Novel Pancreatic Endocrine Maturation Pathways Identified by Genomic Profiling and Causal Reasoning

Gutteridge, Alex; Rukstalis, J. Michael; Ziemek, Daniel; Tié, Mark; Ji, Lin; Ramos-Zayas, Rebeca; Nardone, Nancy A.; Norquay, Lisa D.; Brenner, Martin; Tang, Kim San; McNeish, John D.; Rowntree, Rebecca K.

doi:10.1371/journal.pone.0056024

Cited by 14 publications

(12 citation statements)

References 83 publications

(82 reference statements)

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“…Similar results have been shown in human exocrine pancreatic cells transduced with constitutively active forms of STAT3 and MAPK (Lemper et al, 2015) and in the human ductal cell line PANC1 treated with proinflammatory cytokines (Valdez et al, 2016). Using a global bioinformatic approach and a causal reasoning algorithm, Gutteridge and colleagues suggested that STAT3 signaling pathway is involved in the activation of NEUROG3 in differentiating human embryonic stem cells (Gutteridge et al, 2013). The studies described above show that JAK-mediated phosphorylation of STAT3 results in NEUROG3 transcriptional activation.…”

Section: Discussionsupporting

confidence: 55%

“…Activation of STAT3-mediated signaling pathways with IL-6 has previously been shown to increase NEUROG3 expression and differentiation toward endocrine lineage (Gutteridge et al, 2013). To determine whether ligands for STAT3 signaling would induce NEUROG3 expression, we studied the phosphorylation status of ectopically expressed WT and mutant STAT3 in HEK293 cells.…”

Section: The Mutant Phenotype Is Not Explained By Differential Phosphmentioning

confidence: 99%

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An Activating STAT3 Mutation Causes Neonatal Diabetes through Premature Induction of Pancreatic Differentiation

et al. 2017

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Activating germline mutations in STAT3 were recently identified as a cause of neonatal diabetes mellitus associated with beta-cell autoimmunity. We have investigated the effect of an activating mutation, STAT3, on pancreatic development using induced pluripotent stem cells (iPSCs) derived from a patient with neonatal diabetes and pancreatic hypoplasia. Early pancreatic endoderm differentiated similarly from STAT3 and healthy-control cells, but in later stages, NEUROG3 expression was upregulated prematurely in STAT3 cells together with insulin (INS) and glucagon (GCG). RNA sequencing (RNA-seq) showed robust NEUROG3 downstream targets upregulation. STAT3 mutation correction with CRISPR/Cas9 reversed completely the disease phenotype. STAT3-activating properties were not explained fully by altered DNA-binding affinity or increased phosphorylation. Instead, reporter assays demonstrated NEUROG3 promoter activation by STAT3 in pancreatic cells. Furthermore, proteomic and immunocytochemical analyses revealed increased nuclear translocation of STAT3. Collectively, our results demonstrate that the STAT3 mutation causes premature endocrine differentiation through direct induction of NEUROG3 expression.

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Section: Discussionsupporting

confidence: 55%

Section: The Mutant Phenotype Is Not Explained By Differential Phosphmentioning

confidence: 99%

An Activating STAT3 Mutation Causes Neonatal Diabetes through Premature Induction of Pancreatic Differentiation

et al. 2017

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“…Data analysis suggested the involvement of novel gene networks, such as NEU-ROG3/E2F1/KDM5B and SOCS3/STAT3/IL-6, in endocrine cell differentiation. Finally, they showed that the addition of IL-6 increased Nkx2.2 and NEUROG3 expression [42].…”

Section: Epigenetics Of Human Es Cell-derived Cellsmentioning

confidence: 97%

Profiling of Embryonic Stem Cell Differentiation

2014

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■ AbstractEmbryonic stem (ES) cells have been shown to recapitulate normal developmental stages. They are therefore a highly useful tool in the study of developmental biology. Profiling of ES cell-derived cells has yielded important information about the characteristics of differentiated cells, and allowed the identification of novel marker genes and pathways of differentiation. In this review, we focus on recent results from profiling studies of mouse embryos, human islets, and human ES cell-derived differentiated cells from several research groups. Global gene expression data from mouse embryos have been used to identify novel genes or pathways involved in the developmental process, and to search for transcription factors that regulate direct reprogramming. We introduce gene expression databases of human pancreas cells (Beta Cell Gene Atlas, EuroDia database), and summarize profiling studies of islet-or human ES cell-derived pancreatic cells, with a focus on gene expression, microRNAs, epigenetics, and protein expression. Then, we describe our gene expression profile analyses and our search for novel endoderm, or pancreatic, progenitor marker genes. We differentiated mouse ES cells into mesendoderm, definitive endoderm (DE), mesoderm, ectoderm, and Pdx1-expressing pancreatic lineages, and performed DNA microarray analyses. Genes specifically expressed in DE, and/or in Pdx1-expressing cells, were extracted and their expression patterns in normal embryonic development were studied by in situ hybridization. Out of 54 genes examined, 27 were expressed in the DE of E8.5 mouse embryos, and 15 genes were expressed in distinct domains in the pancreatic buds of E14.5 mouse embryos. Akr1c19, Aebp2, Pbxip1, and Creb3l1 were all novel, and none has been described as being expressed, either in the DE, or in the pancreas. By introducing the profiling results of ES cell-derived cells, the benefits of using ES cells to study early embryonic development will be discussed.

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“…(B) Stem cell directed differentiation. We used a timecourse in vitro differentiation model of pancreatic beta cell development from (25). NEUROG3+ Pancreatic progenitor cells convert to NKX2-2+ endocrine cells, which are able to further differentiate into fully-functional insulin producing cells upon implantation into mice (26).…”

Section: Differential Gene Expression Profilesmentioning

confidence: 99%

“…To test the utility of the CIE platform and the higherorder pathway enrichment on inferred regulators in generating biological insight, we utilized a more complex data set of stem cell directed differentiation of pancreatic beta cells (25) and the mixed signed STRINGdb network with Quaternary scoring method. Figures 5A and B show the CIE causal regulatory inference results.…”

Section: Drivers Of Stem Cell Directed Differentiationmentioning

confidence: 99%

Causal Inference Engine: A platform for directional gene set enrichment analysis and inference of active transcriptional regulators

Farahmand

O’Connor

Macoska

et al. 2019

Preprint

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Inference of active regulatory mechanisms underlying specific molecular and environmental perturbations is essential for understanding cellular response. The success of inference algorithms relies on the quality and coverage of the underlying network of regulator-gene interactions. Several commercial platforms provide large and manuallycurated regulatory networks and functionality to perform inference on these networks. Adaptation of such platforms for open-source academic applications has been hindered by the lack of availability of accurate, high-coverage networks of regulatory interactions and integration of efficient causal inference algorithms. In this work, we present CIE, an integrated platform for causal inference of active regulatory mechanisms form differential gene expression data. Using a regularized Gaussian Graphical Model, we construct a transcriptional regulatory network by integrating publicly available ChIP-Seq experiments with gene-expression data from tissue-specific RNA-Seq experiments. Our GGM approach identifies high confidence TF-gene interactions and annotates the interactions with information on mode of regulation (activation vs. repression). Benchmarks against manually-curated databases of TF-gene interactions show that our method can accurately detect mode of regulation. We demonstrate the ability of our platform to identify active transcriptional regulators by using controlled in vitro overexpression and stem-cell differentiation studies and utilize our method to investigate transcriptional mechanisms of fibroblast phenotypic plasticity.

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Novel Pancreatic Endocrine Maturation Pathways Identified by Genomic Profiling and Causal Reasoning

Cited by 14 publications

References 83 publications

An Activating STAT3 Mutation Causes Neonatal Diabetes through Premature Induction of Pancreatic Differentiation

An Activating STAT3 Mutation Causes Neonatal Diabetes through Premature Induction of Pancreatic Differentiation

Profiling of Embryonic Stem Cell Differentiation

Causal Inference Engine: A platform for directional gene set enrichment analysis and inference of active transcriptional regulators

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