Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA260506 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:7-dehydrocholesterol reductase catalyzes the reduction of 7-dehydrocholesterol to cholesterol. In Smith-Lemli-Opitz syndrome, mutations in DHCR7 prevents this conversion. We have found iPS cells derived from SLOS patients exhibit accelerated differentiation under cholesterol poor conditions. In this dataset, we include expression data obtained from comparision of a control iPS cell line (BJ) and a SLOS iPS cell line (A2). Cell line gene expression was compared in cholesterol rich conditions where the SLOS phenotype is suppressed. Cholesterol deficient culture of control and SLOS iPS cells demonstrated enhanced differentiation of SLOS cells over 7 days. These data are used to obtain 308 genes that are differentially expressed upon cholesterol deficient culture. time-course expression data obtained from control and SLOS patient iPS cells after transfer from cholesterol rich to cholesterol deficient culture.
2015-09-18 | GSE61203 | GEO
Project description:7-dehydrocholesterol reductase catalyzes the reduction of 7-dehydrocholesterol to cholesterol. In Smith-Lemli-Opitz syndrome, mutations in DHCR7 prevents this conversion. We have found iPS cells derived from SLOS patients exhibit accelerated differentiation under cholesterol poor conditions. In this dataset, we include expression data obtained from comparision of a control iPS cell line (BJ) and a SLOS iPS cell line (A2). Cell line gene expression was compared in cholesterol rich conditions where the SLOS phenotype is suppressed. Cholesterol deficient culture of control and SLOS iPS cells demonstrated enhanced differentiation of SLOS cells over 7 days. These data are used to obtain 308 genes that are differentially expressed upon cholesterol deficient culture. time-course expression data obtained from control and SLOS patient iPS cells after transfer from cholesterol rich to cholesterol deficient culture. 48 total RNA samples were isolated and hybridized on Affymetrix arrays. We generated the following pairwise comparisons using Partek: BJ 0hr vs A2 0hr; BJ 2Day vs A2 2Day; BJ 3Day vs A2 3Day; BJ 4Day vs A2 4Day; BJ 5Day vs A2 5Day; BJ 7Day vs A2 7Day. Genes with an FDR≤10% and a fold-change ≥3 were identified as significantly different. We also performed pairwise comparison of BJ and A2 samples within each cell line between subsequent isolations (i.e. BJ 0hr vs BJ 2Day; A2 3Day vs A2 4Day; etc.)
2015-09-18 | E-GEOD-61203 | biostudies-arrayexpress
Project description:This dataset contains raw proteomic data collected from the cell pellets and media from an astrocyte model of Smith-Lemli-Opitz Syndrome.
2022-11-08 | MSV000090664 | MassIVE
Project description:Smith-Lemli-Opitz Syndrome: A Longitudinal Clinical Study of Patients Receiving Cholesterol Supplementation - STAIR 7001
| PRJNA398584 | ENA
Project description:Smith-Lemli-Opitz Syndrome: A Longitudinal Clinical Study of Patients Receiving Cholesterol Supplementation - STAIR 7001
| PRJNA398583 | ENA
Project description:<p>Smith-Lemli-Opitz syndrome (SLOS) is a disorder of cholesterol production by the body. It is caused by changes in the DHCR7 gene, which is the blueprint for an enzyme called 7-dehydrocholesterol- delta7-reductase. This enzyme is necessary for the production of cholesterol by all cells in the body. People with SLOS often have malformations of major organs, slow growth, feeding difficulties and intellectual disability or learning problems.</p> <p>Because patients with SLOS cannot make enough cholesterol, it has been proposed that cholesterol supplementation (either with egg yolk or liquid suspensions of cholesterol) could help improve the symptoms of the disease. However, despite the widespread use of cholesterol supplementation, it is still not known whether it works or not. The study will try to provide an answer to this question by studying the disease and its progression while patients are receiving cholesterol.</p> <p>The clinical features of SLOS are thought to be related to low cholesterol and buildup of toxic cholesterol precursors (substances from which cholesterol is formed). But how exactly low cholesterol and toxic precursors contribute to the disease is poorly understood. This knowledge is critically important because it should help discover new therapeutic targets and develop treatments of the disease in the long run. The study will try to fill this gap with a comprehensive clinical and biochemical testing of the study participants over the course of several years.</p> <p>Last, a limitation of previous SLOS research studies has been their low number of participants. This is understandable because SLOS is a rare diseases and few research groups are working on it. However, in order to fully understand the disease, researchers need to study as many patients as possible. This study is unique in that it is run by a network of several highly specialized clinical research sites across the country. Having several sites involved increases the researcher's ability to recruit and study large number of patients, and centralize patients' information in a comprehensive SLOS clinical registry. This registry will be key to identify markers for diagnostic testing, screening and measuring outcomes in future studies of treatment.</p> <p>The purpose of this study is to learn as much as possible about Smith-Lemli-Opitz Syndrome (SLOS) by following a large group of affected children and adults over time. In this study, we will measure cholesterol and other similar chemicals in blood and urine, evaluate development and behavior, do limited medical evaluation, and carry out brain imaging studies.This study will help researchers: <ul> <li>learn more about what causes SLOS and how SLOS changes with age,</li> <li>note differences in features of SLOS among those affected,</li> <li>evaluate the effect of giving extra cholesterol in this condition, and</li> <li>develop ways to evaluate whether treatments developed in the future will be helpful.</li> </ul> </p>
| phs001430 | dbGaP
Project description:Smith-Lemli-Opitz Syndrome (SLOS) is a developmental disorder caused by autosomal recessive mutations in the Dhcr7 gene. SLOS patients present clinically with multiple dysmorphologies, neurological, behavioral and cognitive defects, and demonstrate impaired cholesterol biosynthesis resulting in markedly elevated 7-DHC in all bodily tissues and fluids. Previous rodent models of SLOS suffered from neonatal mortality or variation in the biochemical phenotype over time. We generated a viable murine model bearing a conditional flosed allele of the Dhcr7 gene, and validated it by generating a mice with liver-specific deletion of Dhcr7 by breeding with a strain expressing Cre recombinase driven by an albumin promoter . These mice demonstrated elevated circulatory and liver 7-DHC levels, but phenotypic characterization of the knockout mice revealed no significant changes in viability, fertility, growth curves, liver architecture, hepatic triglyceride secretion, and parameters of systemic glucose homeostasis. Investigation in to changes in the liver transcriptome were investigated withe RNAseq, and identified enrichment in various pathways, including steroid hormone biosynthesis and various cell signaling and metabolism pathways. Most notably missing from the list are the genes related to cholesterol biosynthesis. Generation of this Dhcr7 conditional knockout model will allow for better studies into the post natal effects of blocking cholesterol biosynthesis, accumulation of 7-DHC, and the role of DHCR7 in specific tissues.
2020-09-04 | GSE146523 | GEO
Project description:Smith-Lemli-Opitz syndrome is an autosomal recessive disorder that arises from mutations in the gene DHCR7, which encodes the terminal enzyme of cholesterol biosynthesis, leading to decreased production of cholesterol and accumulation of the cholesterol precursor, 7-dehydrocholesterol, and its oxysterol metabolites. The disorder displays a wide range of neurodevelopmental defects, intellectual disability and behavioral problems. However, an in-depth study on the temporal changes of gene expression in the developing brains of SLOS mice has not been done before. In this work, we carried out the transcriptomic analysis of whole brains from WT and Dhcr7-KO mice at four time points through postnatal day 0. First, we observed the expected downregulation of the Dhcr7 gene in the Dhcr7-KO mouse model, as well as gene expression changes of several other genes involved in cholesterol biosynthesis throughout all time points. Pathway and GO term enrichment analyses revealed affected signaling pathways and biological processes that were shared amongst time points and unique to individual time points. Specifically, the pathways important for embryonic development, including Hippo, Wnt, and TGF-β signaling pathways are the most significantly affected at the earliest time point, E12.5. Additionally, neurogenesis-related GO terms were enriched in earlier time points, consistent with the timing of development. Conversely, pathways related to synaptogenesis, which occurs later in development compared to neurogenesis, are significantly affected at the later time points, E16.5 and PND0, including the cholinergic, glutamatergic, and GABAergic synapses. The impact of these transcriptomic changes and enriched pathways is discussed in the context of known biological phenotypes of SLOS.
2024-02-15 | GSE247566 | GEO
Project description:Fanconi anemia (FA) is a genetic disorder of DNA repair that manifests as bone marrow dysfunction typically occurring in childhood. The lack of human model systems has impeded progress in identifying effective therapies. To address this, efforts have focused on using directed differentiation of patient-derived human induced pluripotent stem cells (IPSCs) to hematopoietic stem and progenitor cells (HSPCs). However, the requirement for an intact FA DNA repair pathway for efficient reprogramming of patient cells to pluripotency requires genetic complementation of FA pathway defects to efficiently generate IPSCs, precluding derivation of FA pathway-deficient human HSPCs for study. To overcome this barrier, we employed a system of doxycycline-inducible complementation of FANCA deficient patient-derived IPS cells. Doxycycline exposure allowed for the robust maintenance of undifferentiated IPS cells in culture. Removal or retention of doxycycline exposure during directed differentiation of HSPCs allowed for the production of isogenic FANCA-deficient and FANCA-complemented human HSPCs. IPS-derived, FANCA-deficient HSPCs showed impaired response to genotoxic stress, proliferation, and survival compared to complemented HSPCs. Using these cells, we found that FANCA-deficient HSPCs showed expected impaired clonogenicity in methylcellulose culture and unexpected accelerated erythroid differentiation relative to complemented cells. Activation of p53-mediated p21 transactivation in FANCA-deficient HSPCs serves to drive accelerated erythropoiesis as the expense of clonogenicity. This study demonstrates the feasibility of inducible complementation in IPSCs as a method to generate isogenic FA-deficient and FA-complemented human HPSCs for disease modeling and uncovers a novel mechanism by which the FA pathway regulates the balance between stem cell maintenance and terminal differentiation.
2021-02-01 | GSE123194 | GEO
Project description:The genetic defect underlying the human Smith-Lemli-Opitz dysmorphological disorder is loss-of-function mutations affecting the cholesterol synthesis enzyme dehydrocholesterol delta7 reductase, DHCR7. Dhcr7 knockout mice recapitulate the biochemical characteristics, but all knockout pups die within 14h of birth. Tissues of knockout mice accumulate the precursor sterol, 7-dehydrocholesterol, and show reduced levels of cholesterol (J. Clin. Invest. (2001) 108: 905-915). We compared the global gene expression changes in lung, liver and brain from knockout mice to those seen from organs harvested from same-pregnancy wild-type embryos, harvested before birth (E18.5). Since the P0 knockout pups die, we expected that there would be significant changes in gene expression between knockout and wild-type organs, and further comparing the altered genes in common to brain, lung and liver would point to a common mechanistic pathway where disruption of normal sterol synthesis in all cells leads to pathophysiology. Remarkably, these data show that the global gene expression between knockout and wild-type organs is hardly altered, despite the complete loss of cholesterol synthesis. There are so few genes that are altered, and furthermore, those that are altered are very limited in sharing similarities in all three tissues. This suggests that disorganized gene expression is not the cause of the early neonatal lethality.
2012-08-02 | GSE39811 | GEO