Single cell transcriptomic and spatial landscapes of the developing human pancreas
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE197064 | GEO | 2022/12/21
REPOSITORIES: GEO
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Project description:The progress made in directed differentiation of stem cells has shown that understanding human pancreas development can provide cues for generating unlimited amounts of insulin-producing beta cells for transplantation therapy in diabetes. However, current differentiation protocols have not been successful in reproducibly generating functional human beta cells in vitro, partly due to incomplete understanding of human pancreas development. Here, we present detailed transcriptomic analysis of the various cell types of the developing human pancreas, including their spatial gene patterns. We integrated single cell RNA sequencing with spatial transcriptomics at multiple developmental timepoints and revealed distinct temporal-spatial gene cascades in the developing human pancreas.
2022-12-21 | GSE197317 | GEO
Project description:The remarkable differentiation capacity of pluripotent stem cells into any adult cell types have enabled researchers to model human embryonic development and disease process in dishes, as well as deriving specialized cells for replacing damaged tissues. Type 1 diabetes is a degenerative disease characterized by autoimmune destruction of the insulin-producing beta islet cells in the pancreas. Recent advances have led to the establishment of different methods to direct differentiation of human or mouse pluripotent stem cells toward beta cell lineages. However, existing strategies have not yet succeeded in generating fully functional beta cells in vitro. Thus, it remains a major challenge to identify novel regulators of beta cell differentiation and maturation, and the islet-specific genetic and epigenetic regulatory networks are logical targets. To obtain a comprehensive view of the microRNA expression pattern during in vitro directed differentiation of hPSC into pancreatic beta islet cells, we collected 16 samples of 6 stages of differentiated derivatives, 2 samples of human fetal pancreas and 5 samples of purified human beta islet cells for analysis. With these samples, we performed genome-wide microRNA expression profiling using the Illumina Human v2 MicroRNA Expression BeadChips (1,146 assays).
2012-11-07 | E-GEOD-42093 | biostudies-arrayexpress
Project description:The remarkable differentiation capacity of pluripotent stem cells into any adult cell types have enabled researchers to model human embryonic development and disease process in dishes, as well as deriving specialized cells for replacing damaged tissues. Type 1 diabetes is a degenerative disease characterized by autoimmune destruction of the insulin-producing beta islet cells in the pancreas. Recent advances have led to the establishment of different methods to direct differentiation of human or mouse pluripotent stem cells toward beta cell lineages. However, existing strategies have not yet succeeded in generating fully functional beta cells in vitro. Thus, it remains a major challenge to identify novel regulators of beta cell differentiation and maturation, and the islet-specific genetic and epigenetic regulatory networks are logical targets. To obtain a comprehensive view of the mRNA expression pattern during in vitro directed differentiation of hPSC into pancreatic beta islet cells, we collected 16 samples of 6 stages of differentiated derivatives, 2 samples of human fetal pancreas and 5 samples of purified human beta islet cells for analysis. With these samples, we performed genome-wide mRNA expression profiling using the Illumina Infinium HT-12 v4 Gene Expression BeadArray.
2012-11-07 | E-GEOD-42094 | biostudies-arrayexpress
Project description:Maintenance of normal glucose homeostasis is disturbed in diabetes. In the β cell, this involves a glucose sensor converting increased glucose levels to insulin secretion. Understanding the developmental regulatory networks that define a fully functional β cell is important for elucidating the genetic origins of the disease and deriving mature β cells for therapy. Here we show that Aldh1b1 regulates the timing of differentiation in the developing pancreas and the patterning of β cells. In its absence, expression of key β cell transcription factors is deregulated at birth. Null animals become glucose intolerant and hyperglycemic with age. Beta cell dysfunction is associated with extensive transcripteome changes, increased oxidative stress, energy depletion and defects in both glucose sensing and stimulus coupling secretion. These findings identify Aldh1b1 as a central regulator of the transition from the pancreas endocrine progenitor to the committed β cell and demonstrate that changes in the timing of this transition manifest much later in adult life with β cell dysfunction. Islets were isolated from postnatal day one and 8 week old Aldh1b1 null and wt mice. For each P1 samples islets from three mice were combined. Each week 8 sample came from a single mouse. Three samples were analysed per genotype and time point
2015-07-31 | E-GEOD-58025 | biostudies-arrayexpress
Project description:Beta-catenin is an essential mediator of canonical Wnt signaling and a central component of the cadherin-catenin epithelial adhesion complex. Dysregulation of beta-catenin expression has been described in pancreatic neoplasia. Newly published studies have suggested that beta-catenin is critical for normal pancreatic development although these reports reached somewhat different conclusions. In addition, the molecular mechanisms by which loss of beta-catenin affects pancreas development are not well understood. The goals of this study then were; 1] to further investigate the role of beta-catenin in pancreatic development using a conditional knockout approach and 2] to identify possible mechanisms by which loss of beta-catenin disrupts pancreatic development. A Pdx1-cre mouse line was used to delete a floxed beta-catenin allele specifically in the developing pancreas, and embryonic pancreata were studied by immunohistochemistry and microarray analysis. Experiment Overall Design: Parameter: embryonic pancreas from wild type and Pdx1Cre/+; beta-cateninflox/flox Experiment Overall Design: Sample type: RNA Experiment Overall Design: Source name: Embryonic day 14.6 and 16.5 pancreas Experiment Overall Design: Organism: Mus Musculus Experiment Overall Design: Strain: Derived from an intercross of Pdx1Cre/+ ; beta-cateninflox/+ mice. Experiment Overall Design: Extracted molecule:Total RNA Experiment Overall Design: In the study, we hybridized RNA from Embryonic day 14.6 and 16.5 pancreas of wild type (WT) control and Pdx1Cre/+; beta-cateninflox/flox beta-catenin null in the pancreas) embryonic pancreas to Affymetrix MOE430 2.0 GeneChip® arrays containing 45,101 well characterized mouse genes/ESTs.
2007-12-13 | E-GEOD-7430 | biostudies-arrayexpress
Project description:Access to an unlimited number of human pancreatic beta cells represents a major challenge in the field of diabetes to better dissect human beta cell functions and to make significant progress in drug discovery and cell replacement therapies. We previously reported the generation of the EndoC-bH1 human beta cell line that was generated by targeted oncogenesis in human fetal pancreases followed by in vivo cell differentiation in mice. Such cell line displayed many functional properties of adult beta cells. Here we devised a novel strategy to generate conditionally immortalized human beta cell lines based on CRE-mediated excision of immortalizing transgenes. The resulting EndoC-bH2 cell line can be massively amplified in vitro. Transgenes are next efficiently excised upon CRE expression leading to cell proliferation arrest and strong enhancement of beta cell specific features such as insulin expression, content and secretion. Excised EndoC-bH2 cells are close to authentic human beta cells and represent a unique tool to further study beta cell function and to understand why adult human beta cells are refractory to proliferation and how to achieve drug-dependent mobilization towards beta cell expansion. Expression profile of human beta cell lineEndoC-bH2 before and after excision of an immortalization cassette (SV40 LT and hTERT) is compared to human exocrine pancreas cell line SKPC and adult human islets from cadaveric donors. Three replicates were used for each sample group. The three adult human islets samples were taken from GEO series GSE40709 (GSM999550, GSM999551 and GSM999552) and normalized with H357 and SKPC cell line samples using RMA.
2014-03-21 | E-GEOD-48101 | biostudies-arrayexpress
Project description:Intensive efforts are focused on identifying regulators of human pancreatic islet cell growth and maturation to accelerate development of therapies for diabetes. After birth, islet cell growth and function are dynamically regulated; however, establishing these age-dependent changes in humans has been challenging. Here we describe a multimodal strategy for isolating pancreatic endocrine and exocrine cells from children and adults to identify age-dependent gene expression and chromatin changes on a genomic scale. These profiles revealed distinct proliferative and functional states of islet alpha-cells or beta-cells, and histone modifications underlying age-dependent gene expression changes. Expression of SIX2 and SIX3, transcription factors without prior known functions in the pancreas and linked to fasting hyperglycemia risk, increased with age specifically in human islet beta-cells. SIX2 and SIX3 were sufficient to enhance insulin content or secretion in immature beta-cells. Our work provides a unique resource to study human-specific regulators of islet cell maturation and function.
2016-04-14 | GSE65793 | GEO
Project description:Aims/hypothesis Pancreatic beta cells maintain glucose homeostasis and beta cell dysfunction is a major risk factor in developing diabetes. Therefore, understanding the developmental regulatory networks that define a fully functional beta cell is important for elucidating the genetic origins of the disease. Aldehyde dehydrogenase activity has been associated with stem/progenitor cells and we have previously shown that Aldh1b1 is specifically expressed in pancreas progenitor pools. Here we address the hypothesis that Aldh1b1 may regulate the timing of the appearance and eventual functionality of beta cells. Methods We generated an Aldh1b1-knockout mouse line (Aldh1b1tm1lacZ) and used this to study pancreatic development, beta cell functionality and glucose homeostasis in the absence of Aldh1b1 function. Results Differentiation in the developing pancreas of Aldh1b1tm1lacZ null mice was accelerated. Transcriptome analyses of newborn and adult islets showed misregulation of key beta cell transcription factors and genes crucial for beta cell function. Functional analyses showed that glucose-stimulated insulin secretion was severely compromised in islets isolated from null mice. Several key features of beta cell functionality were affected, including control of oxidative stress, glucose sensing, stimulus-coupling secretion and secretory granule biogenesis. As a result of beta cell dysfunction, homozygous mice developed glucose intolerance and age-dependent hyperglycaemia. Conclusions/interpretation These findings show that Aldh1b1 influences the timing of the transition from the pancreas endocrine progenitor to the committed beta cell and demonstrate that changes in the timing of this transition lead to beta cell dysfunction and thus constitute a diabetes risk factor later in life.
2015-07-31 | GSE58025 | GEO
Project description:deBack2012 - Lineage Specification in Pancreas Development
This model of two neighbouring pancreas precursor cells, describes the exocrine versus endocrine lineage specification process. To account for the tissue scale patterns, this couplet model has been extended to hundreds of coupled cells.
This model is described in the article:
On the role of lateral stabilization during early patterning in the pancreas
de Back W., Zhou JX, Brusch L
J. R. Soc. Interface 6 February 2013 vol. 10 no. 79 20120766
Abstract:
The cell fate decision of multi-potent pancreatic progenitor cells between the exocrine and endocrine lineages is regulated by Notch signalling, mediated by cell–cell interactions. However, canonical models of Notch-mediated lateral inhibition cannot explain the scattered spatial distribution of endocrine cells and the cell-type ratio in the developing pancreas. Based on evidence from acinar-to-islet cell transdifferentiation in vitro, we propose that lateral stabilization, i.e. positive feedback between adjacent progenitor cells, acts in parallel with lateral inhibition to regulate pattern formation in the pancreas. A simple mathematical model of transcriptional regulation and cell–cell interaction reveals the existence of multi-stability of spatial patterns whose simultaneous occurrence causes scattering of endocrine cells in the presence of noise. The scattering pattern allows for control of the endocrine-to-exocrine cell-type ratio by modulation of lateral stabilization strength. These theoretical results suggest a previously unrecognized role for lateral stabilization in lineage specification, spatial patterning and cell-type ratio control in organ development.
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2012-11-28 | BIOMD0000000435 | BioModels
Project description:Data accompaning to van Gurp et al. Development 2019. single-cell sequencing of the developing mouse pancreas followed by Seurat analysis to discover genes important for alpha and beta cell differentiation.
2019-06-28 | GSE132364 | GEO