The Zebrafish Pancreas Regulome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB40292 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR5979920.fastq.gz | Fastqsanger.gz | |||
| ERR5979919.fastq.gz | Fastqsanger.gz | |||
| ERR5981173_1.fastq.gz | Fastqsanger.gz | |||
| ERR5981173_2.fastq.gz | Fastqsanger.gz | |||
| ERR5981174_1.fastq.gz | Fastqsanger.gz |
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Project description:A large number of studies have identified and characterized the many transcription factors and cofactors that regulate pancreas organogenesis. Groucho-related genes/Transducin-like Enhancer of Split (Grgs/TLEs) are one such family of cofactors that act as transcriptional co-repressors and are critical for many developmental processes. Several essential pancreatic transcription factors are capable of interacting with GRGs; however, the role of GRG-mediated transcriptional repression in pancreas development is only partially characterized. In this study, we used phenotypic and transcriptomic analyses to determine that GRG3 is essential for β cell development, and in the absence of Grg3 there is compensatory upregulation of Grg4. In Grg3/4 double mutants, mice have severe dysregulation of the pancreas gene program with ectopic expression of liver genes and Foxa1, a master regulator of the liver program. Neurod1, an essential β cell transcription factor and predicted target of Foxa1, becomes downregulated in Grg3/4 mutants, resulting in a loss of β cell proliferation, hyperglycemia, and early lethality. These findings uncover a novel function of GRG-mediated repression in pancreas development.
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Project description:BACKGROUND & AIMS: Acinar cells produce digestive enzymes that impede transcriptomic characterization of the exocrine pancreas. Thus, single-cell RNA-sequencing (scRNA-seq) studies of the pancreas underrepresent acinar cells relative to histological expectations, and a robust approach to capture pancreatic cell responses in disease states is needed. We sought to innovate a method that overcomes these challenges to accelerate study of the pancreas in health and disease. METHODS: We introduce FixNCut, a scRNA-seq approach where tissue is reversibly fixed with dithiobis(succinimidyl propionate) prior to dissociation and single-cell preparation. We apply FixNCut to an established mouse model of acute pancreatitis, validate findings using GeoMx whole transcriptome atlas (WTA) profiling, and integrate our data with prior studies to benchmark our method in both mouse and human pancreas datasets. RESULTS: FixNCut achieves unprecedented definition of challenging pancreatic cells including acinar and immune populations in homeostasis and acute pancreatitis, and identifies changes in all major cell types during injury and recovery. We define the acinar transcriptome during homeostasis and acinar-to-ductal metaplasia and establish a unique gene set to measure deviation from normal acinar identity. We characterize pancreatic immune cells, and analysis of T-cell subsets reveals a polarization of the homeostatic pancreas towards type-2 immunity. We report immune responses during acute pancreatitis and recovery, including early neutrophil infiltration, expansion of dendritic cell subsets, and a substantial shift in the transcriptome of macrophages due to both resident macrophage activation and monocyte infiltration. CONCLUSIONS: FixNCut preserves pancreatic transcriptomes to uncover novel cell states during homeostasis and following pancreatitis, establishing a broadly applicable approach and reference atlas for study of pancreas biology and disease.
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