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Niemann-Pick type C fibroblast analysis

ABSTRACT: 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

ORGANISM(S): Homo sapiens

PROVIDER: GSE8770 | GEO | 2007/08/15

SECONDARY ACCESSION(S): PRJNA102055

REPOSITORIES: GEO

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Niemann-Pick type C fibroblast analysis

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

Transcription profiling of primary skin fibrolasts from Niemann-Pick type C patients homozygous for the I1061T mutation

2007-01-05 | E-SMDB-3835 | biostudies-arrayexpress

Gene expression profile of idiopathic thrombocytopenic purpura (ITP)

Project description:Five ITP and five control whole blood samples were collected with IRB approval. The age range of ITP patients was 1-54 years, and the range in platelet counts was 2,000-98,000 W 109/L. We examined only one ITP sample for antiplatelet antibodies, and found it to be positive. Total RNA was isolated from 2.5 ml whole blood according to the PAXgene Blood RNA System (PreAnalytix, Switzerland). RNA isolated from ITP patients and controls, along with Human Universal Reference RNA (Stratagene, La Jolla, CA) were linearly amplified using the MessageAmp aRNA amplification kit (Ambion, Austin, TX). Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

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Transcription profiling of whole blood samples from humans with Immune Thrombocytopenic Purpura (ITP) and control patients

2006-09-18 | E-SMDB-3822 | biostudies-arrayexpress

Gene expression profile of idiopathic thrombocytopenic purpura (ITP)

2006-09-12 | E-GEOD-5812 | biostudies-arrayexpress

Global gene expression change in the cerebellum of Niemann-Pick disease type C mice with deletion of Ccl3 or Purkinje neuron-specific NPC1 rescue

2012-04-17 | GSE36119 | GEO

Global gene expression change in the cerebellum of Niemann-Pick disease type C mice with deletion of Ccl3 or Purkinje neuron-specific NPC1 rescue

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.

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Transcription profiling of human fibrotic liver samples

Project description:Human liver samples were obtained from Analytical Biological Services Inc.(Wilmington, DE, USA) via autopsy 4-10 hours post-mortem with appropriate consent. The specimens were quickly frozen and stored at -80C. Following pulverization of the liver specimens total RNA was isolated by QIAzol extraction and RNeasy Mini Kit(QIAGEN, Valencia, CA, USA) purification. The RNA was then amplified via Ambion<br>5X MessageAmp II aRNA Amplification Kit (Austin, TX, USA) and profiled using Agilent Human Whole Genome Microarray Kit (Agilent Technologies, Santa Clara, CA, USA).

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CHEMICAL PROTEOMIC ANALYSIS OF ENDOCANNABINOID HYDROLASE ACTIVITY IN NIEMANN-PICK TYPE C MOUSE BRAIN

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

The role of Niemann-Pick type C2 in zebrafish embryonic development

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

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