Calcium-dependent transcriptional changes in human pancreatic islet cells reveal functional diversity in islet cell subtypes.

AIMS/HYPOTHESIS: Pancreatic islets depend on cytosolic calcium (Ca) to trigger the secretion of glucoregulatory hormones and trigger transcriptional regulation of genes important for islet response to stimuli. To date, there has not been an attempt to profile Ca-regulated gene expression in all islet cell types. Our aim was to construct a large single-cell transcriptomic dataset from human islets exposed to conditions that would acutely induce or inhibit intracellular Ca signalling, while preserving biological heterogeneity.

METHODS

We exposed intact human islets from three donors to the following conditions: (1) 2.8 mmol/l glucose; (2) 16 mmol/l glucose and 40 mmol/l KCl to maximally stimulate Ca signalling; and (3) 16 mmol/l glucose, 40 mmol/l KCl and 5 mmol/l EGTA (Ca chelator) to inhibit Ca signalling, for 1 h. We sequenced 68,650 cells from all islet cell types, and further subsetted the cells to form an endocrine cell-specific dataset of 59,373 cells expressing INS, GCG, SST or PPY. We compared transcriptomes across conditions to determine the differentially expressed Ca-regulated genes in each endocrine cell type, and in each endocrine cell subcluster of alpha and beta cells.

RESULTS

Based on the number of Ca-regulated genes, we found that each alpha and beta cell cluster had a different magnitude of Ca response. We also showed that polyhormonal clusters expressing both INS and GCG, or both INS and SST, are defined by Ca-regulated genes specific to each cluster. Finally, we identified the gene PCDH7 from the beta cell clusters that had the highest number of Ca-regulated genes, and showed that cells expressing cell surface PCDH7 protein have enhanced glucose-stimulated insulin secretory function.

CONCLUSIONS/INTERPRETATION: Here we use our large-scale, multi-condition, single-cell dataset to show that human islets have cell-type-specific Ca-regulated gene expression profiles, some of them specific to subpopulations. In our dataset, we identify PCDH7 as a novel marker of beta cells having an increased number of Ca-regulated genes and enhanced insulin secretory function.

DATA AVAILABILITY

A searchable and user-friendly format of the data in this study, specifically designed for rapid mining of single-cell RNA sequencing data, is available at https://lynnlab.shinyapps.io/Human_Islet_Atlas/ . The raw data files are available at NCBI Gene Expression Omnibus (GSE196715).