GEO series
Immune dysregulation and stem-like CD8+ T cell enrichment in type 1 diabetes pancreatic lymph nodes
GSE298811
Homo sapiens
Expression profiling by high throughput sequencing; Other
57 samples
Submitted 2026/07/17
Platform GPL34281Platform GPL24676
Summary
Effector CD8+ T cells are key drivers of type 1 diabetes (T1D) pathogenesis, yet questions remain regarding the molecular defects leading to altered cytotoxicity, peripheral tissue phenotype, and receptor specificity. We analyzed human pancreatic lymph nodes (pLN) using mass cytometry and single-cell RNA sequencing (scRNAseq) with combined T cell receptor (TCR) profiling. Cytometric analysis revealed enrichment of T stem-cell memory (TSCM)-like cells (CD8+CD45RA+CD27+CD28+CCR7+CXCR3+) in T1D pLNs. scRNAseq indicated an elevated inflammatory cytokine gene signature (IFITM3, LTB) along with regulators of terminal differentiation (BCL6, BCL3), coupled with downregulation of exhaustion-associated genes (DUSP2, NR4A2, TSC22D3) in CD8+ T cells in T1D pLN. Immune Response Enrichment Analysis (IREA) indicated IL-15 signaling as a significant driver of these phenotypes. Integrated TCR and transcriptomic analysis revealed a cluster of diverse naïve-like CD8+ T cell clones in T1D pLN. Comparison of pLN and pancreatic slice isolates supported sharing of effector CD8+ T cells, with enhanced terminal effector signatures within the pancreas relative to paired pLN. Multiplex imaging revealed differential localization of TCF1 and TOX-expressing T cells in the pancreas, with islet-proximal TCF1+TOX+ cells displaying a mixture of activation and exhaustion-associated phenotypes. Thus, we provide multimodal cellular profiles enriched in T1D tissues for consideration in therapeutic targeting.
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE298811_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 57 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1271414 and SRA study SRP589533. Searching any of these in the dataset finder brings you back here.
Study design
40 conditions, each sampled once — no replicated groups
Read from the first 40 of 57 sample titles: 40 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
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- GSM9024099 6414 Gene Expression
- GSM9024100 6414 Feature Barcode
- GSM9024101 6414 VDJ
- GSM9024102 6418 Gene Expression
- GSM9024103 6418 Feature Barcode
- GSM9024104 6418 VDJ
- GSM9024105 6461 Gene Expression
- GSM9024106 6461 Feature Barcode
- GSM9024107 6461 VDJ
- GSM9024108 6482 Gene Expression
- GSM9024109 6482 Feature Barcode
- GSM9024110 6482 VDJ
- GSM9024111 6493 Gene Expression
- GSM9024112 6493 Feature Barcode
- GSM9024113 6493 VDJ
- GSM9024114 6548 Gene Expression
- GSM9024115 6548 Feature Barcode
- GSM9024116 6548 VDJ
- GSM9024117 6550 Gene Expression
- GSM9024118 6550 Feature Barcode
- GSM9024119 6550 VDJ
- GSM9024120 6551 Gene Expression
- GSM9024121 6551 Feature Barcode
- GSM9024122 6551 VDJ
- GSM9024123 6578 Gene Expression
- GSM9024124 6578 Feature Barcode
- GSM9024125 6578 VDJ
- GSM9024126 6586 Gene Expression
- GSM9024127 6586 Feature Barcode
- GSM9024128 6586 VDJ
- GSM9024129 6374 Gene Expression
- GSM9024130 6374 Feature Barcode
- GSM9024131 6374 VDJ
- GSM9024132 6457 Gene Expression
- GSM9024133 6457 Feature Barcode
- GSM9024134 6457 VDJ
- GSM9024135 6566 Gene Expression
- GSM9024136 6566 Feature Barcode
- GSM9024137 6566 VDJ
- GSM9024138 6579 Gene Expression
+ 17 more — browse all 57 samples with per-sample file links →
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