Fig. 1: Blood T cell atlas of children with T1D and healthy donors. | Nature Communications

Fig. 1: Blood T cell atlas of children with T1D and healthy donors.

From: Imbalance of stem-like and effector T cell states in children with early type 1 diabetes across conventional and regulatory subsets

Fig. 1

A Experimental design. PBMCs from children with newly diagnosed T1D (T0, n = 30), one-year follow-up (T1, n = 29), and age-matched healthy donors (HD, n = 13) were collected and cryopreserved. Sorted CD4⁺ and CD8⁺ T cells underwent scRNA-seq (gene expression and paired TCR repertoire profiling). Findings were validated in independent published cohorts. B Cohort characteristics. Each dot indicates one donor. Upper panel: group, age, sex, remission at T1 (defined as insulin dose–adjusted HbA1c < 9) and diabetic ketoacidosis at T0 (defined as pH < 7.3 and/or bicarbonate < 15 mEq/L). Middle panel: autoantibody status (GAD, IAA, IA2, ZNT8). Lower panel: T1D risk HLA alleles inferred from scRNA-seq. C–E CD8⁺ T cells (n = 63,068 cells from 43 donors) after quality control and exclusion of contaminants, unconventional subsets, and CD8low NK cells. C UMAP of conventional CD8⁺ T cell populations. Louvain clusters were merged by functional similarity and annotated by marker genes. D Heatmap of selected cluster-defining genes (row-scaled z-scores of average expression). E TCR repertoire analysis: UMAP colored by clonal expansion (log₂ counts of recurrent paired CDR3α/CDR3β). Bottom: quantification of expansion across clusters. F–H CD4⁺ T cells (n = 79,876 cells from 43 donors) after exclusion of low-quality, contaminating, and unconventional subsets. F UMAP of conventional CD4⁺ T cell populations. Louvain clusters merged and annotated as in (C). G Same as (D) but for CD4⁺ clusters. H TCR repertoire analysis: UMAP colored by clonal expansion, calculated as in (E), with quantification across clusters. T1D – Type 1 Diabetes Mellitus, T0 – timepoint at diagnosis, T1 – timepoint one year after diagnosis, Tmk – unconventional KLRC2+ memory T cells, Tmem – memory T cells, Tcm – central memory T cells, Treg – regulatory T cells, Tsig – T cells with signaling transduction signature, ISAGhi – T cells with interferon signaling signature, GAD – Glutamic Acid Decarboxylase, IAA – Insulin Autoantibodies, IA2 – Tyrosine Phosphatase-like Protein IA-2, ZNT8 – Zinc Transporter 8.

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