Transcriptional changes and the role of ONECUT1 in hPSC pancreatic differentiation

Sandra Heller,Cécile Julier,Matthias Hebrok,Thomas Seufferlein,Ryan Geusz,Gopika G Nair,Ivan G Costa,Maike Sander,Markus Breunig,Alexander Kleger,Xi Zhang,Qiong Lin,Meike Hohwieler,Zhijian Li

doi:10.1038/s42003-021-02818-3

Abstract

Cell type specification during pancreatic development is tightly controlled by a transcriptional and epigenetic network. The precise role of most transcription factors, however, has been only described in mice. To convey such concepts to human pancreatic development, alternative model systems such as pancreatic in vitro differentiation of human pluripotent stem cells can be employed. Here, we analyzed stage-specific RNA-, ChIP-, and ATAC-sequencing data to dissect transcriptional and regulatory mechanisms during pancreatic development. Transcriptome and open chromatin maps of pancreatic differentiation from human pluripotent stem cells provide a stage-specific pattern of known pancreatic transcription factors and indicate ONECUT1 as a crucial fate regulator in pancreas progenitors. Moreover, our data suggest that ONECUT1 is also involved in preparing pancreatic progenitors for later endocrine specification. The dissection of the transcriptional and regulatory circuitry revealed an important role for ONECUT1 within such network and will serve as resource to study human development and disease.

Highlights

Cell type specification during pancreatic development is tightly controlled by a transcriptional and epigenetic network
We focused on the functional role of the transcription factors (TFs) ONECUT1 and found an important role as regulator of pancreas progenitor differentiation in our analysis
We observed a similar expression pattern of stage-specific TFs in two further data sets employing distinct cell lines[5,17,29,30], where key markers for pluripotent stem cells (PSC) (SOX2), definitive endoderm (DE) (SOX17, CXCR4), pancreatic endoderm (PE) (PDX1), and pancreatic progenitors (PP) stage (NKX6.1) as well as other TFs such as FOXA2, SOX9, and PROX1 were expressed at the respective stages

Summary

Introduction

Cell type specification during pancreatic development is tightly controlled by a transcriptional and epigenetic network. The precise role of most transcription factors, has been only described in mice To convey such concepts to human pancreatic development, alternative model systems such as pancreatic in vitro differentiation of human pluripotent stem cells can be employed. Transcriptome and open chromatin maps of pancreatic differentiation from human pluripotent stem cells provide a stage-specific pattern of known pancreatic transcription factors and indicate ONECUT1 as a crucial fate regulator in pancreas progenitors. Different forms of diabetes have been appropriately modeled by PSC differentiations[13] Sequencing techniques such as RNA and Assay for Transposase Accessible Chromatin sequencing (RNA-seq and ATAC-seq) can be applied at distinct differentiation stages to allow the global characterization of transcriptional and regulatory changes during pancreatic differentiation. We applied stage-specific RNA-, ChIP-seq, and ATACseq experiments during PSC-based differentiations to dissect transcriptional and regulatory mechanisms during pancreatic development. We could demonstrate that mutations in ONECUT1 contribute to a broad spectrum of diabetes[16]

Methods

Results

Conclusion