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Gene profiling of human iPS-ECs with monoallelic and biallelic mutation in HNF1A gene as compared to isogenic hiPS-ECs control cells

ABSTRACT: Gene profiling of human iPS-ECs with monoallelic and biallelic mutation in HNF1A gene as compared to isogenic hiPS-ECs control cells

PROVIDER: PRJEB44730 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5868820.fastq.gz	Fastqsanger.gz
	ERR5868821.fastq.gz	Fastqsanger.gz
	ERR5868812.fastq.gz	Fastqsanger.gz
	ERR5868822.fastq.gz	Fastqsanger.gz
	ERR5868813.fastq.gz	Fastqsanger.gz

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Gene profiling of human iPS-ECs with monoallelic and biallelic mutation in HNF1A gene as compared to isogenic hiPS-ECs control cells

Project description:Induced pluripotent stem cells (iPSCs) provide a well-defined source of tissue-specific cells and are invaluable disease modeling tools. As HNF1A-MODY patients were shown to exhibit diabetic microvascular complications, their iPSCs can be used to derive endothelial cells (ECs) and investigate possible mechanisms contributing to the complications. However, the clinical phenotype of HNF1A-MODY diabetes varies considerably, and studies examining correlations between genotype and phenotype are still rare. Therefore, in the current study, we looked for possible endothelial dysfunction using iPSCs as disease modeling tools. HNF1A-MODY phenotype was modeled through the introduction of mutations in HNF1A gene in control human induced pluripotent stem cells (hiPSCs) lines, using CRISPR/Cas9, generating both monoallelic and biallelic mutation in HNF1A. The mutations resulted in premature stop codon of HNF1A gene. Subsequently, all lines were differentiated toward ECs (hiPSC-ECs), cell sorted to obtain pure population of CD31+/VE-cad+ cells, and used for global transcriptome analysis.

2026-02-19 | E-MTAB-10404 | biostudies-arrayexpress

Changes in the proteome of human induced pluripotent stem cells derived endothelial cells with CRISPR/Cas9 induced monoallelic and biallelic mutation of the HNF1A gene

Project description:Maturity onset diabetes of the young (MODY) is caused by a mutation in a single gene and leads to diabetes under the age of 25. The mutations in HNF1A gene (leading to HNF1A-MODY) cause about 70% of all MODY cases. It was shown that patients with HNF1A-MODY often develop diabetic microvascular complications, related to endothelial dysfunction, however, it is not clear whether these complications are the result of hyperglycemia or due to the genetic mutation in HNF1A gene. For analysis, monoallelic (MAC) and biallelic (BAC) mutants in the HNF1A gene were used for comparative proteomics to the isogenic control (hiPSCs-EC).

2026-03-01 | PXD039471 | Pride

RNA-seq of hiPSC-ECs from HNF1A-MODY patient and corrected isogenic control lines

Project description:RNA-seq of hiPSC-ECs from HNF1A-MODY patient and corrected isogenic control lines

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RNA-seq of hiPSC-ECs from HNF1A-MODY patient and corrected isogenic control lines

Project description:The experiment aims to find differences in gene expression in endothelial cells due to a heterozygous mutation in HNF1A, which cause maturity-onset diabetes of the young (MODY). For that purpose human induced pluripotent stem cell (hiPSCs) line from an HNF1A-MODY patient was repaired using CRISPR/Cas9, thus generating two isogenic (patient-specific) control lines. The hiPSCs from patient and the respective control lines were differentiated toward endothelial cells, and the gene expression in these cells was compared.

2026-02-22 | E-MTAB-16548 | biostudies-arrayexpress

Biallelic TET2 mutation sensitizes to 5’-azacitidine in acute myeloid leukemia. Stolzel et al. JCI Insight. [RNA-Seq]

Project description:To investigate the impact of TET2 loss on global transcription in HEL acute myeloid leukaemia (AML) cells. HEL AML cells, which have a monoallelic TET2 mutation, were targeted by CRISPR to inactivate the remaining TET2 allele, generating isogenic cell clones with either monoallelic or biallelic TET2 mutation.

2023-03-08 | GSE218227 | GEO

Biallelic TET2 mutation sensitizes to 5’-azacitidine in acute myeloid leukemia. Stolzel et al. JCI Insight. [Illumina Infinium]

Project description:To investigate the impact of TET2 loss on global genomic methylation in HEL acute myeloid leukaemia (AML) cells. HEL AML cells, which have a monoallelic TET2 mutation, were targeted by CRISPR to inactivate the remaining TET2 allele, generating isogenic cell clones with either monoallelic or biallelic TET2 mutation.

2023-03-08 | GSE217940 | GEO

Comparison of transciptome of hiPS-MSC versus MSC (2D culture) and analyze regulated trascripts during differentiation of hiPS-MSC and MSC on a 3D scaffold

Project description:Expression data from hiPS lines after commitment towards mesenchymal lineage (hiPS-MSC) and expression data of mesenchymal lines (MSC), used as positive control of commitment. Following this, hiPS-MSC and MSC are seeded on scaffold to differentiate in a ligamentous (middle) and osseous (edges) part (post 21 days 3D differentiation) We used microarrays to validate efficient commitment of hiPS to generate hiPS-MSC and do whole transcriptome comparison of hiPS-MSC vs isolated MSC (positive control) and then compare the enhanced biological functions after differentiation of these cells on a scaffold

2016-12-20 | GSE58919 | GEO

Single-cell RNA-Seq reveals dynamic, random monoallelic gene expression in mammalian cells

Project description:In the diploid genome, genes come in two copies, which can have different DNA sequence and where one is maternal and one is paternal. In a particular cell, a gene could potentially be expressed from both copies (biallelic expression) or only one (monoallelic). We performed RNA-Sequencing on individual cells, from zygote to the cells of the late blastocyst, and also individual cells from the adult liver. Using first generation crosses between two distantly related mouse strains, CAST/Ei and C57BL/6, we determined the expression separately from the maternal and paternal alleles. We found that half of the genes were expressed by only one allele, randomly so that some cells would express the paternal allele, some the maternal and a few cell both alleles. We also observed the spread of the progressive inactivation of the paternal X chromosome. First generation mouse strain crosses were used to study monoallelic expression on the single cell level

2014-01-10 | E-GEOD-45719 | biostudies-arrayexpress

Gene expression profiles of mono- and biallelic CEBPA mutations in cytogenetically normal AML

Project description:Purpose: CEBPA mutations are found as either biallelic (biCEBPA) or monoallelic (moCEBPA). We set out to explore whether the kind of CEBPA mutation is of prognostic relevance in cytogenetically normal AML (CN-AML). Patients and Methods: 467 homogeneously treated CN-AML patients were subdivided into moCEBPA, biCEBPA and wildtype (wt) CEBPA patients. The subgroups were analyzed for clinical parameters and for additional mutations in the NPM1, FLT3 and MLL genes. Furthermore, we obtained gene expression profiles (GEP) for a subgroup of 61 patients using oligonucleotide microarrays. 61 bone-marrow samples from CN-AML patients were analyzed using Affymetrix HG-U133 oligonucleotide microarrays (Affymetrix, Santa Clara, CA). Sample preparation, hybridization and image acquisition were performed according to standard Affymetrix protocols. Custom chip definition files based on the GeneAnnot database were used for data analysis (Ferrari et al, BMC Bioinformatics 8:446). The twilight algorithm was used to comapre gene expression profiles of patients with wildtype CEBPA and mono- and biallelic CEBPA mutations.

2010-05-16 | E-GEOD-15210 | biostudies-arrayexpress

Genomic and transcriptomic profile of HNF1A-mutated adenomas: molecular signature and potential therapeutic implications

Project description:Background: Hepatocellular adenomas (HAs) are tumors that can develop under different conditions, including in patients harboring a germline mutation in HNF1A. However, little is known about the pathogenesis of such disease. This work aims at better defining what mechanisms lie under the development of this condition. Results: 6 HAs were sampled from the liver of a 17-year-old male affected by diabetes and multiple hepatic adenomatosis harboring the heterozygous pathogenic germline variant c.815G>A, p.(Arg272His) in HNF1A which has a dominant negative effect. All HAs were molecularly characterized and four of them were shown to harbor a second somatic HNF1A variant, one had a mutation in the ARID1A gene while no additional somatic changes were found in the remaining HA and in normal parenchyma. A transcriptomic profile of the same HA samples was also performed. HNF1A biallelic mutations were associated with the up-regulation of several pathways including tricarboxylic acid cycle, the metabolism of fatty acids and mTOR signaling while angiogenesis, endothelial and vascular proliferation, cell migration/adhesion, and immune response were down-regulated. Contrariwise, in the tumor harboring the ARID1A variant, angiogenesis was up-modulated while fatty acid metabolism was down-modulated. Histological analyses confirmed the molecular data. Independently of the second mutation, energetic processes and cholesterol metabolism were up-modulated while immune response was down-modulated. Conclusions: this work provides a complete molecular signature of HNF1A-associated HAs, analyzing the association between specific HNF1A variants and the development of HA, while identifying potential new therapeutic targets for non-surgical treatment.

2024-11-22 | GSE268376 | GEO

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