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Title: A germline mutation in human Oxidation Resistance 1 gene causes developmental delay, epilepsy and cerebellar atrophy      
keywords:
Transcriptome or Gene expression
ID:
PRJNA341845
description:
Purpose: The Oxidation Resistance 1 gene (OXR1) confers neuroprotection against oxidative stress. Oxr1 deficiency in mice resulted in cerebellar neurodegeneration. Genetic causes account for the most proportion of neurodegenerative disorders (early) onset in children. However, the pathological consequence of Oxr1 deficiency in human remains unclear. To assess the effect of OXR1 on the whole transcriptome during neuronal differentiation, we conducted RNA-sequencing of iPS cells, neural aggregates and neurons derivated from OXR1 deficient patient fibroblast and compared with healthy control. Methods: The iPS cells (iPSC) were generated from fibroblast cells of health control (WT) and OXR1 deficient patient (OX), and induced 2 days to form neural aggregate (NA) following to be differentiated into neuron cells in day 20. Total RNA was pooled from triplicate samples in each group and performed RNA sequencing on an Illumina HiSeq2500 platform. The sequence reads that passed quality filters were analyzed at gene level. The GOseq program was used to generate gene ontology (GO) annotation of differentially expressed genes (DEGs). The pathway enrichments were identified by KEGG Pathway Enrichment Analysis. qRT–PCR validation was performed using SYBR Green assays. Results:Totally 1595 DEGs were identified at neuron stage due to Oxr1 disruption, 874 DEGs at iPSC stage and 388 DEGs at NA stage. Among them, there are 61 DEGs commonly regulated by Oxr1 throughout all of the three stages . Further gene oncology (GO) analysis of biological process showed there was a significant enrichment for DEGs related to cell adhesion and extracellular matrix organization (ECM), cell development, cell differentiation, organ development caused by Oxr1 deficiency throughout all developmental stages. Especially neurogenesis and differentiation, axonogensis and guidance, brain and nerves system development were among the top of 50 items when entering neuron stage. In addition, a set of DEGs was significantly enriched in positive regulation of intrinsic apoptotic signaling pathway and regulation of cellular response to stress. Conclusions: Oxr1 regulates transcriptional networks required for modulating oxidative stress, apoptosis and neurogenesis during neuronal differentiation of iPS cells. Overall design: The cells were collected from three stages including iPSC, NA and neuron. The differencial expression profiles were generated by comparsion between health control and OXR1 difficent group in each stage.
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA341845
authentication:
none
authorization:
none
name:
Homo sapiens
ncbiID:
ncbitax:9606
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject