188
Views
0
CrossRef citations to date
0
Altmetric
ORIGINAL RESEARCH

Integrated Analysis of Non-Coding RNA and mRNA Expression Profiles in Exosomes from Lung Tissue with Sepsis-Induced Acute Lung Injury

ORCID Icon, , , , , , , & show all
Pages 3879-3895 | Received 01 May 2023, Accepted 19 Aug 2023, Published online: 01 Sep 2023

References

  • Sevransky JE, Martin GS, Shanholtz C, et al. Mortality in sepsis versus non-sepsis induced acute lung injury. Crit Care. 2009;13(5):R150. doi:10.1186/cc8048
  • Killien EY, Huijsmans RLN, Ticknor IL, et al. Acute respiratory distress syndrome following pediatric trauma: application of pediatric acute lung injury consensus conference criteria. Crit Care Med. 2020;48(1):e26–e33. doi:10.1097/CCM.0000000000004075
  • Fleischmann C, Scherag A, Adhikari NK, et al. International forum of acute care T: assessment of global incidence and mortality of hospital-treated sepsis. Current estimates and limitations. Am J Respir Crit Care Med. 2016;193(3):259–272. doi:10.1164/rccm.201504-0781OC
  • Singer M, Deutschman CS, Seymour CW, et al. The third international consensus definitions for sepsis and septic shock (Sepsis-3). JAMA. 2016;315(8):801–810. doi:10.1001/jama.2016.0287
  • Li Y, Cao Y, Xiao J, et al. Inhibitor of apoptosis-stimulating protein of p53 inhibits ferroptosis and alleviates intestinal ischemia/reperfusion-induced acute lung injury. Cell Death Differ. 2020;27(9):2635–2650. doi:10.1038/s41418-020-0528-x
  • Jiang K, Yang J, Guo S, Zhao G, Wu H, Deng G. Peripheral circulating exosome-mediated delivery of miR-155 as a novel mechanism for acute lung inflammation. Mol Ther. 2019;27(10):1758–1771. doi:10.1016/j.ymthe.2019.07.003
  • Hu Q, Lyon CJ, Fletcher JK, Tang W, Wan M, Hu TY. Extracellular vesicle activities regulating macrophage- and tissue-mediated injury and repair responses. Acta Pharm Sin B. 2021;11(6):1493–1512. doi:10.1016/j.apsb.2020.12.014
  • Zhang D, Lee H, Wang X, Groot M, Sharma L, Dela Cruz CS. Jin Y: a potential role of microvesicle-containing miR-223/142 in lung inflammation. Thorax. 2019;74(9):865–874. doi:10.1136/thoraxjnl-2018-212994
  • Wang S, Zhou H, Zheng L, et al. Global trends in research of macrophages associated with acute lung injury over past 10 years: a bibliometric analysis. Front Immunol. 2021;12:669539. doi:10.3389/fimmu.2021.669539
  • Wang L, Zhang H, Sun L, et al. Manipulation of macrophage polarization by peptide-coated gold nanoparticles and its protective effects on acute lung injury. J Nanobiotechnology. 2020;18(1):38. doi:10.1186/s12951-020-00593-7
  • Xiao K, He W, Guan W, et al. Mesenchymal stem cells reverse EMT process through blocking the activation of NF-kappaB and Hedgehog pathways in LPS-induced acute lung injury. Cell Death Dis. 2020;11(10):863. doi:10.1038/s41419-020-03034-3
  • Yang D, Zhang W, Zhang H, et al. Progress, opportunity, and perspective on exosome isolation - efforts for efficient exosome-based theranostics. Theranostics. 2020;10(8):3684–3707. doi:10.7150/thno.41580
  • Zhang Y, Bi J, Huang J, Tang Y, Du S, Li P. Exosome: a review of its classification, isolation techniques, storage, diagnostic and targeted therapy applications. Int J Nanomedicine. 2020;15:6917–6934. doi:10.2147/IJN.S264498
  • Fabbri M, Girnita L, Varani G, Calin GA. Decrypting noncoding RNA interactions, structures, and functional networks. Genome Res. 2019;29(9):1377–1388. doi:10.1101/gr.247239.118
  • Tang X, Ren H, Guo M, Qian J, Yang Y, Gu C. Review on circular RNAs and new insights into their roles in cancer. Comput Struct Biotechnol J. 2021;19:910–928. doi:10.1016/j.csbj.2021.01.018
  • Wu J, Huang H, Huang W, Wang L, Xia X, Fang X. Analysis of exosomal lncRNA, miRNA and mRNA expression profiles and ceRNA network construction in endometriosis. Epigenomics. 2020;12(14):1193–1213. doi:10.2217/epi-2020-0084
  • Luo D, Dai W, Feng X, et al. Suppression of lncRNA NLRP3 inhibits NLRP3-triggered inflammatory responses in early acute lung injury. Cell Death Dis. 2021;12(10):898. doi:10.1038/s41419-021-04180-y
  • Fowler AA, Truwit JD, Hite RD, et al. Effect of Vitamin C infusion on organ failure and biomarkers of inflammation and vascular injury in patients with sepsis and severe acute respiratory failure: the CITRIS-ALI randomized clinical trial. JAMA. 2019;322(13):1261–1270. doi:10.1001/jama.2019.11825
  • Li X, Ding J, Wang X, Cheng Z, Zhu Q. NUDT21 regulates circRNA cyclization and ceRNA crosstalk in hepatocellular carcinoma. Oncogene. 2020;39(4):891–904. doi:10.1038/s41388-019-1030-0
  • Yu XH, Deng WY, Chen JJ, et al. LncRNA kcnq1ot1 promotes lipid accumulation and accelerates atherosclerosis via functioning as a ceRNA through the miR-452-3p/HDAC3/ABCA1 axis. Cell Death Dis. 2020;11(12):1043. doi:10.1038/s41419-020-03263-6
  • Wang J, Zhao X, Wang Y, et al. circRNA-002178 act as a ceRNA to promote PDL1/PD1 expression in lung adenocarcinoma. Cell Death Dis. 2020;11(1):32. doi:10.1038/s41419-020-2230-9
  • Hu G, Ma J, Zhang J, et al. Hypoxia-induced lncHILAR promotes renal cancer metastasis via ceRNA for the miR-613/206/ 1-1-3p/Jagged-1/Notch/CXCR4 signaling pathway. Mol Ther. 2021;29(10):2979–2994. doi:10.1016/j.ymthe.2021.05.020
  • Guo Z, Wang X, Yang Y, et al. Hypoxic tumor-derived exosomal long noncoding RNA UCA1 promotes angiogenesis via miR-96-5p/AMOTL2 in pancreatic cancer. Mol Ther Nucleic Acids. 2020;22:179–195. doi:10.1016/j.omtn.2020.08.021
  • Rittirsch D, Huber-Lang MS, Flierl MA, Ward PA. Immunodesign of experimental sepsis by cecal ligation and puncture. Nat Protoc. 2009;4(1):31–36. doi:10.1038/nprot.2008.214
  • Vella LJ, Scicluna BJ, Cheng L, et al. A rigorous method to enrich for exosomes from brain tissue. J Extracell Vesicles. 2017;6(1):1348885. doi:10.1080/20013078.2017.1348885
  • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–140. doi:10.1093/bioinformatics/btp616
  • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004;32:D277–80. doi:10.1093/nar/gkh063
  • Mao X, Cai T, Olyarchuk JG, Wei L. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics. 2005;21(19):3787–3793. doi:10.1093/bioinformatics/bti430
  • Crescitelli R, Lasser C, Lotvall J. Isolation and characterization of extracellular vesicle subpopulations from tissues. Nat Protoc. 2021;16(3):1548–1580. doi:10.1038/s41596-020-00466-1
  • Liu B, Jin Y, Yang J, et al. Extracellular vesicles from lung tissue drive bone marrow neutrophil recruitment in inflammation. J Extracell Vesicles. 2022;11(5):e12223. doi:10.1002/jev2.12223
  • Hu C, Li J, Tan Y, et al. Tanreqing injection attenuates macrophage activation and the inflammatory response via the lncRNA-SNHG1/HMGB1 axis in lipopolysaccharide-induced acute lung injury. Front Immunol. 2022;13:820718. doi:10.3389/fimmu.2022.820718
  • Zhao Q, Sheng MF, Wang YY, et al. LncRNA Gm26917 regulates inflammatory response in macrophages by enhancing Annexin A1 ubiquitination in LPS-induced acute liver injury. Front Pharmacol. 2022;13:975250. doi:10.3389/fphar.2022.975250
  • Orecchioni M, Ghosheh Y, Pramod AB, Ley K. Macrophage Polarization: different Gene Signatures in M1(LPS+) vs Classically and M2(LPS-) vs Alternatively Activated Macrophages. Front Immunol. 2019;10:1084. doi:10.3389/fimmu.2019.01084
  • Jiang L, Guo P, Ju J, Zhu X, Wu S, Dai J. Inhalation of L-arginine-modified liposomes targeting M1 macrophages to enhance curcumin therapeutic efficacy in ALI. Eur J Pharm Biopharm. 2022;182:21–31. doi:10.1016/j.ejpb.2022.11.017
  • Zhao J, Yu H, Liu Y, et al. Protective effect of suppressing STAT3 activity in LPS-induced acute lung injury. Am J Physiol Lung Cell Mol Physiol. 2016;311(5):L868–L880. doi:10.1152/ajplung.00281.2016
  • Severgnini M, Takahashi S, Rozo LM, et al. Activation of the STAT pathway in acute lung injury. Am J Physiol Lung Cell Mol Physiol. 2004;286(6):L1282–1292. doi:10.1152/ajplung.00349.2003
  • Wang F, Zhang S, Jeon R, et al. Interferon gamma induces reversible metabolic reprogramming of M1 macrophages to sustain cell viability and pro-inflammatory activity. EBioMedicine. 2018;30:303–316. doi:10.1016/j.ebiom.2018.02.009
  • Ye C, Li H, Bao M, Zhuo R, Jiang G, Wang W. Alveolar macrophage - derived exosomes modulate severity and outcome of acute lung injury. Aging. 2020;12(7):6120–6128. doi:10.18632/aging.103010
  • Zhao R, Wang L, Wang T, Xian P, Wang H, Long Q. Inhalation of MSC-EVs is a noninvasive strategy for ameliorating acute lung injury. J Control Release. 2022;345:214–230. doi:10.1016/j.jconrel.2022.03.025
  • Root-Bernstein R. Innate receptor activation patterns involving TLR and NLR Synergisms in COVID-19, ALI/ARDS and sepsis cytokine storms: a review and model making novel predictions and therapeutic suggestions. Int J Mol Sci. 2021;22(4):2108. doi:10.3390/ijms22042108
  • Billing U, Jetka T, Nortmann L, et al. Robustness and Information Transfer within IL-6-induced JAK/STAT Signalling. Commun Biol. 2019;2:27. doi:10.1038/s42003-018-0259-4
  • Schaper F, Rose-John S. Interleukin-6: biology, signaling and strategies of blockade. Cytokine Growth Factor Rev. 2015;26(5):475–487. doi:10.1016/j.cytogfr.2015.07.004
  • Grommes J, Alard JE, Drechsler M, et al. Disruption of platelet-derived chemokine heteromers prevents neutrophil extravasation in acute lung injury. Am J Respir Crit Care Med. 2012;185(6):628–636. doi:10.1164/rccm.201108-1533OC
  • Bhatia M, Zemans RL, Jeyaseelan S. Role of chemokines in the pathogenesis of acute lung injury. Am J Respir Cell Mol Biol. 2012;46(5):566–572. doi:10.1165/rcmb.2011-0392TR
  • Zarbock A, Allegretti M, Ley K. Therapeutic inhibition of CXCR2 by Reparixin attenuates acute lung injury in mice. Br J Pharmacol. 2008;155(3):357–364. doi:10.1038/bjp.2008.270
  • Grishin AV, Wang J, Potoka DA, et al. Lipopolysaccharide induces cyclooxygenase-2 in intestinal epithelium via a noncanonical p38 MAPK pathway. J Immunol. 2006;176(1):580–588. doi:10.4049/jimmunol.176.1.580
  • Sahoo S, Li Y, de Jesus D, et al. Notch2 suppression mimicking changes in human pulmonary hypertension modulates Notch1 and promotes endothelial cell proliferation. Am J Physiol Heart Circ Physiol. 2021;321(3):H542–H557. doi:10.1152/ajpheart.00125.2021
  • Kiyokawa H, Morimoto M. Notch signaling in the mammalian respiratory system, specifically the trachea and lungs, in development, homeostasis, regeneration, and disease. Dev Growth Differ. 2020;62(1):67–79. doi:10.1111/dgd.12628
  • Chen W, Liu Y, Chen J, et al. The Notch signaling pathway regulates macrophage polarization in liver diseases. Int Immunopharmacol. 2021;99:107938. doi:10.1016/j.intimp.2021.107938
  • Bai X, Li J, Li L, et al. extracellular vesicles from adipose tissue-derived stem cells affect notch-miR148a-3p axis to regulate polarization of macrophages and alleviate sepsis in mice. Front Immunol. 2020;11:1391. doi:10.3389/fimmu.2020.01391
  • Yang Y, Lin S, Yang Z, Huang Y, Zhan F. Circ_0001947 promotes cell proliferation, invasion, migration and inflammation and inhibits apoptosis in human rheumatoid arthritis fibroblast-like synoviocytes through miR-671-5p/STAT3 axis. J Orthop Surg Res. 2022;17(1):54. doi:10.1186/s13018-022-02939-3
  • Zhang HW, Wang Q, Mei HX, et al. RvD1 ameliorates LPS-induced acute lung injury via the suppression of neutrophil infiltration by reducing CXCL2 expression and release from resident alveolar macrophages. Int Immunopharmacol. 2019;76:105877. doi:10.1016/j.intimp.2019.105877
  • Xu Q, Wang M, Guo H, et al. Emodin alleviates severe acute pancreatitis-associated acute lung injury by inhibiting the cold-inducible RNA-binding protein (CIRP)-mediated activation of the NLRP3/IL-1beta/CXCL1 Signaling. Front Pharmacol. 2021;12:655372. doi:10.3389/fphar.2021.655372
  • Cao F, Wang C, Long D, Deng Y, Mao K, Zhong H. Network-based integrated analysis of transcriptomic studies in dissecting gene signatures for LPS-induced acute lung injury. Inflammation. 2021;44(6):2486–2498. doi:10.1007/s10753-021-01518-8
  • Wu X, Yin S, Yan L, Liu Y, Shang L, Liu J. lncRNA DLEU1 modulates proliferation, inflammation, and extracellular matrix degradation of chondrocytes through regulating miR-671-5p. J Immunol Res. 2022;2022:1816217. doi:10.1155/2022/1816217
  • Kaur G, Maremanda KP, Campos M, et al. Distinct Exosomal miRNA Profiles from BALF and Lung Tissue of COPD and IPF Patients. Int J Mol Sci. 2021;22(21):11830. doi:10.3390/ijms222111830
  • Lu Z, Feng H, Shen X, et al. MiR-122-5p protects against acute lung injury via regulation of DUSP4/ERK signaling in pulmonary microvascular endothelial cells. Life Sci. 2020;256:117851. doi:10.1016/j.lfs.2020.117851
  • Xu W, Chen M, Ge N, Xu J. Hemagglutinin from the H5N1 virus activates Janus kinase 3 to dysregulate innate immunity. PLoS One. 2012;7(2):e31721. doi:10.1371/journal.pone.0031721
  • Cao K, Chen M, Jie X, Wang Y, Li Q, Xu J. H5N1 virus hemagglutinin inhibition of cAMP-Dependent CFTR via TLR4-Mediated janus tyrosine kinase 3 activation exacerbates lung inflammation. Mol Med. 2015;21(1):134–142. doi:10.2119/molmed.2014.00189