Single-cell transcriptomics of human islet ontogeny defines the molecular basis of β-cell dedifferentiation in T2D

Abstract

Objective Dedifferentiation of pancreatic β-cells may reduce islet function in type 2 diabetes (T2D). However, the prevalence, plasticity and functional consequences of this cellular state remain unknown. Methods We employed single-cell RNAseq to detail the maturation program of α- and β-cells during human ontogeny. We also compared islets from non-diabetic and T2D individuals. Results Both α- and β-cells mature in part by repressing non-endocrine genes; however, α-cells retain hallmarks of an immature state, while β-cells attain a full β-cell specific gene expression program. In islets from T2D donors, both α- and β-cells have a less mature expression profile, de-repressing the juvenile genetic program and exocrine genes and increasing expression of exocytosis, inflammation and stress response signalling pathways. These changes are consistent with the increased proportion of β-cells displaying suboptimal function observed in T2D islets. Conclusions These findings provide new insights into the molecular program underlying islet cell maturation during human ontogeny and the loss of transcriptomic maturity that occurs in islets of type 2 diabetics.

Multiomics single-cell analysis of human pancreatic islets reveals novel cellular states in health and type 1 diabetes

“…The top 20 clusters are displayed and a stringent cut-off of 1e-6 was applied to determine significant gene ontology pathways. For gene-set-enrichment-analysis (GSEA) analysis, GSEA Preranked (4.0.1) ( 53 ) was run on a pre-ranked gene list using either user-provided pancreatic gene expression sets ( 22, 28 ) or standard hallmark gene signatures provided by the Molecular Signatures Database (MSigDB) ( 54 ).…”

“…S4b). We found that approximately 1.3% of cells from each individual donor (median across all donors) were classified as Hybrid cells, with the exception of one ABB+ donor (AAB+ #3), which was overrepresented in the Hybrid cluster ( Fig To gain further insight into the molecular nature of Hybrid cells, we next compared each Hybrid subpopulation to relevant canonical cell populations to determine their transcriptional divergence (tables S51 to 57) and convergence with respect to gene signatures of common pancreatic cell types (22,28). To this end, we observed the enrichment of the alpha cell signature in Endocrine-like Hybrids, the ductal cell signature in Ductal-like Hybrids, and the acinar cell signature in Acinar-like Hybrids.…”

“…how many principal components to choose when clustering: (1) a Jackstraw-inspired resampling test that Garnett was used for initial cell classification as previously described (9). In brief, a cell type marker file (table S60) with 17 different cell types was compiled using various resources (18)(19)(20)(21)(22)28), and this marker file was checked for specificity using the…”

“…For Metascape analysis (http://metascape.org/gp/index.html#/main/step1; (52)), less than or equal to 3,000 differential genes (FDR< 0.05 and fold change (FC) > 0.1) were subjected to analysis.The top 20 clusters are displayed and a stringent cut-off of 1e-6 was applied to determine significant gene ontology pathways. For gene-set-enrichment-analysis (GSEA) analysis, GSEA Preranked (4.0.1) (53) was run on a pre-ranked gene list using either user-provided pancreatic gene expression sets(22,28) or standard hallmark gene signatures provided by the Molecular Signatures Database (MSigDB) (54).…”

The Anna Karenina model of β cell maturation in development and their dedifferentiation in type 1 and type 2 diabetes

“…To validate our unbiased clustering results, we directly examined the expression of a broad list of published markers of mature β cell identity (20)(21)(22)(23)(24)(25)(26)(27)(28)(29), "β cell disallowed" genes (30-32), markers of immature β cells and non-insulin-expressing β cell precursors (6,8,9,20,(33)(34)(35)(36), and islet hormones ( Figure 4). Several markers of immature β cells and β cell progenitor genes (MafB, Nnat, Sox17, Fev, and Myc), as well as most "β cells disallowed" genes (Ldha, Hk1, Mylk, Igfbp4, Ndrg2, Pcolce, and Slc16a2) showed down-regulation during normal β cell maturation but were not re-expressed in either type of diabetes.…”