Regulation of endocrine cell alternative splicing revealed by single-cell RNA sequencing in type 2 diabetes pathogenesis

The prevalent RNA alternative splicing (AS) contributes to molecular diversity, which has been demonstrated in cellular function regulation and disease pathogenesis. However, the contribution of AS in pancreatic islets during diabetes progression remains unclear. Here, we reanalyze the full-length single-cell RNA sequencing data from the deposited database to investigate AS regulation across human pancreatic endocrine cell types in non-diabetic (ND) and type 2 diabetic (T2D) individuals. Our analysis demonstrates the significant association between transcriptomic AS profiles and cell-type-specificity, which could be applied to distinguish the clustering of major endocrine cell types. Moreover, AS profiles are enabled to clearly define the mature subset of beta-cells in healthy controls, which is completely lost in T2D. Further analysis reveals that RNA-binding proteins (RBPs), heterogeneous nuclear ribonucleoproteins (hnRNPs) and FXR1 family proteins are predicted to induce the functional impairment of beta-cells through regulating AS profiles. Finally, trajectory analysis of endocrine cells suggests the beta-cell identity shift through dedifferentiation and transdifferentiation of beta-cells during the progression of T2D. Together, our study provides a mechanism for regulating beta-cell functions and suggests the significant contribution of AS program during diabetes pathogenesis. Alternative splicing profiles of human pancreatic islets at single-cell resolution define endocrine cell types and reveal the dysregulated splicing programs in beta-cell maturation in type 2 diabetes pathogenesis.