Introduction and Objective: Intra-islet responses to proinflammatory stressors are central to the pathogenesis of type 1 diabetes (T1D), yet the gene-regulatory dynamics triggered by inflammatory and viral insults in islet cell populations are not fully understood. Methods: Here, we leveraged 10x Genomics multiome single nucleus sequencing to jointly profile transcriptomes and chromatin accessibility in human islets from 55 donors under control conditions and following 48-hour exposure to either a pro-inflammatory cytokine cocktail (TNFα, IFN-γ, and IL-1β) or coxsackievirus. To capture transcript diversity at higher resolution, we performed long-read sequencing (Oxford Nanopore) on selected multiome cDNA libraries. Results: By multiplexing samples with a randomized block design and implementing robust quality control and data integration pipelines, we identified 135,565 high quality nuclei and resolved exposure-specific response pathways in nine pancreatic cell types - acinar (41,260 nuclei), ductal (35,662), alpha (19,646), beta (29,419), delta (2,555), gamma (1,401), immune (709), stellate (2,204), and endothelial (3,709) - including dynamic shifts in isoform expression in response to treatments. For example, in ductal cells, cytokine treatment upregulated the transcript isoform ENST00000297350.9 (log2 fold change = 2.0, p = 1.9 × 10−5), a splice variant of TNFRSF11B (osteoprotegerin), a member of the TNF receptor superfamily, consistent with previous reports of cytokine-mediated induction in islets. Conclusion: Through ongoing long-read sequencing and integration with joint chromatin accessibility profiling, we are modeling cell-type-specific gene regulatory dynamics that orchestrate islet response to proinflammatory stimuli. This resource highlights transcripts and regulatory nodes with potential functional relevance for immune-β-cell crosstalk, offering mechanistic insights to inform pathogenic immune-islet interactions in T1D. Disclosure C.C. Robertson: None. Z. Meng: None. S. Lin: None. A.K. Huber: None. X. Wang: None. P. Orchard: None. M.R. Erdos: None. F. Collins: Board Member; Current; ImmunoBrain Checkpoint, Inc. S. Chen: Stock/Shareholder; Current; iOrganBio Inc. Stock/Shareholder; Ended; Oncobeat. S. Parker: Research Support; Current; Pfizer Inc. Consultant; Ended; Novo Nordisk. Funding National Institutes of Health (5U01DK127777)
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