RETRACTED ARTICLE: Calcium-dependent transcriptional changes in human pancreatic islet cells reveal functional diversity in islet cell subtypes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(2+)) 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(2+)-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(2+) 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(2+) signalling; and (3) 16 mmol/l glucose, 40 mmol/l KCl and 5 mmol/l EGTA (Ca(2+) chelator) to inhibit Ca(2+) 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(2+)-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(2+)-regulated genes, we found that each alpha and beta cell cluster had a different magnitude of Ca(2+) response. We also showed that polyhormonal clusters expressing both INS and GCG, or both INS and SST, are defined by Ca(2+)-regulated genes specific to each cluster. Finally, we identified the gene PCDH7 from the beta cell clusters that had the highest number of Ca(2+)-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(2+)-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(2+)-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). GRAPHICAL ABSTRACT: [Image: see text] SUPPLEMENTARY INFORMATION: The online version contains peer-reviewed but unedited supplementary material available at 10.1007/s00125-022-05718-1.