An Integrated Cell Purification and Genomics Strategy Reveals Multiple Regulators of Pancreas Development

Abstract

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 sets in cell subsets that revealed patterns and processes governing progenitor cell development, lineage specification, and endocrine cell maturation. Purification of Neurog3 mutant cells and module network analysis linked established regulators such as Neurog3 to unrecognized gene targets and roles in pancreas development. Iterative module network analysis nominated and prioritized transcriptional regulators, including diabetes risk genes. Functional validation of a subset of candidate regulators with corresponding mutant mice revealed that the transcription factors Etv1, Prdm16, Runx1t1 and Bcl11a are essential for pancreas development. Our integrated approach provides a unique framework for identifying regulatory genes and functional gene sets underlying pancreas development and associated diseases such as diabetes mellitus.

Customizing the genome as therapy for the β-hemoglobinopathies

“…125,126 In principle, the genetic knockout of BCL11A by targeting BCL11A coding sequence in order to create frameshift null alleles represents a potential therapeutic strategy. Roles of BCL11A in nonhematopoietic lineages, including the neural lineage, 127,128 pancreatic progenitors, 129 and the breast epithelium, 130 would not be problematic upon modification of BCL11A in autologous CD34 1 HSPCs. However, this strategy is limited by extraerythroid roles of BCL11A in the hematopoietic system, including its requirement for B-cell development 127,[131][132][133] and HSC function.…”

The mammal-specific Pdx1 Area II enhancer has multiple essential functions in early endocrine-cell specification and postnatal β-cell maturation

“…We further probed the function of Pdx1 in controlling β-cell versus α-cell fate choice by introducing into Pdx1 endo-ΔII mice a Neurog3 GFP knock-in allele (Lee et al, 2002) and combining this with immunodetection of CD133 (Prom1), a lumenal apical surface marker (Benitez et al, 2014;Sugiyama et al, 2007), to flow-sort Neurog3-expressing endocrine progenitors. This process enriched for endocrine progenitor cells by guarding against the inclusion of cells that had passed well beyond the endocrine progenitor state but still contained a long-lived GFP signal from the Neurog3 GFP knockin reporter (Fig.…”

Converting Adult Pancreatic Islet α Cells into β Cells by Targeting Both Dnmt1 and Arx

“…Regulation of islet epigenetics by DNA methylation appears to be an important regulatory mechanism during α- and β-cell differentiation and maturation (Papizan et al, 2011; Avrahami et al, 2015; Dhawan et al, 2011; Dhawan et al, 2015), and prior studies report an unexpected degree of similarity in gene expression and chromatin modifications of α-cells and β-cells in mice and humans (Arda et al, 2016; Bramswig et al, 2013; Benitez et al, 2014; Moran et al, 2012). Adult α-cells and other islet cells express enzymes like DNA methyltransferase 1 (DNMT1) suggesting a requirement for these factors in maintaining α-cell fate (Avrahami et al, 2015; Dhawan et al, 2011; Benitez et al, 2014).…”

“…Adult α-cells and other islet cells express enzymes like DNA methyltransferase 1 (DNMT1) suggesting a requirement for these factors in maintaining α-cell fate (Avrahami et al, 2015; Dhawan et al, 2011; Benitez et al, 2014). Although DNMT1 activity is best understood in the context of maintaining epigenetic ‘memory’ in proliferating cells, recent studies demonstrate DNMT1 function in non-dividing cells (Dhawan et al, 2011).…”