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MiRNA changes in mild and moderate emphysema correlate with target gene expression in vivo and in vitro

ABSTRACT: miRNA changes in mild and moderate emphysema correlate with target gene expression in vivo and in vitro

PROVIDER: PRJNA148963 | ENA |

REPOSITORIES: ENA

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miRNA changes in mild and moderate emphysema correlate with target gene expression in vivo and in vitro

Project description:This SuperSeries is composed of the following subset Series: GSE33336: Development of microRNA expression signature for emphysema in COPD patients GSE33337: miRNA changes in mild and moderate emphysema correlate with target gene expression in vivo and in vitro [target gene expression data] Refer to individual Series

2012-05-31 | E-GEOD-33338 | biostudies-arrayexpress

miRNA changes in mild and moderate emphysema correlate with target gene expression in vivo and in vitro [target gene expression data]

Project description:To define the role of microRNAs and their mRNA targets in emphysema severity in COPD patients. We performed Agilent human miRNA oligo arrays (8x15K array, Part No. G4470A, Agilent Technologies) based on miRBase V9.1 on lung tissues from 9 mild and 20 moderate emphysema lungs obtained from patients undergoing curative resection for lung cancer. We identified 5 miRNAs and two of those were tested and validated technically using qRT-PCR. The predicted mRNA targets for the five miRNAs were identified in MSigDB using GSEA and their expression were negatively correlated in exvivo lung mRNA expression profile obtained from GEO datasets (GSE17770 and GSE1650). Increasing the expression of one of the miRNA target, miR-34c in BEAS-2B and HFL 1 cell lines resulted in the downregulation of 50 TargetScan and Pictar predicted targets of miR-34c.

2012-05-31 | E-GEOD-33337 | biostudies-arrayexpress

miRNA changes in mild and moderate emphysema correlate with target gene expression in vivo and in vitro [target gene expression data]

Project description:To define the role of microRNAs and their mRNA targets in emphysema severity in COPD patients.

2012-06-01 | GSE33337 | GEO

Transcription profiling of human lung tissue from severe emphysema versus normal or mild emphysema human patients

Project description:Comparison of severely emphysematous tissue removed at lung volume reduction surgery to that of normal or mildly emphysematous lung tissue resected from smokers with nodules suspicious for lung cancer. Data obtained from the 18 patients with severe emphysema and 12 patients with mild/no emphysema. Research may provide insights into the pathogenetic mechanisms involved in chronic obstructive pulmonary disease (COPD).

2007-08-13 | E-GEOD-1650 | biostudies-arrayexpress

miRNA changes in mild and moderate emphysema correlate with target gene expression in vivo and in vitro

Project description:This SuperSeries is composed of the SubSeries listed below.

2012-06-01 | GSE33338 | GEO

Hippocampus-Cerebellum Axis Specific Transcriptomic Stratification to Discriminate Mild from Moderate TBI

Project description:The variations of psycho- and physiological deficits caused by TBI correlate with the degree of brain injury. However, the objective stratification of TBI is yet elusive. A modified closed-head injury Marmarou model was used based on the release of a 500 gram steel slug on top of the rat skull from a height of 100 cm or 120 cm to induce differential injury models for mild TBI and moderate TBI, respectively. The skull was covered by a helmet to mimic the warfighter’s condition in theater. The hippocampus was at the focal point of injury, and the cerebellum, was susceptible to diffused shock (secondary injury). The HC-CB axis coordinates visuomotor performance, which is known to be vulnerable to TBI. The rats that received moderate TBI showed deficient visuomotor performance by the Barnes maze test for longer time periods than those inflicted with mild TBI. The time resolved and HC-CB specific transcriptomic analysis focused on genes that enabled discrimination of mild from moderate TBI at 14d post injury which is equivalent to nearly 1.5 years of human lifetime. The functional analysis elucidated an active healing mechanism in the HC exposed to mild TBI. In contrast, moderate TBI caused delayed healing and active cell death in the HC. In conclusion, the graded brain injuries differentially implicated the HC-CB axis, despite the use of a helmet to reduce the impact. Time resolved functional dynamics informed the distinct consequences of mild vs. moderate TBI.

2020-12-31 | GSE131435 | GEO

Development of microRNA expression signature for emphysema in COPD patients

2012-05-31 | E-GEOD-33336 | biostudies-arrayexpress

Mild, moderate and severe enterovirus 71 (EV71) isolates infection in human PBMCs

Project description:Hand, foot and mouth disease (HFMD), caused by enterovirus 71 (EV71), presents mild to severe disease, and sometimes fatal neurological and respiratory manifestations. However, reasons for the severe pathogenesis remain undefined. To investigate this, infection and viral kinetics of EV71 isolates from clinical disease (mild, moderate and severe) from Sarawak, Malaysia, were characterized in human rhabdomyosarcoma (RD), neuroblastoma (SH-SY5Y) and peripheral blood mononuclear cells (PBMCs). High resolution transcriptomics was used to decipher EV71-host interactions in PBMCs. Ingenuity analyses revealed similar pathways triggered by all EV71 isolates, although the extent of activation varied. Importantly, several pathways were found to be specific to the severe isolate, including triggering receptor expressed on myeloid cells 1 (TREM-1) signaling. Depletion of TREM-1 in EV71-infected PBMCs with peptide LP17 resulted in decreased levels of pro-inflammatory genes, and reduced viral loads for the moderate and severe isolates. Mechanistically, this is the first report describing the transcriptome profiles during EV71 infections in primary human cells, and the involvement of TREM-1 in the severe disease pathogenesis, thus providing new insights for future treatment targets.

2020-03-16 | GSE135964 | GEO

miRNA expression in tracheal aspirates in mild/moderate and severe BPD

Project description:miRNA expression in tracheal aspirates in mild/moderate and severe BPD

| PRJNA697980 | ENA

Whole lung transcriptomics of a house dust mite model of mild/moderate asthma

Project description:Purpose: Identify whole lung gene expression patterns in a house dust mite model of mild/moderate asthma Methods: Lung gene expression profiles of 10 week old BALB/c female mice were generated by ribosome-depleted, 150 nt, paired-end, stranded RNA-seq with Illumina HiSeq v4. Sequence reads that passed quality filters after trimming were analyzed with Sailfish-cir to identify linear RNAs and circular RNAs. Differential expression of linear RNAs was assessed with Deseq2 . QRT–PCR validation was performed using TaqMan and SYBR Green methods. Results: 100 million sequence reads per sample were mapped to the mouse genome (build mm10) using Sailfish-cir to identify linear and circular RNA transcripts. Pathway analysis of differentially expressed genes identified upregulation of gene sets for human asthma, mouse lung allergic inflammation, Muc5ac regulated genes and smooth muscle genes after allergic sensitization. Gene level exppression in each asthma-related pathway was reduced by the miR-145 antagonist. The miR-145 antagonist and several nontargeting oligos also upregulated interferon signaling pathways suggesting a general antiinflammatory effect of LNA/DNA oligos in the lung. Conclusions: Lung-directed delivery of LNA/DNA oligonucleotides with cationic lipid nanoparticles is an efffective means to prevent inflammatory gene expression in a house dust mite model of mild/moderate asthma.

2019-06-06 | GSE132263 | GEO

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