. ORCID
  16. Raphael Gottardo: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and.
  17. Gerald T Nepom: Immune Tolerance Network, Bethesda, MD 20814. ORCID
  18. Peter S Linsley: Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101; plinsley@benaroyaresearch.org kcerosaletti@benaroyaresearch.org.
PMID: 28566371 DOI: 10.4049/jimmunol.1700172

Abstract

The significance of islet Ag-reactive T cells found in peripheral blood of type 1 diabetes (T1D) subjects is unclear, partly because similar cells are also found in healthy control (HC) subjects. We hypothesized that key disease-associated cells would show evidence of prior Ag exposure, inferred from expanded TCR clonotypes, and essential phenotypic properties in their transcriptomes. To test this, we developed single-cell RNA sequencing procedures for identifying TCR clonotypes and transcript phenotypes in individual T cells. We applied these procedures to analysis of islet Ag-reactive CD4 memory T cells from the blood of T1D and HC individuals after activation with pooled immunodominant islet peptides. We found extensive TCR clonotype sharing in Ag-activated cells, especially from individual T1D subjects, consistent with in vivo T cell expansion during disease progression. The expanded clonotype from one T1D subject was detected at repeat visits spanning >15 mo, demonstrating clonotype stability. Notably, we found no clonotype sharing between subjects, indicating a predominance of "private" TCR specificities. Expanded clones from two T1D subjects recognized distinct IGRP peptides, implicating this molecule as a trigger for CD4 T cell expansion. Although overall transcript profiles of cells from HC and T1D subjects were similar, profiles from the most expanded clones were distinctive. Our findings demonstrate that islet Ag-reactive CD4 memory T cells with unique Ag specificities and phenotypes are expanded during disease progression and can be detected by single-cell analysis of peripheral blood.

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Grants

  1. DP3 DK106909/NIDDK NIH HHS
  2. DP2 DE023321/NIDCR NIH HHS
  3. UM1 AI109565/NIAID NIH HHS
  4. HHSN272201300006C/NIAID NIH HHS
  5. S10 OD020069/NIH HHS
  6. DP3 DK110867/NIDDK NIH HHS

MeSH Term

Adult
CD4-Positive T-Lymphocytes
Clone Cells
Diabetes Mellitus, Type 1
Female
Gene Expression Profiling
Humans
Immunologic Memory
Islets of Langerhans
Lymphocyte Activation
Male
Peptides
Phenotype
Receptors, Antigen, T-Cell, alpha-beta
Sequence Analysis, RNA
Single-Cell Analysis

Chemicals

Peptides
Receptors, Antigen, T-Cell, alpha-beta
Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

GEN: GEND000221 (Single cell RNA-seq reveals expansion of IGRP-reactive CD4+ T cells in recent onset type I diabetes (single-cell RNA-seq of T-cell clone))
GEN: GEND000222 (Single cell RNA-seq reveals expansion of IGRP-reactive CD4+ T cells in recent onset type I diabetes (single-cell RNA-seq of CD8+ influenza-reactive T cells))

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