Generation and characterization of NGLY1 patient-derived midbrain organoids
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE224294 | GEO | 2023/02/03
REPOSITORIES: GEO
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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.
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Project description:Biallelic mutations in the gene that encodes the enzyme N-glycanase 1 (NGLY1) cause a rare disease with multi-symptomatic features including developmental delay, intellectual disability, neuropathy and seizures. NGLY1’s activity in human neural cells is currently not well understood. To understand how NGLY1 gene loss leads to the specific phenotypes of NGLY1 deficiency, we employed direct conversion of NGLY1 patient-derived induced pluripotent stem cells (iPSCs) to functional cortical neurons. Transcriptomic, proteomic, and functional studies of iPSC-derived neurons lacking NGLY1 function revealed several major cellular processes that were altered, including protein aggregate-clearing functionality, mitochondrial homeostasis, and synaptic dysfunctions. These phenotypes were rescued by introduction of a functional NGLY1 gene and were observed in iPSC-derived mature neurons, but not astrocytes. Finally, laser capture microscopy followed by mass spectrometry provided detailed characterization of the composition of protein aggregates specific to NGLY1-deficient neurons. Future studies will harness this knowledge for therapeutic development.
2025-02-13 | GSE197454 | GEO
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.
2020-12-16 | GSE142143 | GEO
Project description:Biallelic mutations in the gene that encodes the enzyme N-glycanase 1 (NGLY1) cause a rare disease with multi-symptomatic features including developmental delay, intellectual disability, neuropathy and seizures. NGLY1’s activity in human neural cells is currently not well understood. To understand how NGLY1 gene loss leads to the specific phenotypes of NGLY1 deficiency, we employed direct conversion of NGLY1 patient-derived induced pluripotent stem cells (iPSCs) to functional cortical neurons. Transcriptomic, proteomic, and functional studies of iPSC-derived neurons lacking NGLY1 function revealed several major cellular processes that were altered, including protein aggregate-clearing functionality, mitochondrial homeostasis, and synaptic dysfunctions. These phenotypes were rescued by introduction of a functional NGLY1 gene and were observed in iPSC-derived mature neurons, but not astrocytes. Finally, laser capture microscopy followed by mass spectrometry provided detailed characterization of the composition of protein aggregates specific to NGLY1-deficient neurons. Future studies will harness this knowledge for therapeutic development.
2024-05-23 | PXD031091 | Pride
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.
2021-12-21 | PXD026301 | Pride
Project description:Although NGLY1 deficiency has been discovered as a result of mutations in the NGLY1 gene, cellular and molecular mechanisms underlying the neurological abnormalities due to NGLY1 malfunction in the brain remain mostly unknown. Using human cerebral organoid (CO) models and systems biology techniques, we uncovered NGLY1 deficiencyinduced alterations at the early stage of cerebral development. Despite the similar vitality and cellular pluripotency of NGLY1-functional and -deficient WA09 hESCs, COs developed from the NGLY1-deficient hESCs had the defective formation of SATB2+ upper-layer neurons and attenuation of STAT3 and HES1 signaling critical for sustaining radial glia. The NGLY1-deficient CO cells, compared with the NGLY1-functional ones, also presented higher vulnerability to multiple stressors. Bulk and single-cell analysis of transcriptomes revealed that NGLY1-deficient COs showed a propensity for premature neuronal differentiation, accompanied by significant downregulation of secretory and transcription factors, including TTR, IGFBP2, and ID4. Supplementing recombinant TTR to NGLY1-deficient CO cells reduced their susceptibility to proteasome inhibition. Ectopic expression of NGLY1 led to IGFBP2 and ID4 upregulation in CO cells developed from NGLY-deficient patientderived induced pluripotent stem cells (iPSCs). Moreover, ID4 expression, STAT3 signaling, and proliferation were enhanced by treatment of recombinant IGFBP2 in CO cells developed from the NGLY1-deficient WA09 hESCs and patient-derived iPSCs. Our findings indicate that NGLY1 could be critical for regulating various stress responses and maintaining neural stem cells (NSCs) in the developing cerebrum. In patients, NGLY1 deficiencyassociated neurological abnormalities, including microcephaly, may be a consequence of aberrations in NSC signaling sustained by NGLY1.
2022-05-20 | PXD026681 | Pride
Project description:NGLY1 mutations cause protein aggregation in human neurons
| PRJNA810420 | ENA
Project description:Generation and characterization of NGLY1 patient-derived midbrain organoids
| PRJNA930476 | ENA
Project description:N-Glycanase 1 (NGLY1) deficiency is a rare and complex genetic disorder. Although recent studies have shed light on the molecular underpinnings of NGLY1 deficiency, a systematic characterization of gene and protein expression changes in patient-derived cells has been lacking. Here, we performed RNA-sequencing and mass spectrometry to determine the transcriptomes and proteomes of 66 cell lines representing 4 different cell types derived from 14 NGLY1 deficient patients and 17 controls. While gene and protein expression levels agreed well with each other, expression differences were more pronounced at the protein level. Although NGLY1 protein levels were up to 9.5-fold downregulated in patients compared to parent controls, depending on the genotype, NGLY1 protein was still detectable in all patient-derived lymphoblastoid cell lines. Consistent with the role of NGLY1 as a regulator of the transcription factor Nrf1, we observed a cell type-independent downregulation of proteasomal genes in NGLY1 deficient cells. In contrast, genes involved in ribosomal mRNA processing were upregulated in multiple cell types. In addition, we observed cell type-specific effects. For example, genes and proteins involved in glutathione synthesis, such as the glutamate-cystein ligase subunits GCLC and GCLM, were downregulated specifically in lymphoblastoid cells. We provide a web application that enables access to all results generated in this study at https://apps.embl.de/ngly1browser. This resource will guide future studies of NGLY1 deficiency in directions that are most relevant to patients.
| EGAS00001005573 | EGA
Project description:Analysis of human cerebral organoids developed from both WA09 human embryonic stem cells with CRISPR-KO of NGLY1. The hypothesis tested was that NGLY1 is key to normal human brain development and when knocked out would alter cerebral development of organoids through the differential expression of various key genes.
2022-04-19 | GSE169696 | GEO