The miRNA profile of human pancreatic islets and beta-cells and relationship to type 2 diabetes pathogenesis

Abstract

Recent advances in the understanding of the genetics of type 2 diabetes (T2D) susceptibility have focused attention on the regulation of transcriptional activity within the pancreatic beta-cell. MicroRNAs (miRNAs) represent an important component of regulatory control, and have proven roles in the development of human disease and control of glucose homeostasis. We set out to establish the miRNA profile of human pancreatic islets and of enriched beta-cell populations, and to explore their potential involvement in T2D susceptibility. We used Illumina small RNA sequencing to profile the miRNA fraction in three preparations each of primary human islets and of enriched beta-cells generated by fluorescence-activated cell sorting. In total, 366 miRNAs were found to be expressed (i.e. >100 cumulative reads) in islets and 346 in beta-cells; of the total of 384 unique miRNAs, 328 were shared. A comparison of the islet-cell miRNA profile with those of 15 other human tissues identified 40 miRNAs predominantly expressed (i.e. >50% of all reads seen across the tissues) in islets. Several highly-expressed islet miRNAs, such as miR-375, have established roles in the regulation of islet function, but others (e.g. miR-27b-3p, miR-192-5p) have not previously been described in the context of islet biology. As a first step towards exploring the role of islet-expressed miRNAs and their predicted mRNA targets in T2D pathogenesis, we looked at published T2D association signals across these sites. We found evidence that predicted mRNA targets of islet-expressed miRNAs were globally enriched for signals of T2D association (p-values <0.01, q-values <0.1). At six loci with genome-wide evidence for T2D association (AP3S2, KCNK16, NOTCH2, SCL30A8, VPS26A, and WFS1) predicted mRNA target sites for islet-expressed miRNAs overlapped potentially causal variants. In conclusion, we have described the miRNA profile of human islets and beta-cells and provide evidence linking islet miRNAs to T2D pathogenesis.

Figure 1. Islet and beta-cell miRNA profiles.

The top 10 most abundant miRNAs in islets and beta-cells are annotated, with colors denoting those shared between the two top 10s (black), in islet top 10 only (orange), and in beta-cell top 10 only (green). There was good correlation between the two profiles (r² = 0.78). A black dashed line represents equality.

Figure 2. Comparison of miRNA profiles across tissues.

The left panel (A) shows the single-linkage hierarchical clustering of inter-tissue profile correlations. In the right panel (B) the top 10 most tissue specific islet miRNAs are displayed in descending order. The colors indicate the normalized expression levels of these miRNAs across the different profiles used in the analysis.

Figure 3. Results for the T2D association signal enrichment analysis in miRNA target gene sets.

The Venn diagram represents the sets of miRNA target genes for each miRNA as predicted by miRDB, miRanda and TargetScan alone, or overlap of these methods. Annotated are the median number of genes in each set (black text), the number of significantly (p-value <0.001, q-value <0.1) enriched gene sets (green text), and the median enrichment of the significantly enriched gene sets (purple text).