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Screening and verification of differentially expressed long non-coding RNAs in the peripheral blood of patients with asthma

ABSTRACT: Screening and verification of differentially expressed long non-coding RNAs in the peripheral blood of patients with asthma

PROVIDER: PRJNA801410 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17794308_1.fastq.gz	Fastqsanger.gz
	SRR17794308_2.fastq.gz	Fastqsanger.gz
	SRR17794309_1.fastq.gz	Fastqsanger.gz
	SRR17794309_2.fastq.gz	Fastqsanger.gz
	SRR17794310_1.fastq.gz	Fastqsanger.gz

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Screening and verification of differentially expressed long non-coding RNAs in the peripheral blood of patients with asthma

Project description:Purpose: The goals of this study are to explore the differentially expressed long non-coding RNAs in the peripheral blood of patients with asthma. Methods: lncRNA and mRNA profiles of peripheral blood (human) were generated by deep sequencing. Results: There were 1137 differentially expressed lncRNAs in the asthma patients compared to in the healthy controls, of which 485 were upregulated and 652 were downregulated.

2022-01-30 | GSE195599 | GEO

Screening and Verification of Differentially Expressed Long Non-coding RNAs in the Peripheral Blood of Patients With asthma.

Project description:Growing evidence suggests that long non-coding RNAs (lncRNAs) play a key role in the pathogenesis of asthma. Although some differentially expressed lncRNAs have been identified in asthmatic patients, many asthma-related lncRNAs have not been annotated. In the present study, six patients and three healthy subjects were randomly selected from 34 asthmatic patients and 17 healthy subjects. Second-generation high-throughput sequencing was performed on their peripheral blood samples. There were 1,137 differentially expressed lncRNAs in the asthma patients compared to in the healthy controls, of which 485 were upregulated and 652 were downregulated. The top 30 enriched GO and KEGG terms were identified, and the cytosolic ribosome (GO:0022626) and ribosome (hsa03010) were associated with the most differentially expressed lncRNAs. The top 10 differentially expressed lncRNAs associated with asthma were verified by an lncRNA-mRNA co-expression network and RT-qPCR. Seven of the these (NONHSAT015495.2, MSTRG.71212.2, NONHSAT163272.1, NONHSAT181891.1, NONHSAT190964.1, ENST00000564809, and NONHSAT076890.2) were down-regulated in the peripheral blood of asthmatic patients, which was consistent with the sequencing results. Three patients and three healthy subjects were randomly selected from the remaining subjects to verify these seven lncRNAs by RT-qPCR, which further confirmed the sequencing results. Public database GSE106230 was also in agreement with the FPKM (Fragments Per kilobase of exon model per Million mapped reads) trends of ENST00000564809, NONHSAT015495.2, NONHSAT181891.1, and NONHSAT190964.1. In conclusion, the present study identified seven lncRNAs that may serve as potential biological markers for asthma.

| S-EPMC8902465 | biostudies-literature

Differentially expressed profile of LncRNA in PBMCs (peripheral blood mononuclear cells) of asthma patients

Project description:To determine LncRNA transcribed in PBMCs, we have employed whole genome microarray expression profiling as a discovery platform to identify LncRNA expression in PBMCs donated by patients of asthma and healthy volunteers.

2021-05-01 | GSE143192 | GEO

Differentially expressed profile of LncRNA in PBMCs (peripheral blood mononuclear cells) of asthma patients

Project description:Differentially expressed profile of LncRNA in PBMCs (peripheral blood mononuclear cells) of asthma patients

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Functional classes of bronchial mucosa genes that are differentially expressed in asthma

Project description:Asthma pathogenesis and susceptibility involves a complex interplay between genetic and environmental factors. We report the results of expression microarray studies using tissue obtained from bronchial biopsies of healthy controls and of subjects with allergic asthma, both before and following inhaled corticotherapy.

2009-04-24 | GSE15823 | GEO

Gene expression profiling of peripheral blood from uncontrolled and controlled asthma

Project description:We analyzed the transcriptomes of children with controlled and uncontrolled asthma in Taiwanese Consortium of Childhood Asthma Study (TCCAS). Hierarchical clustering, differentially expressed gene (DEG), weighted gene co-expression network analysis (WGCNA) and pathway enrichment methods were performed, to investigate important genes between two groups.

2021-11-09 | GSE188424 | GEO

Transcriptional profiles of peripheral eosinophils in COPD and asthma - a preliminary study

Project description:The role of eosinophilic inflammation in chronic obstructive pulmonary disease (COPD) pathogenesis is unknown and is probably different than in asthma. The molecular processes underlying the differences between eosinophils from asthma and COPD have not been studied. The study group included 5 patients with asthma and 4 patients with COPD. The RNA-Seq data analysis identified 26 differentially expressed genes between COPD and asthma (according to adjusted p-value). In total, 6 genes were up-regulated (CCL3L1, CCL4L2, SERPINB2, PRSS21, GPR82) and 20 were down-regulated (e.g. JUN, IFITM3, DUSP1, GNG7, ZNF107, BCL6) in peripheral eosinophils of COPD patients compared to asthma. Biological processes associated with down-regulated genes were cell differentiation, positive regulation of RNA metabolic process. The genes associated with signaling of IL-4 and IL-13 pathway were down-regulated in COPD eosinophils compared to asthma. Peripheral eosinophils from COPD and asthma patients present different transcriptomic profiles suggesting their different function in pathobiology of both obstructive airway diseases.

2024-01-01 | GSE237284 | GEO

Screening of differentially expressed genes after DBDx treatment

Project description:Screening of differentially expressed genes after DBDx treatment

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Screening and identification of differentially expressed long non-coding RNAs in multidrug-resistant tuberculosis.

Project description:BackgroundEfforts to eradicate tuberculosis are largely threatened by drug-resistant tuberculosis, particularly, multidrug-resistant tuberculosis (MDR-TB). Screening and identification potential biomarkers for MDR-TB is crucial to diagnose early and reduce the incidence of MDR-TB.MethodsTo screen the differentially expressed long non-coding RNAs in MDR-TB, the lncRNA and mRNA expression profiles in serum derived from healthy controls (HCs), individuals with MDR-TB and drug-sensitive tuberculosis (DS-TB) were analyzed by microarray assay and 10 lncRNAs were randomly selected for further validation by reverse transcription-quantitative real-time PCR(RT-qPCR). The biological functions of differentially expressed mRNAs as well as relationships between genes and signaling pathways were investigated using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), respectively.ResultsA total of 353 differentially expressed lncRNAs (312 upregulated) and 202 mRNAs (99 upregulated) were found in the MDR-TB group compared to HCs. And compared with the DS-TB group, 442 differentially expressed lncRNAs (115 upregulated) and 190 mRNAs (87 upregulated) were found in the MDR-TB group. The expression levels of lncRNA n335659 were found to differ significantly between each group by RT-qPCR. Compared with DS-TB group, the GO analysis showed that the differential mRNAs were mainly enriched in the processes associated with the detection of the chemical stimulus, the regulation of mRNA metabolic process and neutrophil activation in the MDR-TB group; the KEGG analysis indicated that the differential mRNAs between DS-TB and MDR-TB were mainly enriched in proteasome and Notch signaling pathway, which might reveal a fraction of the mechanism of MDR-TB. The discovery of the serum lncRNA n335659 might serve as a potential biomarker for MDR-TB and Notch signaling pathway provided a new clue for the investigation of the pathological mechanism of MDR-TB.

| S-EPMC8772445 | biostudies-literature

Genetic characterization of macrophages from induced sputum of asthma and COPD patients

Project description:Background: Macrophages are important cells in pathogenesis of obstructive lung diseases including asthma and chronic obstructive pulmonary disease (COPD). The aim of the study was a multivariate, genetic, comparative analysis of macrophages from patients with asthma and COPD. Methods: Macrophages were isolated from induced sputum (IS) by magnetic bead separation. Transcriptomic measurements were carried out using Affymetrix Human Gene 2.1 ST ArrayStrip in 17 samples: 8 asthma (4 ICS naive , 4 ICS treated), 4 COPD and 5 control samples. The expression of the most significantly differentiating genes was evaluated by real time PCR in 34 samples (15 patients with asthma, 11 patients with COPD and 17 controls). Results: USP53 was the only gene differentially expressed (p adjusted clue =0.09) in the comparison between ICS naïve and ICS treated asthma. The PCR verification showed increased expression of BTF3, CDS2, DNAJC13, DDX5, GNAI2, SCGB1A1, SIRPB1, TRAF3IP, USP53, WDR49 in the asthma compared to COPD group. The changed gene expression profile of macrophages were characterized mostly by gene ontology terms linked with cell motility, cilium function, cell junction and adhesion organization. Conclusions: Gene expression profiling of sputum macrophages revealed distinct molecular capacity in asthma and COPD. The role of sputum macrophages in the pathophysiology of obstructive lung diseases is probably connected with biological processes associated with their motility, cilium dysfunction and cell junction organization.

2018-08-09 | GSE112260 | GEO

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