Twan de Winter1,2, Miha Sovrovic2, Esmée Dekker1, Natascha de Graaf1, Françoise Carlotti1, Eelco de Koning*1, Anna Alemany*2
1Department of Internal Medicine, LUMC, Leiden; 2Department of Anatomy and Embryology, LUMC, Leiden; *shared senior author
Background
Type 2 diabetes (T2D) is a heterogeneous disease of beta cells caused by environmental and genetic factors. There is limited knowledge on how genetic variants regulate gene expression in beta cells, and whether this regulation is affected in T2D. One mechanism of gene regulation involves the binding of microRNAs (miRNA) to the 3’ untranslated region (UTR). 3’UTR variants can act as expression quantitative trait loci (eQTLs) by influencing mRNA stability. Here we set out to investigate the relationship between miRNA expression profiles and eQTL behavior in beta cells from non-diabetic (ND) and T2D donors.
Methods
We identified cell type-specific 3’UTR eQTLs by correlating gene expression with donor-specific variants obtained both from single-cell RNA sequencing datasets of primary human islets. We used four publicly available datasets (ND n=24, T2D n=12), and performed miRNA-seq (ND n=3, T2D n=3). miRNA-eQTL binding score calculation was used to predict miRNA binding. A miRNA-eQTL pair was validated by luciferase assays in human cell lines and glucose stimulated insulin secretion assays in islets.
Results
We detected 31,563 eQTLs in all pancreatic cell types. In beta cells of ND donors, we observed 1321 eQTLs, which was reduced to 434 eQTLs in T2D donors. Reduction in miRNA expression explains the loss of 15 beta cell eQTL signals in T2D. Among these, rs701848, which is located in the 3’UTR of PTEN, alters the binding of miRNA mir-127-5p. This interaction was validated by treatment with mir-127-5p and anti-mir-127-5p in HEK293T and EndoC-BH1 respectively. Lastly, we show that beta cells carrying the alternative variant of rs701848 displayed a reduced function.
Conclusion
eQTLs signals in beta cells are altered in T2D, some of these changes can be explained by differential miRNA expression. Ultimately, understanding beta cell-specific eQTLs offers key insights into gene regulation in health and disease, suggesting pathways for T2D therapy.