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吸烟者和慢性阻塞性肺疾病患者血浆来源的细胞外囊泡微小RNA的小RNA序列分析作为循环生物标志物

Small RNA-sequence analysis of plasma-derived extracellular vesicle miRNAs in smokers and patients with chronic obstructive pulmonary disease as circulating biomarkers.

作者信息

Sundar Isaac Kirubakaran, Li Dongmei, Rahman Irfan

机构信息

Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA.

Department of Clinical & Translational Research, University of Rochester Medical Center, Rochester, NY, USA.

出版信息

J Extracell Vesicles. 2019 Nov 7;8(1):1684816. doi: 10.1080/20013078.2019.1684816. eCollection 2019.

Abstract

Extracellular vesicles (EVs) play a vital role in normal lung physiology to maintain homeostasis in the airways via intercellular communication. EVs include exosomes and microvesicles, and are characterized by their phospholipid bilayers. EVs have been recognized as novel circulating biomarkers of disease, which are released by different cell types. In this study, we used different EV isolation and purification methods to characterize the plasma-derived EV miRNAs from non-smokers, smokers and patients with COPD. A small RNA sequencing (RNA-seq) approach was adapted to identify novel circulating EV miRNAs. We found that plasma-derived EVs from non-smokers, smokers and patients with COPD vary in their size, concentration, distribution and phenotypic characteristics as confirmed by nanoparticle tracking analysis, transmission electron microscopy, and immunoblot analysis of EV surface markers. RNA-seq analysis confirmed the most abundant types of small RNAs, such as miRNAs, tRNAs, piRNAs snRNAs, snoRNAs and other biotypes in plasma-derived EVs. We mainly focused on miRNAs as novel biomarkers in smokers and patients with COPD for further analysis. Differential expression by DESeq2 identified distinct miRNA profiles (up-regulated: miR-22-3p, miR-99a-5p, miR-151a-5p, miR-320b, miR-320d; and down-regulated: miR-335-5p, miR-628-3p, miR-887-5p and miR-937-3p) in COPD versus smokers or non-smokers in a pairwise comparison. Gene set enrichment analysis (GSEA) of differentially expressed miRNAs revealed the top pathways, gene ontology and diseases associated with smokers and patients with COPD. We selectively validated miRNAs in EVs isolated from BEAS-2B cells treated with cigarette smoke extract by quantitative PCR analysis. For the first time, we report that plasma-derived EV miRNAs are novel circulating pulmonary disease biomarkers. Thus, molecular profiling of EV miRNAs has great translational potential for the development of biomarkers that may be used in the diagnosis, prognosis, and therapeutics of COPD.

摘要

细胞外囊泡(EVs)在正常肺生理学中起着至关重要的作用,通过细胞间通讯维持气道内的稳态。EVs包括外泌体和微囊泡,其特征在于具有磷脂双层膜。EVs已被公认为是由不同细胞类型释放的新型疾病循环生物标志物。在本研究中,我们使用不同的EV分离和纯化方法来表征来自非吸烟者、吸烟者和慢性阻塞性肺疾病(COPD)患者的血浆来源的EV微小RNA(miRNAs)。采用小RNA测序(RNA-seq)方法来鉴定新型循环EV miRNAs。我们发现,通过纳米颗粒跟踪分析、透射电子显微镜以及EV表面标志物的免疫印迹分析证实,来自非吸烟者、吸烟者和COPD患者的血浆来源的EVs在大小、浓度、分布和表型特征方面存在差异。RNA-seq分析证实了血浆来源的EVs中最丰富的小RNA类型,如miRNAs、转运RNA(tRNAs)、PIWI相互作用RNA(piRNAs)、小核RNA(snRNAs)、核仁小RNA(snoRNAs)和其他生物类型。我们主要关注miRNAs作为吸烟者和COPD患者的新型生物标志物进行进一步分析。通过DESeq2进行的差异表达分析确定了在COPD与吸烟者或非吸烟者的成对比较中不同的miRNA谱(上调:miR-22-3p、miR-99a-5p、miR-151a-5p、miR-320b、miR-320d;下调:miR-335-5p、miR-628-3p、miR-887-5p和miR-937-3p)。对差异表达的miRNAs进行基因集富集分析(GSEA)揭示了与吸烟者和COPD患者相关的主要通路、基因本体和疾病。我们通过定量PCR分析选择性地验证了从用香烟烟雾提取物处理的BEAS-2B细胞中分离的EVs中的miRNAs。我们首次报道血浆来源的EV miRNAs是新型循环肺部疾病生物标志物。因此,EV miRNAs的分子谱分析对于开发可用于COPD诊断、预后和治疗的生物标志物具有巨大的转化潜力。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb58/6848892/60073ac7ff6c/ZJEV_A_1684816_F0001_OC.jpg

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