Single-cell RNA sequencing reveals preserved pancreatic endocrine cell identity and function by administration of a metabolite-based diet in autoimmune diabetes
Objective: An altered gut bacterial composition is associated with the pathogenesis of type 1 diabetes and short-chain fatty acids are known to play a pivotal role in maintaining gut homeostasis. The effects of short-chain fatty acids on pancreatic islet cell function, insulin production and local immune-infiltration, however, remain elusive.Methods: Five-week-old female NOD mice were fed with an acetylated and butyrylated high-amylose maize-resistant starch (HAMSAB) or control diet for five consecutive weeks. The pancreata were harvested, islets isolated using collagenase, and dispersed into single cells by trypsin. Single-cell RNA sequencing was performed with 10x Chromium. The raw counts were analysed using RStudio with the Seurat package. Human embryonic stem cell-differentiated beta-like cells, mouse islets and INS-1E beta cell line were treated with acetate, butyrate and/or combination. Pro-inflammatory cytokines (IFN-? + IL-1?) were used for stress response and viability assays. Results: single-cell RNA sequencing analysis mapped the gene expression profiles of 4,301 and 4,113 individual islet cells from HAMSAB or HAMS fed mice, respectively. Cells were annotated into 11 clusters: 5 immune, 4 endocrine, acinar and endothelial cell types. The scRNA seq dataset indicated that T cells, B cells, macrophages, and dendritic cell subsets infiltrated the islets of Langerhans from both HAMSAB and HAMS-fed mice. Interestingly, HAMSAB induced an immune tolerogenic profile and lower cytotoxic Gzma+ CD8+ T cells. Moreover, HAMSAB maintained the expression of beta cell functional genes (i.e., Ins1, Ins2, G6pc2, Prlr and Iapp) and decreased the expression of genes associated with cellular stress (i.e., Fos, Impact, Stat1, Dusp1 and Hsp40/Dnajb1). Short-chain fatty acid treatment decreased pro-inflammatory cytokine-induced stress in mouse islets and INS-1E beta cells. In addition, HAMSAB preserved the identity of endocrine cells, evaluated by a decrease in dedifferentiated poly-hormonal cells expressing endocrine progenitor genes (MafA, Nfix). Importantly, short-chain fatty acids increased insulin levels in human embryonic stem cell-differentiated beta-like cells and improve transplantation outcome in NOD/SCID mice. Conclusions: Short-chain fatty acids prevent diabetes development in NOD mice, at least in part, by enhancing beta cell function and preserving the cell identity of endocrine cells under inflammatory-mediated autoimmune stress. Overall design: Single-cell RNA-Seq of mouse pancreata fed with HAMS or HAMSAB diet