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Evalutation of global gene expression changes in NGLY1 deficient mouse embryonic fibroblasts (MEF)

ABSTRACT: Evalutation of global gene expression changes in NGLY1 deficient mouse embryonic fibroblasts (MEF)

PROVIDER: PRJNA497435 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8075050_1.fastq.gz	Fastqsanger.gz
	SRR8075050_2.fastq.gz	Fastqsanger.gz
	SRR8075051_1.fastq.gz	Fastqsanger.gz
	SRR8075051_2.fastq.gz	Fastqsanger.gz
	SRR8075052_1.fastq.gz	Fastqsanger.gz

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Evalutation of global gene expression changes in NGLY1 deficient mouse embryonic fibroblasts (MEF)

Project description:the gene expression profiles of 3 cultured MEFs from NGLY1 knockout mice was compared to 3 cultured MEF from the wild type control mice.

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NGLY1-deficient cerebral organiods display abnormal neuronal differentiation

Project description:We report using a single-cell transcriptomic study of cerebral organiods (COs) developed from WA09 hESCs with gene editing-induced NGLY1 mutations and from NGLY1-deficient patient's hiPSCs at 40 or 80 days of development. WA09 hESC-derived COs with and without mutant NGLY1 and patient's hiPSC-derived COs with and without the ectopic expression NGLY1 were analyzed.

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N-glycoproteomics and proteomics in NGLY1 deficient patient-derived dermal fibroblasts

Project description:In the biological systems, several genes are involved in protein glycosylation and deglycosylation pathways. Congenital disorders of deglycosylation (CDDG) are a set of disorders which occur due to the defect in genes involved in deglycosylation pathways. The only known CDDG so far is the defect in N-glycanase 1 (NGLY1), which primary function is to cleave the N-glycans from misfolded proteins prior to their proteasomal degradation. We used TMT-based N-glycoproteomics and proteomics on patient derived NGLY1 deficient and control fibroblasts to characterize the alteration in glycoproteome and proteome. 24 fractions of enriched glycopeptides after size exclusion chromatography (SEC) and 24 fractions after basic reverse phase liquid chromatography (bRPLC) were analyzed by LC-MS/MS for glycoproteomics and proteomics, respectively. We identified a total of 3,255 N-glycopeptides which were quantified on 550 glycosylation sites of 407 glycoproteins. A site specific aberrant glycosylation was observed for several extracellular matrix and cell adhesion proteins. By using quantitative proteomics, we detected 8,041 proteins. The alteration in expression of several proteins separated the affected individuals and controls. This is the first glycoproteomic study in patient derived NGLY1-CDDG fibroblasts. The glycoproteomics and proteomics analysis in NGLY1-CDDG provides the potential biomarkers and will increase our general understanding of its pathogenesis.

2023-05-10 | PXD034364 | Pride

Nrdc-deficient MEF

Project description:Nrdc-deficient MEF

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Transcriptome profiling of NGLY1 deficient K562 cells

Project description:The data includes a transcriptome analysis of K562 cell lines in which the gene N-glycanase 1 (NGLY1) was mutated in exon 1 and/or exon 3 to include loss of function mutations as described in Mueller and Jakob et al, 2020. The data were used in conjunction with whole proteome MS/MS experiments to show a gene expression profile consistent with NGLY1 deficiency, a human disease. The experiments demonstrate the wide ranging effect of the loss of NGLY1 on a cellular system.

2020-04-20 | E-MTAB-8876 | biostudies-arrayexpress

Transcriptome profiling of NGLY1 deficient K562 cells

Project description:Transcriptome profiling of NGLY1 deficient K562 cells

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Comparative proteomics reveal elevated CCN2 in NGLY1 deficient cells

Project description:N-glycanase 1(NGLY1) catalyzes the removal of N-linked glycans from newly synthesized or misfolded protein to exert protein quality control function via the process of endoplasmic reticulum-associated degradation (ERAD). NGLY1 deficiency (OMIM 615273) is a newly diagnosed rare genetic disorder with ~60 patients worldwide to date. The affected individuals present a broad spectrum of clinical features, including developmental delay, seizures, muscle weakness, liver failure, and the reduced secretion of sweats and tears. Recent studies explored several possible molecular mechanisms of NGLY1 deficiency including in vivo proteostasis, mitochondrial homeostasis, innate immunity, water and ion transport, with the goal of linking these findings to the pathophysiology of the disease. This study focuses on the dysregulation of ERAD in NGLY1 deficiency. We demonstrate the abnormal accumulation of ERAD substrates in NGLY1 deficient cells. Comprehensive global quantitative proteomics discovered elevated levels of novel endogenous proteins in NGLY1 defective human and mouse cells. Further biological validation assays confirmed the altered abundance of several key candidates’ that were observed in the isobarically labeled proteomic experiments. CCN2 was selected for further analysis due to its high fold change in different cell models of NGLY1 deficiency. Functional assays show elevated CCN2 and over-stimulated TGF-β signaling in NGLY1 deficient cells. Given the important role of CCN2 and TGF-β pathway in mediating systemic fibrosis, we propose a potential link of increased CCN2 and TGF-β signaling to microscopic liver fibrosis in NGLY1 patients.

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NGLY1-deficient cerebral organiods display abnormal neuronal differentiation

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Project description:Gene expression of Retinoblastoma deficient mouse embryonic fibroblasts (Rb-/- MEF, ME3) and wildtype mouse embryonic fibroblasts (Rb+/+ MEF,MEFA) during adipocyte differentiation were studied by cDNA microarray analysis. 2-day postconfluent cells (day 0) were treated with a hormonal cocktail including Rosiglitzone for differentiation into adipocytes. Gene expression at day 1, day 3, and day 8 after hormonal induction were compared to that before induction (day 0).

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Project description:NGlY1 deficiency is an ultra-rare, autosomal recessive genetic disease caused by mutations in the NGLY1 gene encoding N-glycanase one that removes N-linked glycan. Patients with pathogenic mutations in NGLY1 have complex clinical symptoms including global developmental delay, motor disorder, and liver dysfunction. To better understand disease pathogensis and neurological symptoms of NGLY1 deficiency we generated and characterized midbrain organoids using patient-derived iPSCs from two patients with disease causing mutations.

2023-02-03 | GSE224294 | GEO

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