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

• Published in: The Journal of immunology (1950) Vol. 199; no. 1; pp. 323 - 335
• Main Authors: Cerosaletti, Karen, Barahmand-pour-Whitman, Fariba, Yang, Junbao, DeBerg, Hannah A, Dufort, Matthew J, Murray, Sara A, Israelsson, Elisabeth, Speake, Cate, Gersuk, Vivian H, Eddy, James A, Reijonen, Helena, Greenbaum, Carla J, Kwok, William W, Wambre, Erik, Prlic, Martin, Gottardo, Raphael, Nepom, Gerald T, Linsley, Peter S
• Format: Journal Article
• Language: English
• Published: United States American Association of Immunologists 01.07.2017
• Subjects: Adult; CD4 antigen; CD4-Positive T-Lymphocytes - immunology; Cell activation; Clone Cells; Diabetes; Diabetes mellitus; Diabetes Mellitus, Type 1 - blood; Diabetes Mellitus, Type 1 - immunology; Female; Gene Expression Profiling; Humans; Immunologic Memory; Immunological memory; Islets of Langerhans - immunology; Lymphocyte Activation; Lymphocytes; Lymphocytes T; Male; Memory cells; Peptides - immunology; Peripheral blood; Phenotype; Receptors, Antigen, T-Cell, alpha-beta - immunology; Ribonucleic acid; RNA; Sequence Analysis, RNA; Single-Cell Analysis; T cell receptors; Transcription
• ISSN: 0022-1767; 1550-6606; 1550-6606
• DOI: 10.4049/jimmunol.1700172

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.