The role of Niemann-Pick type C2 in zebrafish embryonic development
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA679737 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13091257_1.fastq.gz | Fastqsanger.gz | |||
| SRR13091257_2.fastq.gz | Fastqsanger.gz | |||
| SRR13091258_1.fastq.gz | Fastqsanger.gz | |||
| SRR13091258_2.fastq.gz | Fastqsanger.gz | |||
| SRR13091259_1.fastq.gz | Fastqsanger.gz |
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Project description:Niemann-Pick disease type C (NPC) is a rare fatal neurodegenerative lysosomal storage disease caused by mutations of either NPC1 or NPC2. NPC2 is a soluble lysosomal protein that in coordination with NPC1 is responsible for the efflux of unesterified cholesterol from the lysosome. Mutations of both genes cause a similar cellular pathology, that includes the accumulation of unesterified cholesterol and other lipids in the late endosome/lysosome, while reducing cholesterol bioavailability. Here we describe a npc2 null zebrafish model generated by CRISPR/Cas9 gene targeting. Zygotic npc2m/m zebrafish from the intercross of npc2+/m individuals showed significant unesterified cholesterol accumulation at larval stages, and a reduction in body size in adulthood. Additionally, zygotic npc2m/m adults exhibited motor and balance defects shortly before a premature death. These findings mimic defects found in human and mice, however the phenotype at embryonic stages were milder than expected. To address the possible dose protection effects of npc2 mRNA present in the oocyte at the time of fertilization we intercrossed npc2m/m zebrafish to generate Maternal-zygotic (MZ) npc2m/m embryos. MZnpc2m/m zebrafish exhibited significant developmental defects including absent otolith, abnormal head/brain development, curved/twisted body axis, no circulating blood cells, and died by 72 hpf. These developmental defects have not previously been reported in connection with either NPC2 or NPC1. RNA-seq analysis conducted on 30 hpf npc2+/m and MZnpc2m/m embryos revealed a significant reduction in notch3 expression as well as reduction in other downstream genes in the signally pathway such as hey1 and her12 that could be partially rescued by microinjection of a plasmid containing the constitutively active notch3 ICD at the 1-cell stage, suggesting that impaired Notch3 signaling likely underlies some aspects of the developmental defects observed in MZnpc2m/m zebrafish.
2021-03-20 | GSE161867 | GEO
Project description:Niemann-Pick disease type C (NPC) is a rare, fatal, neurodegenerative lysosomal disease caused by mutations of either NPC1 or NPC2. NPC2 is a soluble lysosomal protein that functions in coordination with NPC1 to efflux cholesterol from the lysosomal compartment. Mutations of either gene result in the accumulation of unesterified cholesterol and other lipids in the late endosome/lysosome, and reduction of cellular cholesterol bioavailability. Zygotic null npc2m/m zebrafish showed significant unesterified cholesterol accumulation at larval stages, a reduction in body size, and motor and balance defects in adulthood. However, the phenotype at embryonic stages was milder than expected, suggesting a possible role of maternal Npc2 in embryonic development. Maternal-zygotic npc2m/m zebrafish exhibited significant developmental defects, including defective otic vesicle development/absent otoliths, abnormal head/brain development, curved/twisted body axes and no circulating blood cells, and died by 72 hpf. RNA-seq analysis conducted on 30 hpf npc2+/m and MZnpc2m/m embryos revealed a significant reduction in the expression of notch3 and other downstream genes in the Notch signaling pathway, suggesting that impaired Notch3 signaling underlies aspects of the developmental defects observed in MZnpc2m/m zebrafish.
| S-EPMC8077516 | biostudies-literature
Project description:Primary skin fibroblasts from four Niemann-Pick type C patients homozygous for the I1061T mutation and four control individuals were cultured under identical conditions in DMEM containing 10% fetal bovine serum. Cells were harvested at 50-70% confluency. mRNA was isolated with the FastTrack 2.0 mRNA isolation kit according to the manufacturer's instructions (Invitrogen, Carlsbad, CA). A reference RNA comprised of 10 cell lines was used as the control for each hybridized sample (Stratagene, La Jolla, CA). Both sample and reference RNAs were amplified using the MessageAmp II aRNA amplification kit (Ambion, Austin, TX). Set of arrays that are part of repeated experiments Biological Replicate Complex
2007-08-15 | E-GEOD-8770 | biostudies-arrayexpress
Project description:Macrophage inflammatory protein 1alpha/CCL3 protein is a known pro-inflammatory cytokine that can mediate chemotaxis of monocytes and promote cell degranulation. Ccl3 gene expression is elevated in the CNS and visceral tissue of many lysosomal storage disorders. The deletion of Ccl3 in a mouse model of Sandhoff disease was reported to result in reduced monocyte-associated pathology in the brain, delayed neurodegeneration, and prolonged health. However, deletion of Ccl3 in a mouse model of Niemann-Pick C disease was dentrimental or neutral instead of beneficial. Prevention of neuronal loss was instead mediated by providing NPC1 to neurons. We used microarrays to detail the global change in gene expression of the cerebellum in Niemann-Pick C disease animals, Niemann-Pick C disease animals with Ccl3 gene deletion, and Niemann-Pick C disease animals with Purkinje neuron-specific NPC1-YFP rescue.
2012-04-17 | GSE36119 | GEO
Project description:Primary skin fibroblasts from four Niemann-Pick type C patients homozygous for the I1061T mutation and four control individuals were cultured under identical conditions in DMEM containing 10% fetal bovine serum. Cells were harvested at 50-70% confluency. mRNA was isolated with the FastTrack 2.0 mRNA isolation kit according to the manufacturer's instructions (Invitrogen, Carlsbad, CA). A reference RNA comprised of 10 cell lines was used as the control for each hybridized sample (Stratagene, La Jolla, CA). Both sample and reference RNAs were amplified using the MessageAmp II aRNA amplification kit (Ambion, Austin, TX). Set of arrays that are part of repeated experiments Keywords: Biological Replicate
2007-08-15 | GSE8770 | GEO
Project description:Macrophage inflammatory protein 1alpha/CCL3 protein is a known pro-inflammatory cytokine that can mediate chemotaxis of monocytes and promote cell degranulation. Ccl3 gene expression is elevated in the CNS and visceral tissue of many lysosomal storage disorders. The deletion of Ccl3 in a mouse model of Sandhoff disease was reported to result in reduced monocyte-associated pathology in the brain, delayed neurodegeneration, and prolonged health. However, deletion of Ccl3 in a mouse model of Niemann-Pick C disease was dentrimental or neutral instead of beneficial. Prevention of neuronal loss was instead mediated by providing NPC1 to neurons. We used microarrays to detail the global change in gene expression of the cerebellum in Niemann-Pick C disease animals, Niemann-Pick C disease animals with Ccl3 gene deletion, and Niemann-Pick C disease animals with Purkinje neuron-specific NPC1-YFP rescue. To identify the top ~50 genes elevated in NPC disease Npc1-/- (NPC) and Npc1+/- (WT) mice were compared at age P50; To profile changes in gene expression as a result of Ccl3 gene deletion Ccl3-/-;Npc1-/- mice were compared against Npc1-/- mice across various ages; To profile changes in gene expression as a result of Purkinje neuron-sepcific NPC1 rescue P;N;Npc1-/- mice were compared against Npc1-/- mice across various ages.
2012-04-16 | E-GEOD-36119 | biostudies-arrayexpress
Project description:Primary skin fibroblasts from four Niemann-Pick type C patients homozygous for the I1061T mutation and four control individuals were cultured under identical conditions in DMEM containing 10% fetal bovine serum. Cells were harvested at 50-70% confluency. mRNA was isolated with the FastTrack 2.0 mRNA isolation kit according to the manufacturer's instructions (Invitrogen, Carlsbad, CA). A reference RNA comprised of 10 cell lines was used as the control for each hybridized sample (Stratagene, La Jolla, CA). Both sample and reference RNAs were amplified using the MessageAmp II aRNA amplification kit (Ambion, Austin, TX).
2007-01-05 | E-SMDB-3835 | biostudies-arrayexpress
Project description:The endocannabinoid system is considered to be an endogenous protective system in various neurodegenerative diseases. Niemann-Pick Type C is a neurodegenerative disease in which the role of the endocannabinoid system has not been studied yet. Here, we report the endocannabinoid hydrolase activity in brain proteomes of a Niemann-Pick type C mouse model as measured by activity-based protein profiling. Diacylglycerol lipase α, α/β-hydrolase domain-containing protein 4 (ABHD4), ABHD6, ABHD12, fatty acid amide hydrolase and monoacylglycerol lipase activities were quantified. Chemical proteomics showed no difference in endocannabinoid hydrolase activity in the brain of wildtype compared to Niemann-Pick C1 protein (NPC1) knockout mice. Three lysosomal serine hydrolases were identified with increased activity in NPC1 knockout mouse brain: retinoid-inducible serine carboxypeptidase, cathepsin A and palmitoyl-protein thioesterase 1, and we conclude that these might be interesting therapeutic targets for future validation studies.
2018-04-19 | PXD008979 | Pride
Project description:RNA-seq of Niemann-Pick Type C mouse microglia throughout disease course
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Project description:Niemann-Pick type C disease is a rare neurodegenerative disorder mainly caused by mutations in Npc1, resulting in abnormal late endosomal/lysosomal lipid storage. Although microgliosis is a prominent pathological feature, direct consequences of NPC1 loss on microglial function remain uncharacterized. Previously, we have characterized microglial proteome alterations in the NPC1 KO mouse model (PXD019447). In order to investigate similar changes in humans, we have cultured monocyte derived macrophages of NPC1 patients and control donors.
2021-02-09 | PXD020659 | Pride