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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA sequencing analysis of miR-603 overexpression

ABSTRACT: Alzheimer’s disease (AD) is a serious neurodegenerative disease in which miRNAs have been linked to its pathogenesis. miR-603 is a primate-specific miRNA. Through ADNI data analysis, we found a SNP rs11014002 in pre-miR-603 which promotes the biogenesis of mature miR-603 is associated with AD risk. We further identified that LRPAP1, a protein which antagonizes the function of LRP1 in Aβ clearance and AD susceptibility, is a target gene of miR-603. Moreover, overexpression of miR-603 increased the protein level of LRP1, suggesting the protective role of miR-603 in AD. Both significant increase and loss of regulatory function of miR-603 hint the existence of a compensatory mechanism in hippocampus of AD subjects. Furthermore, we found that miR-603 could directly downregulate E2F1 and prevent cells from H2O2 induced-apoptosis. This work provides the first evidence that miR-603 may modulate AD susceptibility and the SNP rs11014002 (T-carrier genotype) might be a protective factor for AD. There are two groups: Negative Control and miR-603 overexpression. We performed experiments on HEK293 cell and Hela cell.

ORGANISM(S): Homo sapiens

SUBMITTER: jin fan

PROVIDER: E-GEOD-68987 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNA sequencing analysis of miR-603 overexpression

Project description:Alzheimer’s disease (AD) is a serious neurodegenerative disease in which miRNAs have been linked to its pathogenesis. miR-603 is a primate-specific miRNA. Through ADNI data analysis, we found a SNP rs11014002 in pre-miR-603 which promotes the biogenesis of mature miR-603 is associated with AD risk. We further identified that LRPAP1, a protein which antagonizes the function of LRP1 in Aβ clearance and AD susceptibility, is a target gene of miR-603. Moreover, overexpression of miR-603 increased the protein level of LRP1, suggesting the protective role of miR-603 in AD. Both significant increase and loss of regulatory function of miR-603 hint the existence of a compensatory mechanism in hippocampus of AD subjects. Furthermore, we found that miR-603 could directly downregulate E2F1 and prevent cells from H2O2 induced-apoptosis. This work provides the first evidence that miR-603 may modulate AD susceptibility and the SNP rs11014002 (T-carrier genotype) might be a protective factor for AD.

2015-05-18 | GSE68987 | GEO

Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans

Project description:Comparative proteomic study between C. elegans wild type, mir-58.1 single, mir-80; mir-58.1 double and mir-80; mir-58.1; mir-81-82 quadruple mutants.

2015-08-06 | PXD001998 | Pride

microRNA-132/212 deficiency enhances Ab production and senile plaque deposition in Alzheimerâs disease triple transgenic mice

Project description:The abnormal regulation of amyloid-b (Ab) metabolism (e.g., production, cleavage, clearance) plays a central role in Alzheimerâs disease (AD). Among endogenous factors believed to participate in AD progression are the small regulatory non-coding microRNAs (miRs). In particular, the miR-132/212 cluster is severely reduced in the AD brain. In previous studies we have shown that miR-132/212 deficiency in mice leads to impaired memory and enhanced Tau pathology as seen in AD patients. Here we demonstrate that the genetic deletion of miR-132/212 promotes Ab deposition and amyloid (senile) plaque formation in triple transgenic AD (3xTg-AD) mice. Using RNA-Seq and bioinformatics, we identified genes of the miR-132/212 network with documented roles in the regulation of Ab metabolism, including Tau, Mapk, and Sirt1. We used RNA-Seq to analyse the hippocampus of 3xTg-AD mice lacking the miR-132/212 cluster as well as Neuro2a cells overexpressing miR-132 mimics.

2016-07-17 | E-GEOD-84481 | biostudies-arrayexpress

Aging aggravates aortic aneurysm and dissection via the miR-1204-MYLK signaling axis

Project description:The mechanism by which aging induces aortic aneurysm and dissection (AAD) remains unclear. A total of 430 subjects were recruited for screening of differentially expressed plasma microRNAs. We found that miR-1204 was significantly increased in both plasma and aorta of elder patients with AAD, and was positively correlated with age. Cell senescence induced the expression of miR-1204 through p53 interaction with plasmacytoma variant translocation 1, and miR-1204 induced vascular smooth muscle cell (VSMC) senescence to form a positive feedback loop. miR-1204 aggravated angiotensin II-induced AAD formation, and inhibition of miR-1204 attenuated β-aminopropionitrile monofumarate-induced AAD formation. Mechanistically, miR-1204 directly targeted myosin light chain kinase (MYLK) to promote VSMCs to acquire senescence-associated secretory phenotype (SASP) and lose their contractile phenotype. Overexpression of MYLK reversed miR-1204-induced VSMC senescence, SASP and contractile phenotype changes, and the decrease of transforming growth factor-β signaling pathway. Our findings suggest aging aggravates AAD via miR-1204-MYLK signaling axis.

2024-04-01 | PXD048658 | Pride

A miR-494 dependent feedback loop regulates ER stress (ANAN-376 Project)

Project description:Defects in stress responses are important contributors in many chronic conditions including cancer, cardiovascular disease, diabetes, and obesity-driven pathologies like non-alcoholic steatohepatitis (NASH). Specifically, endoplasmic reticulum (ER) stress is linked with these pathologies and control of ER stress can ameliorate tissue damage. MicroRNAs have a critical role in regulating diverse stress responses including ER stress. Here we show that miR-494-3p plays a functional role during ER stress. ER stress inducers (tunicamycin and thapsigargin) robustly increase the expression of miR-494 in vitro in an ATF6 dependent manner. Surprisingly, miR-494 pretreatment dampens the induction and magnitude of ER stress in response to tunicamycin in endothelial cells. Conversely, inhibition of miR-494 increases ER stress de novo and amplifies the effects of ER stress inducers. Using Mass Spectrometry (TMT-MS) we identified many proteins that are downregulated by both tunicamycin and miR-494 in cultured human umbilical vein endothelial cells (HUVECs). Among these, we found 6 transcripts which harbor a putative miR-494 binding site. Our data indicates that ER stress driven miR-494 may act in a feedback inhibitory loop to dampen downstream ER stress signaling. We propose that RNA-based approaches targeting miR-494 or its targets may be attractive candidates for inhibiting ER stress dependent pathologies in human disease.

2021-09-09 | PXD019992 | Pride

microRNA-222 Attenuates Mitochondrial Dysfunction Induced by Transmissible Gastroenteritis Virus via Targeting Thrombospondin-1 and Inhibiting Cluster of Differentiation 47

Project description:Transmissible gastroenteritis virus (TGEV) is a member of Coronaviridae family. Our previous research showed that TGEV infection could induce mitochondrial dysfunction and up-regulat miR-222 level. Therefore, we presumed that miR-222 might be implicated in regulating mitochondrial dysfunction induced by TGEV infection. To verify the hypothesis, the effect of miR-222 on mitochondrial dysfunction was detected and showed that miR-222 attenuated TGEV-induced mitochondrial dysfunction. To investigate the underlying molecular mechanism of miR-222 in TGEV-induced mitochondrial dysfunction, a quantitative proteomic analysis of PK-15 cells that were transfected with miR-222 mimics and infected with TGEV was performed. In total, 4151 proteins were quantified and 100 differentially expressed proteins were obtained (57 up-regulated, 43 down-regulated), among which thrombospondin-1 (THBS1) and cluster of differentiation 47 (CD47) were down-regulated. THBS1 was identified as the target of miR-222. Knockdown of THBS1 and CD47 increased mitochondrial Ca2+ level and decreased mitochondrial membrane potential (MMP) level. Together, our data establish a significant role of miR-222 in regulating mitochondrial dysfunction in response to TGEV infection.

2018-12-19 | PXD010927 | Pride

Expression data from human blood samples

Project description:Genetic factors contribute to the development of ischemic stroke but their identity remains largely unknown. We tested the association with ischemic stroke of 210 single nucleotide polymorphisms (SNPs) associated with pathways functionally related to stroke. We observed an association between the rs7956957 SNP in LRP1 and next performed microarrays analysis in healthy individuals to investigate possible associations of LRP genotypes with the expression of other genes. Twelve blood samples were obtained from twelve different healthy subjects carrying different genotypes for the rs7956957 SNP of the LRP1 gene (GG, CG or CC). Blood was extracted from 12 subjects. EDTA tubes were centrifuged at 3500rpm for 15 min to obtain the white blood cell fraction and the samples were stored at -80ºC until RNA isolation. RiboPureTM -Blood kit from Ambion (Ambion, Woodward st. Austin, USA) was used to extract total RNA following manufacturer’s instructions. Globin RNA from erythrocytes that causes interference was extracted using the Globin-Clear kit (Ambion, Woodward st. Austin, USA).

2010-11-17 | E-GEOD-25414 | biostudies-arrayexpress

The effect of transfected miR-10a in IL-1beta-stimulated and non-stimulated keratinocytes

Project description:miR-10a has been shown to regulate proliferation and invasiveness of cancer cells and inflammatory responses of endothelial cells. The function of miR-10a in the skin has not been studied before. Here we examined miR-10a expression, regulation and functions in keratinocytes (KCs) in association with atopic dermatitis (AD).

2019-09-01 | E-MTAB-7245 | biostudies-arrayexpress

Target proteins of miR-200b in AIPC by label free proteomics

Project description:For androgen-independent prostate cancer (AIPC), the current treatment is limited and the prognosis is poor. We previously found miR-200b could inhibit androgen independent proliferation ability of prostate cancer cells, but the mechanism is unclear. MiRNAs plays their role by blocking translation through base-pairing with complementary mRNA and by promoting degradation of target mRNA. Unraveling the miRNA translational silencing network remains a challenge in part because a single miRNA can inhibit multiple mRNA targets and because a single mRNA can be regulated by several distinct miRNAs that act cooperatively. However, proteomics methods provide us useful tools to unravel the target genes network. This study identified the target genes of miR-200b in AIPC. It helps us to understand the mechanism of AIPC and applies several new candidate targets of AIPC treatment.

2020-08-05 | PXD006350 | Pride

Expression data from human blood samples

2010-11-17 | GSE25414 | GEO

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