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

References

• Hogg JC, Timens W. The pathology of chronic obstructive pulmonary disease. Annu Rev Pathol. 2009;4:435–21. PubMed PMID: 18954287. .
   PubMed Web of Science ®Google Scholar
• Pouwels SD, Heijink IH, Ten Hacken NH, et al. DAMPs activating innate and adaptive immune responses in COPD. Mucosal Immunol. 2014 Mar;7(2):215–226. PubMed PMID: 24150257.
   PubMed Web of Science ®Google Scholar
• Kumar M, Seeger W, Voswinckel R. Senescence-associated secretory phenotype and its possible role in chronic obstructive pulmonary disease. Am J Respir Cell Mol Biol. 2014 Sep;51(3):323–333. PubMed PMID: 25171460. .
   PubMed Web of Science ®Google Scholar
• Yao H, Rahman I. Current concepts on oxidative/carbonyl stress, inflammation and epigenetics in pathogenesis of chronic obstructive pulmonary disease. Toxicol Appl Pharmacol. 2011 Jul 15;254(2):72–85. PubMed PMID: 21296096; PubMed Central PMCID: PMCPMC3107364. .
   PubMed Web of Science ®Google Scholar
• Sundar IK, Yao H, Rahman I. Oxidative stress and chromatin remodeling in chronic obstructive pulmonary disease and smoking-related diseases. Antioxid Redox Signal. 2013 May 20;18(15):1956–1971. PubMed PMID: 22978694; PubMed Central PMCID: PMCPMC3624634. .
   PubMed Web of Science ®Google Scholar
• Lerner CA, Sundar IK, Rahman I. Mitochondrial redox system, dynamics, and dysfunction in lung inflammaging and COPD. Int J Biochem Cell Biol. 2016 Dec;81(Pt B):294–306. PubMed PMID: 27474491; PubMed Central PMCID: PMCPMC5154857. .
   Web of Science ®Google Scholar
• Stolzenburg LR, Harris A. The role of microRNAs in chronic respiratory disease: recent insights. Biol Chem. 2018 Feb 23;399(3):219–234. PubMed PMID: 29148977.
   PubMed Web of Science ®Google Scholar
• De Smet EG, Mestdagh P, Vandesompele J, et al. Non-coding RNAs in the pathogenesis of COPD. Thorax. 2015 Aug;70(8):782–791. PubMed PMID: 25995155.
   PubMed Web of Science ®Google Scholar
• Molina-Pinelo S, Pastor MD, Suarez R, et al. MicroRNA clusters: dysregulation in lung adenocarcinoma and COPD. Eur Respir J. 2014 Jun;43(6):1740–1749. PubMed PMID: 24743967.
   PubMed Web of Science ®Google Scholar
• Hough KP, Chanda D, Duncan SR, et al. Exosomes in immunoregulation of chronic lung diseases. Allergy. 2017 Apr;72(4):534–544. PubMed PMID: 27859351; PubMed Central PMCID: PMCPMC5462600.
   PubMed Web of Science ®Google Scholar
• Yanez-Mo M, Siljander PR, Andreu Z, et al. Biological properties of extracellular vesicles and their physiological functions. J Extracell Vesicles. 2015;4:27066. PubMed PMID: 25979354; PubMed Central PMCID: PMCPMC4433489. .
   PubMed Web of Science ®Google Scholar
• Nana-Sinkam SP, Acunzo M, Croce CM, et al. Extracellular vesicle biology in the pathogenesis of lung disease. Am J Respir Crit Care Med. 2017 Dec 15;196(12):1510–1518. PubMed PMID: 28678586; PubMed Central PMCID: PMCPMC5754438.
   PubMed Web of Science ®Google Scholar
• Osei ET, Florez-Sampedro L, Timens W, et al. Unravelling the complexity of COPD by microRNAs: it’s a small world after all. Eur Respir J. 2015 Sep;46(3):807–818. 10.1183/13993003.02139-2014. PubMed PMID: 26250493.
   PubMed Web of Science ®Google Scholar
• Ezzie ME, Crawford M, Cho JH, et al. Gene expression networks in COPD: microRNA and mRNA regulation. Thorax. 2012 Feb;67(2):122–131. PubMed PMID: 21940491.
   PubMed Web of Science ®Google Scholar
• Shen Y, Yu X, Zhu L, et al. Transfer RNA-derived fragments and tRNA halves: biogenesis, biological functions and their roles in diseases. J Mol Med (Berl). 2018 Nov;96(11):1167–1176. 10.1007/s00109-018-1693-y. PubMed PMID: 30232504.
   PubMed Web of Science ®Google Scholar
• Sun T, Han X. The disease-related biological functions of PIWI-interacting RNAs (piRNAs) and underlying molecular mechanisms. ExRNA. 2019;1(1):21.
   Google Scholar
• Fujita Y, Kosaka N, Araya J, et al. Extracellular vesicles in lung microenvironment and pathogenesis. Trends Mol Med. 2015 Sep;21(9):533–542. PubMed PMID: 26231094.
   PubMed Web of Science ®Google Scholar
• Gould SJ, Raposo G. As we wait: coping with an imperfect nomenclature for extracellular vesicles. J Extracell Vesicles. 2013;2. PubMed PMID: 24009890; PubMed Central PMCID: PMCPMC3760635. DOI:10.3402/jev.v2i0.20389.
   PubMedGoogle Scholar
• Colombo M, Raposo G, Thery C. Biogenesis, secretion, and intercellular interactions of exosomes and other extracellular vesicles. Annu Rev Cell Dev Biol. 2014;30:255–289. PubMed PMID: 25288114. .
   PubMed Web of Science ®Google Scholar
• Abels ER, Breakefield XO. Introduction to extracellular vesicles: biogenesis, RNA cargo selection, content, release, and uptake. Cell Mol Neurobiol. 2016 Apr;36(3):301–312. PubMed PMID: 27053351; PubMed Central PMCID: PMCPMC5546313.
   PubMed Web of Science ®Google Scholar
• Clayton A, Buschmann D, Byrd JB, et al. Summary of the ISEV workshop on extracellular vesicles as disease biomarkers, held in Birmingham, UK, during December 2017. J Extracell Vesicles. 2018;7(1):1473707.
   PubMed Web of Science ®Google Scholar
• Tan DBA, Armitage J, Teo TH, et al. Elevated levels of circulating exosome in COPD patients are associated with systemic inflammation. Respir Med. 2017 Nov;132:261–264. PubMed PMID: 28476471.
   PubMed Web of Science ®Google Scholar
• Sundar IK, Yao H, Huang Y, et al. Serotonin and corticosterone rhythms in mice exposed to cigarette smoke and in patients with COPD: implication for COPD-associated neuropathogenesis. PloS One. 2014;9(2):e87999. PubMed PMID: 24520342; PubMed Central PMCID: PMC3919731. .
   Web of Science ®Google Scholar
• Sundar IK, Li D, Rahman I. Proteomic analysis of plasma-derived extracellular vesicles in smokers and patients with chronic obstructive pulmonary disease. ACS Omega. 2019;4(6):10649–10661.
   Web of Science ®Google Scholar
• Mateescu B, Kowal EJ, van Balkom BW, et al. Obstacles and opportunities in the functional analysis of extracellular vesicle RNA - an ISEV position paper. J Extracell Vesicles. 2017;6(1):1286095. PubMed PMID: 28326170; PubMed Central PMCID: PMCPMC5345583. .
   PubMed Web of Science ®Google Scholar
• El-Mogy M, Lam B, Haj-Ahmad TA, et al. Diversity and signature of small RNA in different bodily fluids using next generation sequencing. BMC Genomics. 2018 May 29;19(1):408. PubMed PMID: 29843592; PubMed Central PMCID: PMCPMC5975555.
   PubMed Web of Science ®Google Scholar
• Thery C, Amigorena S, Raposo G, et al. Isolation and characterization of exosomes from cell culture supernatants and biological fluids. In: Bonifacino JS, et al., editor. Current protocols in cell biology/editorial board; 2006 Apr. p. 22. Chapter 3: Unit3 PubMed PMID: 18228490. doi:10.1002/0471143030.cb0322s30.
   Google Scholar
• Gardiner C, Ferreira YJ, Dragovic RA, et al. Extracellular vesicle sizing and enumeration by nanoparticle tracking analysis. J Extracell Vesicles. 2013;2:19671. PubMed PMID: 24009893; PubMed Central PMCID: PMC3760643. .
   Google Scholar
• Hong CS, Funk S, Muller L, et al. Isolation of biologically active and morphologically intact exosomes from plasma of patients with cancer. J Extracell Vesicles. 2016;5:29289. PubMed PMID: 27018366; PubMed Central PMCID: PMCPMC4808740. .
   PubMed Web of Science ®Google Scholar
• Consortium E-T, Van Deun J, Mestdagh P, et al. EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research. Nat Methods. 2017 Feb 28;14(3):228–232. PubMed PMID: 28245209.
   PubMed Web of Science ®Google Scholar
• Subramanian SL, Kitchen RR, Alexander R, et al. Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. J Extracell Vesicles. 2015;4:27497. PubMed PMID: 26320941; PubMed Central PMCID: PMCPMC4553261. .
   Web of Science ®Google Scholar
• Kalra H, Simpson RJ, Ji H, et al. Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation. PLoS Biol. 2012;10(12):e1001450. PubMed PMID: 23271954; PubMed Central PMCID: PMCPMC3525526. .
   PubMed Web of Science ®Google Scholar
• Keerthikumar S, Chisanga D, Ariyaratne D, et al. ExoCarta: a web-based compendium of exosomal cargo. J Mol Biol. 2016 Feb 22;428(4):688–692. PubMed PMID: 26434508; PubMed Central PMCID: PMCPMC4783248. .
   PubMed Web of Science ®Google Scholar
• Wong N, Wang X. miRDB: an online resource for microRNA target prediction and functional annotations. Nucleic Acids Res. 2015 Jan;43(D1):D146–52. PubMed PMID: 25378301; PubMed Central PMCID: PMCPMC4383922.
   PubMed Web of Science ®Google Scholar
• Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11(3):R25. PubMed PMID: 20196867; PubMed Central PMCID: PMCPMC2864565. .
   PubMed Web of Science ®Google Scholar
• Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. PubMed PMID: 25516281; PubMed Central PMCID: PMCPMC4302049. .
   PubMed Web of Science ®Google Scholar
• Backes C, Khaleeq QT, Meese E, et al. miEAA: microRNA enrichment analysis and annotation. Nucleic Acids Res. 2016 Jul 8;44(W1):W110–6. PubMed PMID: 27131362; PubMed Central PMCID: PMCPMC4987907.
   PubMed Web of Science ®Google Scholar
• Akbas F, Coskunpinar E, Aynaci E, et al. Analysis of serum micro-RNAs as potential biomarker in chronic obstructive pulmonary disease. Exp Lung Res. 2012 Aug;38(6):286–294. PubMed PMID: 22686440.
   PubMed Web of Science ®Google Scholar
• Schembri F, Sridhar S, Perdomo C, et al. MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2319–2324. PubMed PMID: 19168627; PubMed Central PMCID: PMCPMC2650144.
   PubMed Web of Science ®Google Scholar
• Dang X, Qu X, Wang W, et al. Bioinformatic analysis of microRNA and mRNA regulation in peripheral blood mononuclear cells of patients with chronic obstructive pulmonary disease. Respir Res. 2017 Jan 5;18(1):4. PubMed PMID: 28057018; PubMed Central PMCID: PMCPMC5217451.
   PubMed Web of Science ®Google Scholar
• Esquinas C, Janciauskiene S, Gonzalo R, et al. Gene and miRNA expression profiles in PBMCs from patients with severe and mild emphysema and PiZZ alpha1-antitrypsin deficiency. Int J Chron Obstruct Pulmon Dis. 2017;12:3381–3390. PubMed PMID: 29238183; PubMed Central PMCID: PMCPMC5713702. .
   PubMed Web of Science ®Google Scholar
• Shen Z, Tang W, Guo J, et al. miR-483-5p plays a protective role in chronic obstructive pulmonary disease. Int J Mol Med. 2017 Jul;40(1):193–200. PubMed PMID: 28534971.
   Web of Science ®Google Scholar
• Soeda S, Ohyashiki JH, Ohtsuki K, et al. Clinical relevance of plasma miR-106b levels in patients with chronic obstructive pulmonary disease. Int J Mol Med. 2013 Mar;31(3):533–539. PubMed PMID: 23338559.
   Web of Science ®Google Scholar
• Mizuno S, Bogaard HJ, Gomez-Arroyo J, et al. MicroRNA-199a-5p is associated with hypoxia-inducible factor-1alpha expression in lungs from patients with COPD. Chest. 2012 Sep;142(3):663–672. PubMed PMID: 22383663; PubMed Central PMCID: PMCPMC3435138.
   PubMed Web of Science ®Google Scholar
• Chatila WM, Criner GJ, Hancock WW, et al. Blunted expression of miR-199a-5p in regulatory T cells of patients with chronic obstructive pulmonary disease compared to unaffected smokers. Clin Exp Immunol. 2014 Jul;177(1):341–352. PubMed PMID: 24634990; PubMed Central PMCID: PMCPMC4089184.
   Web of Science ®Google Scholar
• Christenson SA, Brandsma CA, Campbell JD, et al. miR-638 regulates gene expression networks associated with emphysematous lung destruction. Genome Med. 2013;5(12):114. PubMed PMID: 24380442; PubMed Central PMCID: PMCPMC3971345.
   PubMed Web of Science ®Google Scholar
• Sinha A, Yadav AK, Chakraborty S, et al. Exosome-enclosed microRNAs in exhaled breath hold potential for biomarker discovery in patients with pulmonary diseases. J Allergy Clin Immunol. 2013 Jul;132(1):219–222. PubMed PMID: 23683467.
   PubMed Web of Science ®Google Scholar
• Njock MS, Guiot J, Henket MA, et al. Sputum exosomes: promising biomarkers for idiopathic pulmonary fibrosis. Thorax. 2018 Sep 22. PubMed PMID: 30244194. DOI:10.1136/thoraxjnl-2018-211897.
   Web of Science ®Google Scholar
• Sanchez-Vidaurre S, Eldh M, Larssen P, et al. RNA-containing exosomes in induced sputum of asthmatic patients. J Allergy Clin Immunol. 2017 Nov;140(5):1459–1461 e2. PubMed PMID: 28629752.
   PubMed Web of Science ®Google Scholar
• Bagnato G, Roberts WN, Roman J, et al. A systematic review of overlapping microRNA patterns in systemic sclerosis and idiopathic pulmonary fibrosis. Eur Respir Rev. 2017 Sep;26(144):160125. PubMed PMID: WOS:000412288100012; English.
   PubMed Web of Science ®Google Scholar
• Fujii T, Shimada K, Nakai T, et al. MicroRNAs in smoking-related carcinogenesis: biomarkers, Functions, and Therapy. J Clin Med. 2018 May 7;(5):98. PubMed PMID: WOS:000435194400011; English. DOI:10.3390/jcm7050098.
   Web of Science ®Google Scholar
• Sato T, Liu XD, Nelson A, et al. Reduced miR-146a increases prostaglandin E-2 in chronic obstructive pulmonary disease fibroblasts. Am J Respir Crit Care Med. 2010 Oct 15;182(8):1020–1029. PubMed PMID: WOS:000283384000008; English.
   PubMed Web of Science ®Google Scholar
• Xie LH, Wu MH, Lin H, et al. An increased ratio of serum miR-21 to miR-181a levels is associated with the early pathogenic process of chronic obstructive pulmonary disease in asymptomatic heavy smokers. Mol Biosyst. 2014;10(5):1072–1081. PubMed PMID: WOS:000333581100010; English. .
   PubMedGoogle Scholar
• Hu G, Drescher KM, Chen XM. Exosomal miRNAs: biological properties and therapeutic potential. Front Genet. 2012;3:56. PubMed PMID: 22529849; PubMed Central PMCID: PMCPMC3330238. .
   PubMedGoogle Scholar
• Kumar P, Anaya J, Mudunuri SB, et al. Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biol. 2014 Oct;1(12):78. PubMed PMID: 25270025; PubMed Central PMCID: PMCPMC4203973. .
   PubMed Web of Science ®Google Scholar
• Maute RL, Schneider C, Sumazin P, et al. tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma. Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1404–1409. PubMed PMID: 23297232; PubMed Central PMCID: PMCPMC3557069.
   PubMed Web of Science ®Google Scholar
• Goodarzi H, Liu X, Nguyen HC, et al. Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement. Cell. 2015 May 7;161(4):790–802. PubMed PMID: 25957686; PubMed Central PMCID: PMCPMC4457382.
   PubMed Web of Science ®Google Scholar
• Li S, Xu Z, Sheng J. tRNA-derived small RNA: a novel regulatory small non-coding RNA. Genes (Basel). 2018 May 10;9(5):246. PubMed PMID: 29748504; PubMed Central PMCID: PMCPMC5977186. .
   Web of Science ®Google Scholar
• Qu AL, Wang WF, Yang YM, et al. A serum piRNA signature as promising non-invasive diagnostic and prognostic biomarkers for colorectal cancer. Cancer Manag Res. 2019;11:3703–3720. PubMed PMID: WOS:000467153800001; English. .
   PubMed Web of Science ®Google Scholar
• Muhammad A, Waheed R, Khan NA, et al. piRDisease v1.0: a manually curated database for piRNA associated diseases. Database (Oxford). 2019 Jan;1. DOI:10.1093/database/baz052. PubMed PMID: 31267133; PubMed Central PMCID: PMCPMC6606758.
   Web of Science ®Google Scholar
• Krishnan P, Ghosh S, Graham K, et al. Piwi-interacting RNAs and PIWI genes as novel prognostic markers for breast cancer. Oncotarget. 2016 Jun 21;7(25):37944–37956. PubMed PMID: WOS:000378229100042; English.
   PubMedGoogle Scholar
• Ravo M, Cordella A, Rinaldi A, et al. Small non-coding RNA deregulation in endometrial carcinogenesis. Oncotarget. 2015 Mar 10;6(7):4677–4691. PubMed PMID: WOS:000352792000011; English.
   Google Scholar