Neural and Metabolic Dysregulation in PMM2 deficient human in vitro neural models
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE251886 | GEO | 2024/03/12
REPOSITORIES: GEO
Similar Datasets
Project description:PMM2-CDG is a rare inborn error of metabolism caused by deficiency of the phosphomannomutase (PMM2) enzyme, which leads to impaired protein glycosylation. While the disorder presents primarily with neurological symptoms, there is limited knowledge about the specific brain-related changes that result from PMM deficiency. We found aberrant neural activity in 2D neuronal networks from individuals with PMM2-CDG. Multi-omics datasets from 3D brain organoids derived from individuals with PMM2-CDG revealed widespread decrease in protein glycosylation, highlighting impaired glycosylation as a key pathological feature of PMM2-CDG. Further, we identified impaired mitochondrial structure and abnormal glucose metabolism in PMM2-CDG organoids indicating disturbances in energy metabolism. Correlation between PMM2 enzymatic activity in brain organoids and symptom severity suggests that the level of PMM2 enzyme function directly influences neurological manifestations. These findings enhance our understanding of specific brain-related perturbations associated with PMM2-CDG, offering insights into the underlying mechanisms and potential directions for therapeutic interventions.
2024-04-25 | PXD044647 | Pride
Project description:Glycosylation of proteins is an important post-translational modification that comprises two major stages: synthesis and attachment of glycans in the endoplasmic reticulum (ER), and glycan remodeling in the ER and Golgi apparatus (GA). Genetic disorders impairing a step of this process give rise to a group of pathologies named congenital disorders of glycosylation (CDG). The most common CDG type is PMM2-CDG, caused by mutations on PMM2 (phosphomannomutase 2) genes. PMM2-CDG clinical presentation vary among affected individuals. CDG condition is considered a form of chronic ER stress. Inhibition of glycosylation results in the accumulation of misfolded proteins in the ER, which induces a complex protective reaction known as the unfolded protein response (UPR), which includes translational repression, transcriptional activation of ER chaperones, and ER-associated degradation of unfolded proteins. In search for CDG biomarkers, EBV-transformed CDG B-lymphoblastoid cell lines (B-LCL) were used as cellular models due to two main advantages: first, B-LCL are secretory cells that are forced to continuously synthetize proteins such as immunoglobulins, cytokines or other cell to cell communication molecules, so their ER is chronically stressed; second, as immune system cells, they express common genes and share common regulatory mechanisms with nervous system cells such as neurons (affected cell in most CDG patients). In this work we generated a collection of 7 EBV-transformed PMM2-CDG B-LCL by culture of patients' purified blood B lymphocytes with supernatants of the marmoset EBV-leukocyte cell line B95-8, and compared their transcriptome with that of 7 EBV-transformed healthy B-LCL. Our analysis revealed 348 significantly up-regulated and 106 down-regulated protein-coding genes compared to non-CDG cell lines, which included response to stress, transcription factors, glycosylation, motility and cell junction, development and cell (neuron) differentiation and synapse genes. Gene Set Enrichment Analysis (GSEA) identified biological consequences associated to gene expression changes in PMM2-CDG cells related to the unfolded protein response (UPR), RNA metabolism and the endoplasmic reticulum, Golgi apparatus and mitochondria components. Dysregulated important genes were MAN1A1, MGAT2, CHST4, LARGE, ADAM23, SEMA4D, UNC13C, AUTS2, CA2, SMN1, EXOSC2 expressed not only in the immune system but in other tissues including the nervous system that were compatible with CDG pathophysiology. Our results confirm PMM2-CDG EBV-transformed B-LCL as a suitable cell model that expands both our knowledge and tools to study CDG pathology at the cellular level, useful for functional characteristics and potential therapeutic drugs testing.
2022-01-22 | GSE145082 | GEO
Project description:Disruption of N-linked glycosylation has a broad impact on proper glycosylation of nascent glycoproteins in the endoplasmic reticulum, which affect multiple signalling pathways( by changing the stability of membrane proteins or the signalling ability of membrane receptors) and may be responsible of the fibrotic stage associated to CDG type-I. We used microarrays to characterize the global changes in gene expression in three distinct groups of CDG-I patients and we identified a common perturbation in the expression of genes encoding for proteins involved in the stress as well as in the fibrotic responses. Experiment Overall Design: Primary fibroblasts, obtained from forearm skin biopsies of healthy control subjects and three distinct groups of CDG-I patients, were cultured in F12 DMEM supplemented with 4.5 g/l glucose and 10% fetal calf serum prior to RNA extraction and Hybridization on human HG 133 A Affymetrix Microarrays. To avoid bias related to the analysis of a specific CDG-I type or to a specific individual expression pattern, we have considered three patients for the CDG-Ic and -Ie group and two patients for the CDG-Ig group. Moreover the total RNA was extracted from three different independent biological replicates.
2008-10-18 | E-GEOD-8440 | biostudies-arrayexpress
Project description:Phosphomannomutase 2 (PMM2) converts mannose-6-phospahate to mannose-1-phosphate; the substrate for GDP-mannose, a building block of the glycosylation biosynthetic pathway. Pathogenic variants in the PMM2 gene have been shown to be associated with protein hypoglycosylation causing PMM2-congenital disorder of glycosylation (PMM2-CDG). While mannose supplementation improves glycosylation in vitro, but not in vivo, we hypothesized that liposomal delivery of mannose-1-phosphate could increase the stability and delivery of the activated sugar to enter the targeted compartments of cells. Thus, we studied the effect of liposome-encapsulated mannose-1-P (GLM101) on global protein glycosylation and on the cellular proteome in skin fibroblasts from individuals with PMM2-CDG, as well as in individuals with two N-glycosylation defects early in the pathway, namely ALG2-CDG and ALG11-CDG. We leveraged multiplexed proteomics and N-glycoproteomics in fibroblasts derived from different individuals with various pathogenic variants in PMM2, ALG2 and ALG11 genes. Proteomics data revealed a moderate but significant change in the abundance of some of the proteins in all CDG fibroblasts upon GLM101 treatment. On the other hand, N-glycoproteomics revealed the GLM101 treatment enhanced the expression levels of several high-mannose and complex/hybrid glycopeptides from numerous cellular proteins in individuals with defects in PMM2 and ALG2 genes. Both PMM2-CDG and ALG2-CDG exhibited several-fold increase in glycopeptides bearing Man6 and higher glycans and a decrease in Man5 and smaller glycan moieties, suggesting that GLM101 helps in the formation of mature glycoforms. These changes in protein glycosylation were observed in all individuals irrespective of their genetic variants. ALG11-CDG fibroblasts also showed increase in high mannose glycopeptides upon treatment; however, the improvement was not as dramatic as the other two CDG. Overall, our findings suggest that treatment with GLM101 overcomes the genetic block in the glycosylation pathway and can be used as a potential therapy for CDG with enzymatic defects in early steps in protein N-glycosylation.
2024-11-13 | PXD050018 | Pride
Project description:Disruption of N-linked glycosylation has a broad impact on proper glycosylation of nascent glycoproteins in the endoplasmic reticulum, which affect multiple signalling pathways( by changing the stability of membrane proteins or the signalling ability of membrane receptors) and may be responsible of the fibrotic stage associated to CDG type-I. We used microarrays to characterize the global changes in gene expression in three distinct groups of CDG-I patients and we identified a common perturbation in the expression of genes encoding for proteins involved in the stress as well as in the fibrotic responses. Keywords: disease state analysis
2008-07-11 | GSE8440 | GEO
Project description:Exposure to microgravity in low-Earth orbit (LEO) has been shown to affect human health. Post-flight brain imaging and studies of astronauts and mouse models suggest that microgravity may cause intracranial fluid shifts and possibly alter white and gray matter of the brain. To focus on the effects of microgravity on brain cells, we used induced pluripotent stem cells (iPSCs) to produce three-dimensional (3D) human neural organoids as models of the nervous system. We studied iPSC-derived organoids from four individuals, including people with the neurological diseases primary progressive multiple sclerosis (PPMS) and Parkinson’s disease (PD) and non-symptomatic controls. We patterned the organoids toward cortical and dopaminergic fates representing regions of the brain affected by MS and PD, respectively. Microglia were generated from the same cell lines and integrated into a portion of the organoids. The organoids were maintained for a month in a novel static culture system on the International Space Station (ISS) and live samples were returned to Earth. The post-flight samples were evaluated using transcriptome analysis. Microglia-specific genes were detectable in the microglia-containing organoid cultures. Differential gene expression analyses of individual organoids cultured in LEO and on Earth suggest that cell proliferation was lower and neural cells were more mature in samples that were cultured in LEO. These experiments lay the groundwork for further studies, including long term studies to investigate the effects of microgravity on the brain.
2024-08-14 | GSE259421 | GEO
Project description:In the biological systems, several genes are involved in protein glycosylation pathway. Congenital Disorders of Glycosylation (CDG) is known to be a multisystem disorder. Pathogenic variants in the glycosylation genes lead to abnormal N- or O-linked glycosylation that causes cellular stress. We used TMT-based N-glycoproteomics and proteomics on different patient-derived CDG and control fibroblasts to characterize the alteration in glycoproteome and proteome. 12 fractions of enriched glycopeptides after size exclusion chromatography (SEC) and 12 fractions after basic reverse phase liquid chromatography (bRPLC) were analyzed by LC-MS/MS for glycoproteomics and proteomics, respectively. A site-specific aberrant glycosylation was observed for several proteins such as mitochondrial, autophagy, extracellular matrix and cell adhesion proteins. By using quantitative proteomics, we observed alteration in abundances of several proteins separated the affected individuals and controls. The glycoproteomics and proteomics analysis in CDG patients provides the potential biomarkers and will increase our general understanding of its pathogenesis.
2023-10-24 | PXD044327 | Pride
Project description:<p>Urea cycle disorders represent a group of rare inborn errors of metabolism that lead to accumulation of ammonia, a toxic product of protein metabolism. Individuals with urea cycle disorders cannot metabolize the ammonia that accumulates due to enzyme deficiency. The symptoms of these disorders may present at birth, childhood or adulthood (milder deficiencies). There are currently eight enzyme deficiencies that constitute the range of inborn errors of ureagenesis. This project will focus on the most common enzyme disorder of the urea cycle, ornithine transcarbamylase deficiency, inherited as an X-linked trait.</p> <p>This project will study cognitive and motor dysfunction in patients who are female carriers of ornithine transcarbamylase deficiency (OTCD) or are males with late onset presentation of OTCD, utilizing state of the art MRI (magnetic resonance imaging), a non -invasive technique. This project seeks to improve our understanding of the underlying neural mechanisms that contribute to metabolic, cognitive, sensory and motor abnormalities in urea cycle disorders, which although individually rare, collectively constitute a major cause of neonatal encephalopathy, leading to significant morbidity and mortality. As a result of this study, a greater understanding of the anatomic, cognitive, motor, and biochemical underpinnings of neurologic damage attributable to this metabolic disorder will be gained. Experimental approaches will combine sensory, cognitive and motor testing with structural, functional and molecular magnetic resonance imaging to study symptomatic and asymptomatic heterozygous female carriers of X-linked ornithine transcarbamylase deficiency (OTCD), and late onset hemizygous males. Participants to be included in the studies will range from ages 18-60 years and will be compared to an age-matched typically developed (TD) comparison group.</p> <p>For our research, we use anatomic MRI, functional Magnetic Resonance Imaging (fMRI), and magnetic resonance spectroscopy (MRS) to monitor brain activity. The technique of fMRI provides detailed maps of the brain areas underlying human mental activities. By using fMRI, we are able to observe how the brain is functioning while a person is performing a specific task, such as reading. We can not only observe differences in the structure of the brain, but can also measure differences in brain function and activity as well. This information will ultimately be used to provide a basis for designing more effective interventions and methods for early identification of learning disabilities in patients with OTCD and related disorders. We will also use MRS to study various brain chemicals such as glutamine using the non-invasive MRI imaging techniques.</p>
| phs001108 | dbGaP
Project description:The most common congenital disorder of glycosylation (CDG) is caused by pathogenic variants in PMM2 (PMM2-CDG) that reduce phosphomannomutase activity and impair N-glycan synthesis. Patients present early in life with multi-system disabilities. Traditional diagnosis relies on measuring carbohydrate-deficient transferrin (CDT) and confirmation by genetic testing. However, tests for CDT can be normal in some patients, or normalize with age. Because patients also show subtle alterations in serum glycan structures, we considered that site-specific glycosylation changes might be diagnostic. We analyzed serum from 35 individuals with PMM2-CDG for discovery and validation of glycoproteomic changes. We carried out mass spectrometry-based discovery studies to profile the glycoproteome in an initial set of well-characterized affected individuals and matched controls. Next, we developed a streamlined method for analyzing additional affected individuals. Finally, targeted mass spectrometry was used to validate selected N-glycopeptides in an independent set of samples in a blinded fashion. Of the 3,342 N-glycopeptides derived from 284 glycoproteins identified in discovery experiments, individuals with PMM2-CDG exhibited a general decrease in complex-type N-glycans and an increase in truncated, mannose-rich and hybrid species. We identified a glycopeptide from complement C4 carrying the glycan Man5GlcNAc2, which was not detected in controls. Notably, this glycopeptide was also detected in five affected individuals with normal CDT, including one individual after liver transplant, two individuals with a known genetic variant associated with mild disease and two individuals with well characterized variants, indicating that this glycopeptide is more sensitive than CDT. Finally, this marker was also detected by targeted analysis in two individuals with variants of uncertain significance (VUS) in PMM2 gene. Overall, we believe that C4-derived Man5GlcNAc2 glycopeptide could serve as a novel next-generation biomarker for more accurate diagnosis and tracking progress of patients in therapeutic trials.
2024-03-12 | PXD042446 | Pride
Project description:Human cerebral cortex development is a highly complex and orchestrated process that is under tight genetic regulation. Rare mutations that alter gene expression or function can disrupt the structure of the cerebral cortex, resulting in a variety of neurological cAonditions1. Lissencephaly (“smooth brain”) spectrum disorders comprise a group of rare, genetically heterogeneous congenital brain malformations commonly associated with epilepsy and intellectual disability2. However, the molecular mechanisms underlying disease pathogenesis remain unknown. Here, we establish hypoactivity of the mammalian target of rapamycin (mTOR) pathway as a clinically relevant molecular mechanism in lissencephaly spectrum disorders. We characterized cerebral organoids from individuals with two genetically distinct lissencephalies harboring a recessive mutation in P53-Induced Death Domain Protein 1 (PIDD1) or a heterozygous chromosome 17p13.3 microdeletion leading to Miller-Dieker Lissencephaly Syndrome (MDLS). We found that PIDD1-mutant and MDLS organoids recapitulate the thickened cortex typical of human lissencephaly and demonstrated dysregulation of protein translation, metabolism, and the mTOR pathway. We found that a brain-selective activator of mTOR complex 1 (mTORC1) prevents, and even reverses, cellular and molecular defects in lissencephaly organoids. Our findings unveil an unexpected converging molecular mechanism contributing to genetically heterogeneous lissencephaly spectrum disorders.
2024-10-04 | PXD056364 | Pride