Genome-wide differential expression profiling of long non-coding RNAs in FOXA2 knockout iPSC-derived pancreatic cells

Abstract

Background Our recent studies have demonstrated the crucial involvement of FOXA2 in the development of human pancreas. Reduction of FOXA2 expression during the differentiation of induced pluripotent stem cells (iPSCs) into pancreatic islets has been found to reduce α-and β-cell masses. However, the extent to which such changes are linked to alterations in the expression profile of long non-coding RNAs (lncRNAs) remains unraveled. Methods Here, we employed our recently established FOXA2-deficient iPSCs (FOXA2−/− iPSCs) to investigate changes in lncRNA profiles and their correlation with dysregulated mRNAs during the pancreatic progenitor (PP) and pancreatic islet stages. Furthermore, we constructed co-expression networks linking significantly downregulated lncRNAs with differentially expressed pancreatic mRNAs. Results Our results showed that 442 lncRNAs were downregulated, and 114 lncRNAs were upregulated in PPs lacking FOXA2 compared to controls. Similarly, 177 lncRNAs were downregulated, and 59 lncRNAs were upregulated in islet cells lacking FOXA2 compared to controls. At both stages, we observed a strong correlation between lncRNAs and several crucial pancreatic genes and TFs during pancreatic differentiation. Correlation analysis revealed 12 DE-lncRNAs that strongly correlated with key downregulated pancreatic genes in both PPs and islet cell stages. Selected DE-lncRNAs were validated using RT-qPCR. Conclusions Our data indicate that the observed defects in pancreatic islet development due to the FOXA2 loss is associated with significant alterations in the expression profile of lncRNAs. Therefore, our findings provide novel insights into the role of lncRNA and mRNA networks in regulating pancreatic islet development, which warrants further investigations.

Identifying miRNA Signatures Associated with Pancreatic Islet Dysfunction in a FOXA2-Deficient iPSC Model

“…Recent studies conducted in our laboratory have unveiled that the absence of FOXA2 during the differentiation of induced pluripotent stem cells (iPSCs) into pancreatic and hepatic cells results in pancreatic islets' and hepatic cells' developmental defects [18,19]. Furthermore, our findings have brought to light changes in mRNA profiles associated with FOXA2 deficiency that are accompanied by significant alterations in the expression of long non-coding RNAs (lncRNAs) at the pancreatic progenitor (PP) and pancreatic islet stages [20]. Recently, we have also unraveled the connection between dysregulated miRNAs and differentially expressed genes (DEGs) in PPs lacking FOXA2 [21].…”

“…MicroRNAs (miRNAs), a group of conserved non-coding RNAs consisting of [19][20][21][22][23][24][25] nucleotides, exert significant influence on diverse biological processes and are implicated in various diseases. Primarily, they function by suppressing the translation or facilitating the degradation of their target mRNAs [8].…”