Like mapping a river’s branches, mapping the links between genes can be a hefty task, especially when the same gene might control entirely different genes downstream. Take HNF4A and HNF1A, for example: two genes essential for our pancreas, liver and other tissues.
“Both genes encode transcriptional regulators, meaning that they control the expression of a complex network of gene targets that, in turn, contribute to how our organs develop and work,” said Adrian Teo, a Senior Principal Scientist from the A*STAR Institute of Molecular and Cell Biology (A*STAR IMCB).
Mutations in either gene are linked to rare genetic forms of diabetes and an increased risk of developing type 2 diabetes (T2D). These links are likely due to the genes’ influence on beta cells: specialised pancreatic cells that produce insulin, a blood sugar-regulating hormone.
For researchers like Teo, a key question is what that influence looks like at a genetic level, and whether it causes different effects depending on its target. “Given the links between these two genes and the onset of diabetes, if we can identify their downstream gene targets, we’ll also find potential targets for new or better diabetes drugs,” Teo explained.
Teaming up with colleagues at A*STAR IMCB and the A*STAR Bioinformatics Institute (A*STAR BII), as well as researchers at the National University of Singapore, Teo explored HNF4A and HNF1A’s regulatory effects on various genes in pancreatic and liver cells, aiming to shed light on their diverse roles therein.
Top: Venn diagram of the number of overlapping HNF4A-bound target genes in models of human pancreatic islet and beta cells, with the most common target genes listed. Some targets (in green) were also replicated in endocrine progenitor cells. Across: Human induced pluripotent stem cell (iPSC)-derived pancreatic islet spheroids displaying their expression of PDX1, a transcription factor that plays a central role in pancreatic β-cell function, and C-peptide, a pro-insulin marker.
© A*STAR Research
Using gene-mapping techniques such as ChIP-Seq, the team surveyed the duo’s target genes across human stem cell-derived pancreatic and liver cells, which helped them observe their interactions and control over those genes.
“From this analysis, we derived a comprehensive resource of HNF4A and HNF1A downstream targets in human beta cells and liver cells, which enables the follow up of selected gene targets for new mechanistic insights,” said Natasha Ng, A*STAR IMCB Senior Scientist and lead author.
The team uncovered valuable clues about the links between the two genes and diabetes. Among the genes strongly bound and regulated by HNF4A are ACY3 and HAAO, which encode metabolic enzymes; their reduced expression led to beta cells secreting less insulin. Several new genes, including HAAO and USH1C, were also identified as key players in beta cell function.
The team also explored how specific variants of HNF4A and HNF1A, already linked with higher T2D risk, might alter gene function differently from their normal counterparts. By tracing the work of rs1800961, a T2D risk variant of HNF4A, they found that it bound to different targets from normal HNF4A.
“This suggests that the variant, rather than being a disabled form of HNF4A, could instead be upregulating certain genes that add to diabetes predisposition,” noted Teo.
Besides providing a rich resource for more investigations into diabetes and related diseases, the team’s genomic survey could lead to new targeted gene therapies which improve beta cell function.
Moving forward, the team aims to further investigate several promising gene targets from their study, eyeing their potential roles in future diabetes treatments.
The A*STAR-affiliated researchers contributing to this research are from the A*STAR Institute of Molecular and Cell Biology (A*STAR IMCB) and A*STAR Bioinformatics Institute (A*STAR BII).
