MicroRNA Expression in Extracellular Vesicles from Nasal Lavage Fluid in Chronic Rhinosinusitis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Human Subjects
2.2. NLF Collection
2.3. Isolation of EVs from the NLF
2.4. EV Characterization
2.5. MicroRNA Isolation from EVs
2.6. Nanostring nCounter System MiRNA Assay
2.7. Prediction of Target Genes and Associated Pathways
2.8. Statistical Analysis
3. Results
3.1. Clinical Characteristics of the Study Participants
3.2. Phenotypic Characterization of NLF-EVs
3.3. MicroRNAs Were Differentially Expressed in NLF-EVs of CRS Patients
3.4. Gene Ontology and Pathway Classification of In Silico Analysis of MiRNA Target Genes in CRS vs. Healthy NLF-EVs
3.5. Gene Ontology and Pathway Classification of in Silico Analysis of MiRNA Target Genes in CRSsNP vs. CRSwNP NLF-EVs
3.6. Functional Validation of Representative MiRNA Analysis Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
CRS | Chronic rhinosinusitis |
EVs | Extracellular vesicles |
miRNA | MicroRNA |
NLF | Nasal lavage fluid |
JESREC | Japanese Epidemiological Survey of Refractory Eosinophilic Chronic Rhinosinusitis |
KEGG | Kyoto Encyclopedia Gene and Genome database |
GalNAc-Ts | N-acetylgalactosanimyltransferases |
GalNAc | N-acetylgalactosamine |
TGF-β | Transforming growth factor beta |
MET | MET proto-oncogene |
EGFR | Epidermal growth factor receptor |
ACTB | Beta-actin |
PARP1 | Poly(ADP-ribose) polymerase 1 |
TGFBR | Transforming growth factor beta receptor |
SMAD | Small mothers against decapentaplegic |
MAPK | Mitogen-activated protein kinase |
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Variables | CRSwNP 1 (n = 7) | CRSsNP 2 (n = 8) | HC 3 (n = 7) |
---|---|---|---|
Sex, male (%) | 3 (42.9%) | 4 (50.0%) | 6 (85.7%) |
Age, years | 47.4 ± 23.2 | 42.0 ± 20.6 | 40.3 ± 15.2 |
JESREC score 4 | 9.67 ± 3.27 | 7.29 ± 5.25 | NA |
Allergy | |||
(+) | 4 (57.1%) | 3 (37.5%) | 2 (28.6%) |
(−) | 3 (42.9%) | 5 (62.5%) | 5 (71.4%) |
Asthma | |||
(+) | 7 (100%) | 7 (100%) | 7 (100%) |
(−) | 0 (0%) | 0 (0%) | 0 (0%) |
Subject | Median Size (IQR) (nm) | Mean Count (Cell Count/10 mm2 ± SD) |
---|---|---|
CRSwNP 1 | 131.56 (107.99–166.29) | 75 ± 19 |
CRSsNP 2 | 82.32 (75.43–102.77) | 66 ± 20 |
HC 3 | 183.93 (157.14–216.07) | 3 ± 3 |
Total | 124.57 (93.78–157.14) | N/A |
KEGG Pathway | MiRNA | CRS vs. HC | CRSwNP vs. CRSsNP | Target MRNA Name | Putative Disease Associations (Human Studies) |
---|---|---|---|---|---|
Mucin type O-Glycan biosynthesis | miR-23a-3p | Up | p > 0.05 | MET; CTNND1; LMO7; IQGAP1; EGFR; TJP1; NLK; CDH1; SMAD4; CTNNB1; CTNNA1; WASF2; CSNK2A1; FARP2; PTPRJ; ACTN4; MAPK1; TGFBR2 | Fibrosis [12], Disease Progression [13], Folic Acid Deficiency [14], Genetic Predisposition to Diseases [15] |
miR-15a-5p | Up | p > 0.05 | ACTB; SMAD2; PVRL2; ACTG1; LMO7; IQGAP1; IGF1R; PTPRF; ACP1; CDH1; CTNNB1; CSNK2A1; RAC1; CDC42; EP300; YES1; FGFR1; MAP3K7; CREBBP; PVRL1 | Disease Progression [16] | |
miR-223-3p | Up | p > 0.05 | PARP1; SCARB1; RASGRP1; DDIT4; GFPT1; RGS1; MECP2; MT1E; TTBK2; WDR7; FADS1; STMN1; GDI1; CHUK; SOX5; SERINC1; TMEM69; CPEB4; RNF213; ARTN; COX7A2L | Inflammation [17,18] *, Disease Progression [19,20] *, Genetic Predisposition to Disease [21], primary myelofibrosis [12,22] | |
miR-1285-3p | Down | p > 0.05 | WBSCR17 | Inflammation [23] | |
TGF-beta signaling pathway | miR-548q | p > 0.05 | Up | IGF1R | Disease Progression [24,25] *, Genetic Predisposition to Disease [26,27], Inflammation [28] * |
miR-1290 | p > 0.05 | Up | CDKN2B; SKP1; ACVR2A; SP1; MAPK1; BMPR2; RPS6KB1 | Inflammation [29] | |
miR-548l | p > 0.05 | Up | FST; SMAD2; INHBB; SKP1; ACVR2B; SMAD4; E2F5; SMAD5; ACVR2A; SP1; ACVR1C; TGFB2; BMPR1A; E2F4; PPP2R1B | Acute diseases, Acute Lung Injury [30], Inflammation [31] |
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Cha, S.; Seo, E.-H.; Lee, S.H.; Kim, K.S.; Oh, C.-S.; Moon, J.-S.; Kim, J.K. MicroRNA Expression in Extracellular Vesicles from Nasal Lavage Fluid in Chronic Rhinosinusitis. Biomedicines 2021, 9, 471. https://doi.org/10.3390/biomedicines9050471
Cha S, Seo E-H, Lee SH, Kim KS, Oh C-S, Moon J-S, Kim JK. MicroRNA Expression in Extracellular Vesicles from Nasal Lavage Fluid in Chronic Rhinosinusitis. Biomedicines. 2021; 9(5):471. https://doi.org/10.3390/biomedicines9050471
Chicago/Turabian StyleCha, Seungbin, Eun-Hye Seo, Seung Hyun Lee, Kyung Soo Kim, Chung-Sik Oh, Jong-Seok Moon, and Jin Kook Kim. 2021. "MicroRNA Expression in Extracellular Vesicles from Nasal Lavage Fluid in Chronic Rhinosinusitis" Biomedicines 9, no. 5: 471. https://doi.org/10.3390/biomedicines9050471