Extended Data Fig. 6: Pseudotemporal analysis recapitulates the development of exhaustion in intra-islet CD8+ T cells and reveals key differences between Lag3ΔTM and Cre Controls.
From: Autoreactive CD8+ T cells are restrained by an exhaustion-like program that is maintained by LAG3
Diffusion maps were constructed and pseudotemporal ordering was inferred (Methods) using single-cell RNAseq data described in Ext. Data Fig. 5. (a-d) CD8+ T cells from the islets and ndLN were isolated from 4 Cre Control and 4 Lag3∆TM 8-week NOD female mice and were subjected to 5’ paired single cell RNAseq (scRNAseq) and single cell T cell receptor sequencing (scTCRseq). Unless otherwise noted, red is representative of Lag3∆TM dominated clusters (3 + 4) and blue is representative of Cre Control dominated clusters (6). Diffusion component 1 and 2 portray the trajectory of CD8+ T cell differentiation. (a) Diffusion pseudotime colored by DRAGON cluster (Fig. 3b). (b-d) Differential gene expression as a function of diffusion pseudotime. Genes associated with early pseudotime (b), mid-pseudotime (c), and late pseudotime (d). Red corresponds to ORA markers of Lag3∆TM dominated clusters and blue is representative of Cre Control dominated cluster markers derived from ORA analysis. Two sided Pearson’s correlation was used to calculated the Pearson’s correlation coefficient where P < 2.2×10-16 (indicated as ****) in all cases.
