Proinflammatory islet antigen reactive CD4 T cells are linked with response to alefacept in type 1 diabetes.

Abstract

Variation in the preservation of β cell function in clinical trials in type 1 diabetes (T1D) has emphasized the need to define biomarkers to predict treatment response. The T1DAL trial targeted T cells with alefacept (LFA-3-Ig) and demonstrated C-peptide preservation in ~30% of new onset T1D subjects. We analyzed islet antigen reactive (IAR) CD4 T cells in PBMC samples collected prior to treatment from alefacept- and placebo-treated subjects using flow cytometry and single cell RNA-sequencing. IAR CD4 T cells at baseline had heterogenous phenotypes. Transcript profiles formed phenotypic clusters of cells along a trajectory based on increasing maturation and activation, and T cell receptor (TCR) chains showed clonal expansion. Notably, the frequency of IAR CD4 T cells with a memory phenotype and a unique transcript profile (Cluster 3) were inversely correlated with C-peptide preservation in alefacept-, but not placebo-treated subjects. Cluster 3 cells had a proinflammatory phenotype characterized by expression of the transcription factor BHLHE40 and the cytokines GM-CSF and TNF-α, and shared TCR chains with effector memory-like clusters. Our results suggest IAR CD4 T cells as a potential baseline biomarker of response to therapies targeting the CD2 pathway and warrant investigation for other T cell-related therapies.