Single-cell mRNA-regulation analysis reveals cell type-specific mechanisms of type 2 diabetes

Perturbed secretion of insulin and other pancreatic islet hormones is the main cause of type 2 diabetes (T2D). The islets harbor five cell types that are potentially altered differently by T2D. Whole-islet transcriptomics and single-cell RNA-sequencing (scRNAseq) studies have revealed differentially expressed genes without reaching consensus. Here, we demonstrate that further insights into T2D disease mechanisms can be obtained by network-based analysis of scRNAseq data from individual cell types. We developed differential gene coordination network analysis (dGCNA) and analyzed islet SmartSeq2 scRNAseq data from 16 T2D and 16 non-T2D individuals. dGCNA reveals T2D-induced cell type-specific networks of dysregulated genes with remarkable ontological specificity, thus allowing for a comprehensive and unbiased functional classification of genes involved in T2D. In beta cells eleven networks of genes are detected, revealing that mitochondrial electron transport chain, glycolysis, cytoskeleton organization, cell proliferation, unfolded protein response and three networks of beta cell transcription factors are perturbed, whereas exocytosis, lysosomal regulation and insulin translation programs are instead enhanced in T2D. Furthermore, we validated the ability of dGCNA to reveal disease mechanisms and predict the functional context of genes by showing that TMEM176A/B regulates beta cell microfilament organization and that CEPBG is an important regulator of the unfolded protein response. In addition, when comparing beta- and alpha cells, we found substantial differences, reproduced across independent datasets, confirming cell type-specific alterations in T2D. We conclude that analysis of networks of differentially coordinated genes provides detailed insight into cell type-specific gene function and T2D pathophysiology.