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An integrative single-cell multiomics profiling of human pancreatic islets identifies T1D associated genes, regulatory regions, and single nucleotide polymorphism [ATAC-seq]

ABSTRACT: To investigate the mechanism of DLK1 and RASGRP1 knockout in inducing beta cell apoptosis, we performed chromatin access profiling analysis using data obtained from ATAC-seq of DLK1 WT vs DLK1-/- and RASGRP1 WT VS RASGRP1-/- hPSCs differentiated beta cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE233474 | GEO | 2023/11/13

REPOSITORIES: GEO

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An integrative single-cell multiomics profiling of human pancreatic islets identifies T1D associated genes, regulatory regions, and single nucleotide polymorphism [bulk RNA-seq]

Project description:To investigate the mechanism of DLK1 and RASGRP1 knockout in inducing beta cell apoptosis, we performed gene expression profiling analysis using data obtained from RNA-seq of DLK1 WT vs DLK1-/- and RASGRP1 WT VS RASGRP1-/- hPSCs differentiated beta cells.

2023-11-13 | GSE233475 | GEO

An integrative single-cell multiomics profiling of human pancreatic islets identifies T1D associated genes, regulatory regions, and single nucleotide polymorphism

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A statistical method for detecting genomic aberrations in heterogeneous tumour samples from single nucleotide polymorphism genotyping data

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Unravelling the Biological Functions of Type 1 Diabetes Associated Noncoding Single-Nucleotide Polymorphism in Human Pancreatic β Cells

Project description:Over 90% of disease associated single nucleotide polymorphisms (SNPs) identified by genome wide association studies (GWAS) are noncoding variants. Platform to efficiently validate the biological function of variants thus discovered remain distinctly lacking. Here, we used β-like cells derived from isogenic human pluripotent stem cells (hPSCs), carrying the type 1 diabetes (T1D)-associated noncoding SNP rs2542151T>G or the knockout of the SNP-associated gene PTPN2−/−, to systematically examine the role of the T1D associated noncoding variant in β cell function and survival. PTPN2−/− and rs2542151T>G both decrease insulin production and elevate cell apoptosis in vitro as well as in vivo. A high content chemical screen identified sodium butyrate, a short-chain fatty acid, to rescue the defects of PTPN2−/−and rs2542151G/G β-like cells in vitro and a humanized mouse model. The combined phosphoproteomics, proteomics and RNA-seq analyses discovered a LAMIN A/HDAC/ERK/complex 1 axis as the downstream pathway of PTPN2 to control β cell survival. Together, this study proved the principle to apply hPSC-derived β cells to study diabetes associated noncoding SNP, and identified a drug candidate for the precision therapy of T1D.

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Single Nucleotide Polymorphism Genotyping in Single-Molecule Electronic Circuits.

Project description:Establishing low-cost, high-throughput, simple, and accurate single nucleotide polymorphism (SNP) genotyping techniques is beneficial for understanding the intrinsic relationship between individual genetic variations and their biological functions on a genomic scale. Here, a straightforward and reliable single-molecule approach is demonstrated for precise SNP authentication by directly measuring the fluctuations in electrical signals in an electronic circuit, which is fabricated from a high-gain field-effect silicon nanowire decorated with a single hairpin DNA, in the presence of different target DNAs. By simply comparing the proportion difference of a probe-target duplex structure throughout the process, this study implements allele-specific and accurate SNP detection. These results are supported by the statistical analyses of different dynamic parameters such as the mean lifetime and the unwinding probability of the duplex conformation. In comparison with conventional polymerase chain reaction and optical methods, this convenient and label-free method is complementary to existing optical methods and also shows several advantages, such as simple operation and no requirement for fluorescent labeling, thus promising a futuristic route toward the next-generation genotyping technique.

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Single-nucleotide polymorphism phylotyping of Escherichia coli.

Project description:We describe a rapid and easily automated phylogenetic grouping technique based on analysis of bacterial genome single-nucleotide polymorphisms (SNPs). We selected 13 SNPs derived from a complete sequence analysis of 11 essential genes previously used for multilocus sequence typing (MLST) of 30 Escherichia coli strains representing the genetic diversity of the species. The 13 SNPs were localized in five genes, trpA, trpB, putP, icdA, and polB, and were selected to allow recovery of the main phylogenetic groups (groups A, B1, E, D, and B2) and subgroups of the species. In the first step, we validated the SNP approach in silico by extracting SNP data from the complete sequences of the five genes for a panel of 65 pathogenic strains belonging to different E. coli pathovars, which were previously analyzed by MLST. In the second step, we determined these SNPs by dideoxy single-base extension of unlabeled oligonucleotide primers for a collection of 183 commensal and extraintestinal clinical E. coli isolates and compared the SNP phylotyping method to previous well-established typing methods. This SNP phylotyping method proved to be consistent with the other methods for assigning phylogenetic groups to the different E. coli strains. In contrast to the other typing methods, such as multilocus enzyme electrophoresis, ribotyping, or PCR phylotyping using the presence/absence of three genomic DNA fragments, the SNP typing method described here is derived from a solid phylogenetic analysis, and the results obtained by this method are more meaningful. Our results indicate that similar approaches may be used for a wide variety of bacterial species.

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Single Nucleotide Polymorphism in Patients with Moyamoya Disease.

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