Extended Data Fig. 2: Intra-islet CD8⁺ T cells express LAG3, which marks exhausted CD8⁺ T cells, though total intra-islet CD8⁺ T cells also share features of effector T cells.

Transcriptional and epigenetic analysis was performed on intra-islet CD8⁺ T cells (a) WT Lag3 locus is shown in the top panel. The Lag3^L/L-YFP construct is generated by inserting LoxP sites flanking the transmembrane region, exon 7, of the Lag3 gene (middle panel). (b) YFP expression is demonstrated in the Lag3^L/L-YFP.NOD, marking those CD8⁺ T cells which have transcribed Lag3. (c-d) Bulk population RNAseq was preformed comparing intra-islet YFP⁺ and YFP^– CD8⁺ T cells, along with YFP^– ndLN and pLN controls. Cells are pooled from 3 Lag3^L/L-YFP.NOD 8 week old females in 2 independent experiments. (c) Relative expression of selected co-stimulatory or co-inhibitory receptors in the YFP⁺ vs YFP^– intra-islet CD8⁺ T cells. (d) Leading-edge gene set enrichment analysis was preformed comparing YFP⁺ and YFP^– intra-islet CD8⁺ T cells to published exhaustion⁶⁴ and activation⁶⁵ datasets. NES = Normalized Enrichment score, fdr = false discovery rate. (Methods) (e) scATACseq was preformed comparing E8i^CRE/CRE-GFP.NOD CD8⁺ T cells derived from islets and ndLN (n = 4, 8 week Females). Enrichment for effector signature peaks is shown.