CtBP2 beta cell KO islet RNA-seq
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA913646 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22805152_1.fastq.gz | Fastqsanger.gz | |||
| SRR22805152_2.fastq.gz | Fastqsanger.gz | |||
| SRR22805153_1.fastq.gz | Fastqsanger.gz | |||
| SRR22805153_2.fastq.gz | Fastqsanger.gz | |||
| SRR22805154_1.fastq.gz | Fastqsanger.gz |
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Project description:RNA-seq analysis was performed using pancreatic islet samples from flox mice and beta-cell specific CtBP2 KO mice.
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Project description:Purpose: The goal of this study is to investigate how METTL3 regulates islet β-cell function. Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from pancreatic islets of Mettl3flox/flox and β-Mettl3-KO mice at 8 weeks old. Each RNA sample was pooled from four Mettl3flox/flox and β-Mettl3-KO mice, respectively. Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina Novaseq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome(GRCm38.p6) with Hisat2 v2.0.5, and the aligned reads were used to quantify mRNA expression by using featureCounts v1.5.0-p3. Conclusion: Our study represents the first detailed analysis of islet transcriptomes from Mettl3flox/flox and β-Mettl3-KO mice, generated by RNA-seq technology. The RNA-seq analysis showed that 2560 genes were downregulated and 3408 genes were upregulated in the pancreatic islets of β-Mettl3-KO mice. GO analysis showed that the downregulated genes were primarily related to insulin secretion, SNARE binding, and mitochondrial respiratory chain, whereas the upregulated genes were associated with the immune response, B cell activation, and antigen binding.
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Project description:Purpose: Through mRNA m6A-profiling, we aim to characterize the mRNA m6A changes in pancreatic islets obtained from Mettl3flox/flox and β-Mettl3-KO mice. Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from pancreatic islets of Mettl3flox/flox and β-Mettl3-KO mice at 8 weeks old. A total of 2-3 μg RNAs were pooled from nine Mettl3flox/flox mice and twelve β-Mettl3-KO mice, respectively. Three independent biological replicates of each group were used for MeRIP-seq. Fragmented RNA (~100 nt) was incubated for 2 hr at 4oC with anti-m6A polyclonal antibody (Merk Millipore) in the immunoprecipitation experiment. Then, immunoprecipitated RNAs or Input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols. After mapping reads to the reference genome, exomePeak R package (version 2.16.0) was used for the m6A peak identification in each anti-m6A immunoprecipitation group with the corresponding input samples serving as a control, and q-value threshold of enrichment of 0.05 was used for all data sets. The m6A-enriched motifs of each group were identified by HOMER (version 4.9.1). Conclusion: The islet mRNA m6A profiles in Mettl3flox/flox and β-Mettl3-KO mice were characterized.
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Project description:We measured changes in the human islet proteome following 72-hr exposure to 3 mM R-beta-hydroxybutyrate. Islets from 12 metabolically healthy human islet donors were obtained from the Alberta Diabetes Institute Islet Core
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Project description:Blood vessels play a critical role in pancreatic islet health and function, yet current culture methods to generate islet organoids from human pluripotent stem cells (SC-islets) lack a vascular component. Here, we engineered 3D vascularized SC-islet organoids by assembling SC-islet cells, human primary endothelial cells (ECs) and fibroblasts both in a non-perfused model and a microfluidic device with perfused vessels. Vasculature improved stimulus-dependent Ca2+ influx into SC-β-cells; a hallmark of β-cell function that is blunted in non-vascularized SC-islets. We show that an islet-like basement membrane is formed by vasculature and contributes to the functional improvement of SC-β-cells. Furthermore, cell-cell communication networks based on scRNA-seq data predicted BMP2/4-BMPR2 signaling from ECs to SC-β-cells. Correspondingly, BMP4 augmented the SC-β-cell Ca2+ response and insulin secretion. The here-described vascularized SC-islet models will enable further studies of crosstalk between β-cells and ECs and serve as an in vivo-mimicking platform for disease modeling and therapeutic testing.
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Project description:We found that in rodents, postnatal beta-cell maturation is associated with changes in the expression of several islet microRNAs and discovered that these modifications are driven by changes in the nutrient supply. Mimicking the microRNA changes observed during β-cell maturation in newborn rat islet cells was sufficient to promote glucose-induced insulin release and to achieve a mature β-cell secretory phenotype. Moreover, the modifications in the level of some of these microRNAs reduced the proliferation of newborn β-cells, suggesting that they contribute to the limited proliferative capacity of adult β-cells. These findings demonstrated that miRNAs contribute to postnatal beta-cell maturation and development. Their role is likely to promote beta-cell adaptation to fule supply and to maintain glucose homeostasis by regulating insulin release and proliferation. Islets from 10-day-old rats (P10) (n=3) or 3-month-old male rat (n=3) were taken. Total RNA was extracted and mRNA profiling via Illumina single-end sequencing of mRNA-seq libraries was performed.
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Project description:Altered islet architecture is associated with β cell dysfunction and Type 2 Diabetes (T2D) progression, but molecular effectors of islet spatial organization remain mostly unknown. Although Notch signaling is known to regulate pancreatic development, we observed “re-activated” β cell Notch activity in obese mouse models. To test the repercussions and reversibility of Notch effects, we generated doxycycline-dependent, β cell-specific Notch gain-of-function mice. As predicted, we found that Notch activation in post-natal β cells impaired glucose stimulated insulin secretion (GSIS) and glucose intolerance, but we observed a surprising remnant glucose intolerance after doxycycline withdrawal and cessation of Notch activity, associated with a marked disruption of normal islet architecture. Transcriptomic screening of Notch-active islets revealed increased Ephrin signaling. Commensurately, exposure to Ephrin ligands increased β cell repulsion, and impaired murine and human pseudo-islet formation. Consistent with our mouse data, Notch and Ephrin signaling are increased in metabolically-inflexible β cells in patients with T2D. These studies suggest than islet architecture can be permanently altered by β cell Notch/Ephrin signaling during a morphogenetic window in early life.
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Project description:MeRIP-Seq of pancreatic islets in Mettl3flox/flox and islet β cell-specific Mettl3 knockout (β-Mettl3-KO) mice
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