A single cell map of the developing endoderm implicates fxr in hepatopancreatic development
PhD student: Margrit Kamel
Supervisor at TUD: Nikolay Ninov
Supervisor at KCL: Shanta Persaud
Start date: 15.04.2017 Date of defense: 16.09.2021 Joint PhD
Development is a universal process encoded in our DNA, beginning with a single cell that proliferates and gives rise to multipotent stem cells that differentiate to form the complex systems that make up an adult human. It is crucial that we identify the genetic regulators governing cell fate specification as that will help us understand the molecular mechanisms leading to developmental disorders in organogenesis and adult organ function. Recent advances in single-cell sequencing technologies and computational analysis have allowed defining the transcriptional trajectories underlying germ layer specification and organogenesis. However, a detailed map of endodermal organ development is missing. Here, we established a new single-cell atlas of endodermal development in zebrafish. To this end, we performed single-cell transcriptomics of the endodermal cells of zebrafish embryos at critical early stages of development during which the endodermal organs undergo specification.
Using novel computational methods, we generated a transcriptomic map of the lineage decisions in the developing endoderm called a URD tree (named after the Norse goddess of fate). Our URD tree illustrated that the bile acid receptor farnesoid X receptor (fxr) is enriched in the liver lineage of zebrafish embryos. To define its role in endoderm development, we utilized CRISPR/Cas9 to generate fxr-/- embryos. The mutant embryos showed perturbation in liver and ventral pancreas development, abrogated biliary duct expansion, aberrant bile acid filling of the gallbladder and changes in glucose metabolism. These phenotypes are reminiscent of the human condition where FXR mutations result in progressive familial intrahepatic cholestasis and eventually liver failure.
Thus, we describe a novel role for fxr in early hepatopancreas development in zebrafish. This zebrafish model may allow defining the cellular mechanism underlying the human disease. Finally, to study the role of additional genes in endodermal development, we established a rapid reverse genetic screen to explore how disease-causing genes regulate fate specification in the early endoderm and maintenance of function during organogenesis.
Publications:
Catching new targets in metabolic disease with a zebrafish. M. Kamel, N. Ninov. Curr Opin Pharmacol. 2017;37:41-50.