Single-cell chromatin accessibility of developing murine pancreas identifies cell state-specific gene regulatory programs

Identification of mouse and human embryonic pancreatic cells with adult Procr+ progenitor transcriptomic and epigenomic characteristics

Background

The quest to find a progenitor cell in the adult pancreas has driven research in the field for decades. Many potential progenitor cell sources have been reported, but so far this is a matter of debate mainly due to reproducibility issues. The existence of adult Procr+ progenitor cells in mice islets has been recently reported. These were shown to comprise ~1% of islet cells, lack expression of Neurog3 and endocrine hormones, and to be capable of differentiating into all endocrine cell types. However, these findings had limited impact, as further evidence supporting the existence and function of Procr+ progenitors has not emerged.

Methods and findings

We report here an unbiased comparison across mouse and human pancreatic samples, including adult islets and embryonic tissue, to track the existence of Procr+ progenitors originally described based on their global gene expression signature. We could not find Procr+ progenitors on other mouse or human adult pancreatic islet samples. Unexpectedly, our results revealed a transcriptionally close mesothelial cell population in the mouse and human embryonic pancreas. These Procr-like mesothelial cells of the embryonic pancreas share the salient transcriptional and epigenomic features of previously reported Procr+ progenitors found in adult pancreatic islets. Notably, we report here that Procr-like transcriptional signature is gradually established in mesothelial cells during mouse pancreas development from E12.5 to E17.5, which has its largest amount. Further supporting a developmentally relevant role in the human pancreas, we additionally report that a transcriptionally similar population is spontaneously differentiated from human pluripotent stem cells cultured in vitro along the pancreatic lineage.

Conclusions

Our results show that, although the previously reported Procr+ progenitor cell population could not be found in other adult pancreatic islet samples, a mesothelial cell population with a closely related transcriptional signature is present in both the mouse and human embryonic pancreas. Several lines of evidence presented in this work support a developmentally relevant function for these Procr-like mesothelial cells.

Cell identity dynamics and insight into insulin secretagogues when employing stem cell-derived islets for disease modeling

Stem cell-derived islets (SC-islets) are not only an unlimited source for cell-based therapy of type 1 diabetes but have also emerged as an attractive material for modeling diabetes and conducting screening for treatment options. Prior to SC-islets becoming the established standard for disease modeling and drug development, it is essential to understand their response to various nutrient sources in vitro. This study demonstrates an enhanced efficiency of pancreatic endocrine cell differentiation through the incorporation of WNT signaling inhibition following the definitive endoderm stage. We have identified a tri-hormonal cell population within SC-islets, which undergoes reduction concurrent with the emergence of elevated numbers of glucagon-positive cells during extended in vitro culture. Over a 6-week period of in vitro culture, the SC-islets consistently demonstrated robust insulin secretion in response to glucose stimulation. Moreover, they manifested diverse reactivity patterns when exposed to distinct nutrient sources and exhibited deviant glycolytic metabolic characteristics in comparison to human primary islets. Although the SC-islets demonstrated an aberrant glucose metabolism trafficking, the evaluation of a potential antidiabetic drug, pyruvate kinase agonist known as TEPP46, significantly improved in vitro insulin secretion of SC-islets. Overall, this study provided cell identity dynamics investigation of SC-islets during prolonged culturing in vitro, and insights into insulin secretagogues. Associated advantages and limitations were discussed when employing SC-islets for disease modeling.

Spatiotemporal role of SETD2-H3K36me3 in murine pancreatic organogenesis

Pancreas development is tightly controlled by multilayer mechanisms. Despite years of effort, large gaps remain in understanding how histone modifications coordinate pancreas development. SETD2, a predominant histone methyltransferase of H3K36me3, plays a key role in embryonic stem cell differentiation, whose role in organogenesis remains elusive. Here, by combination of cleavage under targets and tagmentation (CUT&Tag), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and bulk RNA sequencing, we show a dramatic increase in the H3K36me3 level from the secondary transition phase and decipher the related transcriptional alteration. Using single-cell RNA sequencing, we define that pancreatic deletion of Setd2 results in abnormalities in both exocrine and endocrine lineages: hyperproliferative tip progenitor cells lead to abnormal differentiation; Ngn3+ endocrine progenitors decline due to the downregulation of Nkx2.2, leading to insufficient endocrine development. Thus, these data identify SETD2 as a crucial player in embryonic pancreas development, providing a clue to understanding the dysregulation of histone modifications in pancreatic disorders.

NEUROD2 function is dispensable for human pancreatic β cell specification

Introduction

The molecular programs regulating human pancreatic endocrine cell induction and fate allocation are not well deciphered. Here, we investigated the spatiotemporal expression pattern and the function of the neurogenic differentiation factor 2 (NEUROD2) during human endocrinogenesis.

Methods

Using Crispr-Cas9 gene editing, we generated a reporter knock-in transcription factor (TF) knock-out human inducible pluripotent stem cell (iPSC) line in which the open reading frame of both NEUROD2 alleles are replaced by a nuclear histone 2B-Venus reporter (NEUROD2nVenus/nVenus).

Results

We identified a transient expression of NEUROD2 mRNA and its nuclear Venus reporter activity at the stage of human endocrine progenitor formation in an iPSC differentiation model. This expression profile is similar to what was previously reported in mice, uncovering an evolutionarily conserved gene expression pattern of NEUROD2 during endocrinogenesis. In vitro differentiation of the generated homozygous NEUROD2nVenus/nVenus iPSC line towards human endocrine lineages uncovered no significant impact upon the loss of NEUROD2 on endocrine cell induction. Moreover, analysis of endocrine cell specification revealed no striking changes in the generation of insulin-producing b cells and glucagon-secreting a cells upon lack of NEUROD2.

Discussion

Overall, our results suggest that NEUROD2 is expendable for human b cell formation in vitro.