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Exhausted-like CD8+ T cell phenotypes linked to C-peptide preservation in alefacept-treated T1D subjects
Kirsten E. Diggins, Elisavet Serti, Virginia Muir, Mario Rosasco, TingTing Lu, Elisa Balmas, Gerald Nepom, S. Alice Long, Peter S. Linsley
Kirsten E. Diggins, Elisavet Serti, Virginia Muir, Mario Rosasco, TingTing Lu, Elisa Balmas, Gerald Nepom, S. Alice Long, Peter S. Linsley
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Research Article Immunology

Exhausted-like CD8+ T cell phenotypes linked to C-peptide preservation in alefacept-treated T1D subjects

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Abstract

Clinical trials of biologic therapies in type 1 diabetes (T1D) aim to mitigate autoimmune destruction of pancreatic β cells through immune perturbation and serve as resources to elucidate immunological mechanisms in health and disease. In the T1DAL trial of alefacept (LFA3-Ig) in recent-onset T1D, endogenous insulin production was preserved in 30% of subjects for 2 years after therapy. Given our previous findings linking exhausted-like CD8+ T cells to beneficial response in T1D trials, we applied unbiased analyses to sorted CD8+ T cells to evaluate their potential role in T1DAL. Using RNA sequencing, we found that greater insulin C-peptide preservation was associated with a module of activation- and exhaustion-associated genes. This signature was dissected into 2 CD8 memory phenotypes through correlation with cytometry data. These cells were hypoproliferative, shared expanded rearranged TCR junctions, and expressed exhaustion-associated markers including TIGIT and KLRG1. The 2 phenotypes could be distinguished by reciprocal expression of CD8+ T and NK cell markers (GZMB, CD57, and inhibitory killer cell immunoglobulin-like receptor [iKIR] genes), versus T cell activation and differentiation markers (PD-1 and CD28). These findings support previous evidence linking exhausted-like CD8+ T cells to successful immune interventions for T1D, while suggesting that multiple inhibitory mechanisms can promote this beneficial cell state.

Authors

Kirsten E. Diggins, Elisavet Serti, Virginia Muir, Mario Rosasco, TingTing Lu, Elisa Balmas, Gerald Nepom, S. Alice Long, Peter S. Linsley

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Figure 1

CD8+ T cell activation and exhaustion-associated gene signature was associated with response to alefacept.

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CD8+ T cell activation and exhaustion-associated gene signature was asso...
(A) Schematic diagram shows analysis workflow. (B) WGCNA cluster dendrogram is shown for analysis of 5000 most variable genes in CD8 samples (n = 24; including 2 placebo). (C) Pearson correlation between module eigengene and C-peptide change. Significance of correlation was determined by Student’s asymptotic 2-tailed t test. Only the blue module was significantly correlated with C-peptide change (*P < 0.05). Correlation and significance calculations included all 24 subjects used for WGCNA module generation. (D) Graph shows blue module eigengene expression versus C-peptide change at week 104 across the same 24 subjects (r = 0.47, P = 0.023, FDR = 0.14). Pearson correlation and the corresponding 1-tailed t test of correlation significance were performed using cor.test function in R. (E) Change from baseline median expression of blue module genes in responders, partial responders, and nonresponders over time. See Supplemental Table 1 for sample numbers per group and visit. Significant differences at week 52 and 104 were seen between responders and nonresponders (*P < 0.05). Significance was determined by repeated-measures 1-way ANOVA, with multiplicity adjustment applied to P values. (F) A selection of significantly enriched terms identified by GO enrichment analysis of blue module genes are shown with their respective enrichment P value (–log10[FDR]). (G) Blue module genes categorized as “leukocyte activation” by GO analysis were clustered using string (string-db.org) and visualized in Cytoscape. Inhibitory marker names colored red.

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