HNF1A regulates a β-cell RNA splicing program that is disrupted in type 2 diabetes [RNA-seq]

Type 2 diabetes (T2D) is a complex chronic disease that results from pancreatic β-cell dysfunction and insulin resistance. Human genetic evidence supports a pivotal role of HNF1A, encoding hepatocyte nuclear factor 1A, in the pathophysiology of mendelian and type 2 diabetes. Recent single-cell genomic studies also reveal HNF1A as a key transcription factor underlying β-cell heterogeneity and disease progression. We now demonstrate that HNF1A-deficient diabetes is caused by β-cell-autonomous defects, and show that HNF1A governs not only β-cell transcription, but also a broad RNA splicing program. We uncover a regulatory hierarchy in which HNF1A controls transcription of A1CF, which in turn regulates splicing of genes important for membrane transport, lysosome, and secretory functions. Genetic variants that increase human pancreatic islet A1CF expression are associated with improved glycemia, increased insulin secretion, and decreased T2D susceptibility. Furthermore, β-cells from T2D individuals exhibit a profound disruption of A1CF-dependent splicing. These findings link HNF1A-deficiency to a β-cell RNA splicing defect that is impaired in Mendelian diabetes and T2D.