Predicting the Key Regulators of Cell Identity in Human Adult Pancreas

Abstract

SUMMARYCellular identity during development is under the control of transcription factors that form gene regulatory networks. However, the transcription factors and gene regulatory networks underlying cellular identity in the human adult pancreas remain largely unexplored. Here, we integrate multiple single-cell RNA sequencing datasets of the human adult pancreas, totaling 7393 cells, and comprehensively reconstruct gene regulatory networks. We show that a network of 142 transcription factors forms distinct regulatory modules that characterize pancreatic cell types. We present evidence that our approach identifies key regulators of cell identity in the human adult pancreas. We predict that HEYL and JUND are active in acinar and alpha cells, respectively, and show that these proteins are present in the human adult pancreas as well as in human induced pluripotent stem cell-derived pancreatic cells. The comprehensive gene regulatory network atlas can be explored interactively online. We anticipate our analysis to be the starting point for a more sophisticated dissection of how transcription factors regulate cell identity in the human adult pancreas. Furthermore, given that transcription factors are major regulators of embryo development and are often perturbed in diseases, a comprehensive understanding of how transcription factors work will be relevant in development and disease biology.HIGHLIGHTS-Reconstruction of gene regulatory networks for human adult pancreatic cell types-An interactive resource to explore and visualize gene expression and regulatory states-Predicting putative transcription factors driving pancreatic cell identity-HEYL and JUND as candidate regulators of acinar and alpha cell identity, respectively

Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers

“…Of note, the motif for Pbx3, a transcription factor driving Sst expression in delta cells [84], was enriched in accessible chromatin at promoter-proximal regions. The motif for Stat4, recently implicated in establishing alpha cell identity [85] was concentrated exonic chromatin. Lastly, the motif for Ptf1a, a transcription factor identified in early pancreatic endocrine cell development [86], was preferentially associated with areas of open chromatin at distal intergenic regions.…”

PDX1 directs a core developmentally and evolutionarily conserved gene program in the pancreatic islet

“…The comparison between fetal and adult stages revealed stage-specific and conserved signature genes in fetal beta cells, ductal cells, and acinar cells (Figure 3C). For example, ASCL2 is a target gene of Wnt signaling (27) and expressed in human mature beta cells (28), which was enriched in fetal beta cells and bound by PDX1 only in fetal beta cells. MEIS2 and MAFB were directly regulated by PDX1 in both fetal and adult beta cells.…”

A multimodal cross-species comparison of pancreas development

“…MEIS2 encodes a homeobox TF in the three amino acid loop extension (TALE) family and acts together with PBX and HOX TFs to form dimeric or trimeric complexes to enhance DNA binding specificity and affinity for target gene regulation 59 . MEIS2 was detected in human embryonic 25 and adult beta cells 60 and shown to regulate PAX6 expression during pancreas development 61 . To understand the role of MEIS2 in beta cell differentiation, we performed in silico perturbation using CellOracle to mimic a MEIS2 knockout (KO, Fig.…”