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The Impact of Pro-Inflammatory Cytokines on Alternative Splicing Patterns in Human Islets

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posted on 25.10.2021, 22:26 authored by Wenting Wu, Farooq Syed, Edward Simpson, Chih-Chun Lee, Jing Liu, Garrick Chang, Chuanpeng Dong, Clayton Seitz, Decio L. Eizirik, Raghavendra G. Mirmira, Yunlong Liu, Carmella Evans-Molina
Alternative splicing (AS) within the β cell has been proposed as one potential pathway that may exacerbate autoimmunity and unveil novel immunogenic epitopes in type 1 diabetes (T1D). We employed a computational strategy to prioritize pathogenic splicing events in human islets treated with IL-1β + IFN-γ as an ex vivo model of T1D and coupled this analysis with a k-mer based approach to predict RNA binding proteins involved in AS. In total, 969 AS events were identified in cytokine-treated islets, with the majority (44.8%) involving a skipped exon. ExonImpact identified 129 events predicted to impact protein structure. AS occurred with high frequency in MHC Class II-related mRNAs, and targeted qPCR validated reduced inclusion of Exon5 in the MHC Class II gene HLA-DMB. Single-molecule RNA FISH confirmed increased HLA-DMB splicing in pancreatic sections from human donors with established T1D and autoantibody positivity. Serine and Arginine Rich Splicing Factor 2 was implicated in 37.2% of potentially pathogenic events, including Exon5 exclusion in HLA-DMB. Together, these data suggest that dynamic control of AS plays a role in the β cell response to inflammatory signals during T1D evolution.

Funding

This work was supported by NIH grants R01 DK093954 and DK127308 (to C.E-M.), R01 DK060581 and R01 DK105588 (to R.G.M), UC4 DK 104166 (to C.E.M. and R.G.M.), U01 DK127786 (to C.E.M., D.L.E., and R.G.M), VA Merit Award I01BX001733 (to C.E-M.), JDRF 2-SRA-2018-493-A-B (to C.E.M. and R.G.M.) and gifts from the Sigma Beta Sorority, the Ball Brothers Foundation, and the George and Frances Ball Foundation (to C.E.M.).

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