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Homo sapiens isolate:Human pancreatic islets, EndoC-ßH1 cells

ABSTRACT: EndoC-βH1 multiomic profiling defines gene regulatory programs intrinsic to human β cell identity and function

PROVIDER: PRJNA480287 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7585370.fastq.gz	Fastqsanger.gz
	SRR7585380_1.fastq.gz	Fastqsanger.gz
	SRR7585380_2.fastq.gz	Fastqsanger.gz
	SRR7585371_1.fastq.gz	Fastqsanger.gz
	SRR7585371_2.fastq.gz	Fastqsanger.gz

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Dexamethasone effect on gene expression in human pancreatic islets and human pancreatic EndoC-βH1 cells

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EndoC-βH1 multiomic profiling defines gene regulatory programs intrinsic to human β cell identity and function

Project description:EndoC-βH1 is emerging as a critical human β cell model to study the genetic and environmental etiologies of β cell (dys)function and diabetes. Comprehensive knowledge of its molecular landscape is lacking, yet required, for effective use of this model. Here, we report chromosomal (spectral karyotyping), genetic (genotyping), epigenomic (ChIP-seq and ATAC-seq), chromatin interaction (Hi-C and Pol2 ChIA-PET), and transcriptomic (RNA-seq and miRNA-seq) maps of EndoC-βH1. Analyses of these maps define known (e.g., PDX1 and ISL1) and putative (e.g., PCSK1 and mir-375) β cell-specific transcriptional cis-regulatory networks and identify allelic effects on cis-regulatory element use. Importantly, comparison with maps generated in primary human islets and/or β cells indicates preservation of chromatin looping but also highlights chromosomal aberrations and fetal genomic signatures in EndoC-βH1. Together, these maps, and a web application we created for their exploration, provide important tools for the design of experiments to probe and manipulate the genetic programs governing β cell identity and (dys)function in diabetes.

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Project description:EndoC-BH1 multiomic profiling defines gene regulatory programs intrinsic to human beta cell identity and function

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Project description:We have developped a novel human pancreatic beta cell line: EndoC-βH5. EndoC-βH5 cells are ready-to-use and storable cells with physiological insulin secretion. EndoC-βH5 cells were generated by integrative gene transfer of immortalizing transgenes hTERT and SV40 large T along with Herpes Simplex Virus-1 thymidine kinase into human fetal pancreas. Immortalizing transgenes were removed after amplification using CRE activation and remaining non-excized cells eliminated using ganciclovir. Resulting cells were distributed as ready to use EndoC-βH5 cells. We performed comparative transcriptome analysis with EndoC-βH1 cells , extensive functional and immunological assays. RNA-seq confirmed abundant expression of beta cell transcription factors and functional markers, including incretin receptors.

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Project description:We report the actively transcribed chromatin regions in EndoC-βH1 Cells that are associated with histone H3 lysine 27 acetylation mark.

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RNAsequencing of control and STAT3 knocked down transriptomes of EndoC cells

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Project description:Type 1 diabetes (T1D) is a chronic disease characterized by an autoimmune-mediated destruction of insulin-producing pancreatic β cells. Environmental factors such as viruses play an important role in the onset of T1D and interact with predisposing genes. Recent data suggest that viral infection of human islets leads to a decrease in insulin production rather than β cell death, suggesting loss of β cell identity. We undertook this study to examine whether viral infection could induce human ß cell dedifferentiation. Using the functional human β cell line EndoC-βH1, we demonstrate that polyinosinic-polycitidilic acid (PolyI:C), a synthetic double-stranded RNA that mimics a by-product of viral replication induces a decrease in β cell-specific gene expression. In parallel to this loss, the expression of progenitor-like genes such as SOX9 was activated following PolyI:C treatment or enteroviral infection. SOX9 was induced by the NF-kB pathway and also in a paracrine non-cell autonomous fashion through the secretion of IFNA. Finally, we identified new SOX9 targets in human β cells as new markers of dedifferentiation in T1D. These findings reveal that inflammatory signaling has clear implications in human β cell dedifferentiation.

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