An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development.. Mus musculus

The regulatory logic underlying global transcriptional programs controlling development of visceral organs like the pancreas remains undiscovered. Here, we profiled gene expression in 12 purified populations of fetal and adult pancreatic epithelial cells representing crucial progenitor cell subsets, and their endocrine or exocrine progeny. Using probabilistic models to decode the general programs organizing gene expression, we identified co-expressed gene modules in cell subsets that revealed patterns and processes governing progenitor cell development, lineage specification, and endocrine cell maturation. Module network analysis linked established regulators like Neurog3 to unrecognized roles in endocrine secretion and protein transport, and nominated multiple candidate regulators of pancreas development. Phenotyping mutant mice revealed that candidate regulatory genes encoding transcription factors, including Bcl11a, Etv1, Prdm16 and Runx1t1, are essential for pancreas development or glucose control. Our integrated approach provides a unique framework for identifying regulatory networks underlying pancreas development and diseases like diabetes mellitus. Overall design: Gene expression analysis: 12 primary cell populations from wild-type pancreas and 1 cell type from a mutant background (E15 Ngn3-null cells) pancreas (in fetal and adult stage) were purified using a combination of cell surface markers and transgenic reporters. Total RNA was isolated from each cell type in at least biological triplicates, amplified and hybridized to Affymetrix Mouse 430 2.0 arrays.