Differences in transcription in Angelman syndrome and control person iPSC-derived neurons
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA611562 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11271979_1.fastq.gz | Fastqsanger.gz | |||
| SRR11271979_2.fastq.gz | Fastqsanger.gz | |||
| SRR11271980_1.fastq.gz | Fastqsanger.gz | |||
| SRR11271980_2.fastq.gz | Fastqsanger.gz | |||
| SRR11271981_1.fastq.gz | Fastqsanger.gz |
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Project description:Angelman syndrome is caused by loss of funtional ubiquitin E3 ligase UBE3A and results in severe deley in cognitive and motor development. In neurons, UBE3A locates to the synapse and to the nucleus. Loss of nuclear UBE3A results in development of Angelman syndrome like symptoms in mice. UBE3A can function as transcriptional coactivator of steroid hormone receptors, but the entire function of UBE3A in the nucleus is still not clear. So we wanted to study differences in the transcriptome in neurons differentiated from iPSCs that were derived from patients with Angleman syndrome and normal controls.
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Project description:mRNAseq on (1) isogenic control and Angelman Syndrome pluripotent stem cell-derived neurons or (2) antisense oligonucleotide-treated H9 hESC-derived neurons
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Project description:Angelman syndrome (AS) is a neurogenetic developmental disorder that results from the loss of E3 ubiquitin ligase UBE3A due to mutations in or deletions of the maternally inherited UBE3A allele. While mouse models of AS have implicated abnormal synaptic signaling and plasticity underlying behavioral dysfunction, how the loss of UBE3A contributes to hyperactivity of neuronal networks seen in AS patients remains unclear. Here, by utilizing human induced neurons and 3D cortical organoids derived from AS patient iPSCs and CRISPR-Cas9 mediated UBE3A KO hESCs, we uncovered a novel role of UBE3A in suppressing neuronal hyperexcitability via ubiquitin-mediated degradation of BK channels. More importantly, augmented BK channel activity in neurons manifested as increased intrinsic excitability of neurons and network level bursting and synchronization, which can be pharmacologically normalized by BK antagonists. Our study has illustrated the utility of modeling neurological diseases with human neural cells, and our results have provided new insights into underlying pathophysiological mechanisms and potential therapeutic strategy in Angelman syndrome.
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Project description:Establishing a molecular phenotype for Angelman Syndrome stem cell-derived neurons
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Project description:Angelman syndrome (AS) and interstitial duplication 15q autism (int dup(15)) are reciprocal genomic disorders caused by maternal deletion or duplication of the 15q11.2-q13 region. While AS is caused by maternal loss of 15q and maternal duplications of 15q can cause autism implicating the maternally expressed UBE3A gene in these phenotypes. We investigated chromatin and gene expression changes in blood and cell lines from three int dup(15) and three reciprocal AS deletion subjects to identify global genomic and gene expression changes that may influence both the AS and autism phenotypes. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) we identified 1104 regions of differential open chromatin in AS deletion and 2344 regions int dup(15) indicating changes in chromatin could influence gene expression in these regions. Microarray analysis revealed 1225 genes that were elevated in AS deletion vs int dup(15) and 976 genes that were elevated in int dup(15) vs AS deletion PBMC (pvalue<0.05). Significant differences in expression were found for genes at the 15q locus like UBE3A, ATP10A and HERC2. A larger set of genes involved in chromatin remodeling, DNA repair and neurogenesis were found, at FAIRE peaks in AS deletion samples but had increased transcription in int dup(15) samples. There was a significant enhancement for genes with FOXP1 binding sites in the int dup(15) gene set and elevated FOXP1 protein could be detected in the nucleus of int dup(15) as compared to AS deletion cell lines. This analysis provides the first insights into transcriptional changes which may unveil new sets of genes and pathways contributing to both AS and autism pathogenesis. Gene expression was performed using 100ng of total RNA from each subject as starting material for amplification and cRNA synthesis in accordance Affymetrix protocols (http://tinyurl.com/3j7dcp6). Hybridizations were performed to the Affy HumanGene_st_v1 chip and the signal data normalized using internal chip controls. Normalized expression data was then exported to a text file for subsequent expression analysis using the EXPANDER software analysis suite.
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Project description:Mouse fibroblasts can be reprogrammed into iPSC by Yamanaka factor. iPSC can be derived into iMSC under certain induction conditions. iMSC and MSC have similar cellular properties. However, the genomic differences of these cell types are not clear. RNA-seq sequencing was used to clarify the possible genetic differences.
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Project description:Angelman syndrome (AS) is a genetic disorder which entails autism, intellectual disability, lack of speech, motor deficits, andseizure susceptibility. It is caused by the lack of UBE3A protein expression, which is an E3-ubiquitin ligase. Despite AS equalprevalence in males and females, not much data on how sex affects the syndrome was reported. In the herein study, we thoroughlycharacterized many behavioral phenotypes of AS mice. The behavioral data acquired was analyzed with respect to sex. Inaddition, we generated a new mRNA sequencing dataset. We analyzed the coding transcriptome expression profiles with respectto the effects of genotype and sex observed in the behavioral phenotypes. We identified several neurobehavioral aspects,especially sensory perception, where AS mice either lack the male-to-female differences observed in wild-type littermates oreven show opposed differences. However, motor phenotypes did not show male-to-female variation between wild-type (WT) andAS mice. In addition, by utilizing the mRNA sequencing, we identified genes and isoforms with expression profiles that mirrorthe sensory perception results. These genes are differentially regulated in the two sexes with inverse expression profiles in ASmice compared to WT littermates. Some of these are known pain-related and estrogen-dependent genes. The observed differ-ences in sex-dependent neurobehavioral phenotypes and the differential transcriptome expression profiles in AS mice strengthenthe evidence for molecular cross talk between Ube3a protein and sex hormone receptors or their elicited pathways. Theseinteractions are essential for understanding Ube3a deletion effects, beyond its E3-ligase activity.
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Project description:Huntington's disease is caused by an expanded CAG repeat in the huntingtin gene, yeilding a Huntingtin protein with an expanded polyglutamine tract. Patient-derived induced pluripotent stem cells (iPSCs) can help understand disease; however, defining pathological biomarkers in challanging. Here we used LC-MS/MS to determine differences in mitochondrial proteome between iPSC-derived neurons from healthy donors and Huntington's disease patients.
2023-02-10 | PXD037526 | Pride
Project description:Genetic aberrations of the maternal UBE3A allele, which encodes the E3 ubiquitin ligase E6AP, are the cause of Angelman syndrome (AS), an imprinting disorder. In most cases, the maternal UBE3A allele is not expressed. Yet, approximately 10 percent of AS individuals harbor distinct point mutations in the maternal allele resulting in the expression of full-length E6AP variants that frequently display compromised ligase activity. In a high-throughput screen, we identified cyanocobalamin, a vitamin B12-derivative, and several alloxazine derivatives as activators of the AS-linked E6AP-F583S variant. Furthermore, we show by cross-linking coupled to mass spectrometry that cobalamins affect the structural dynamics of E6AP-F583S and apply limited proteolysis coupled to mass spectrometry to obtain information about the regions of E6AP that are involved in, or are affected by, binding cobalamins and alloxazine derivatives. Our data suggest that dietary supplementation with vitamin B12 could be beneficial for AS individuals.
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