Childhood Asthma Biomarkers Derived from Plasma and Saliva Exosomal miRNAs
Abstract
1. Introduction
2. Results
2.1. Clinical Differences in Pediatrics Severe Asthma
2.2. Characterization of Plasma- and Saliva-Derived Exosomes
2.3. Exosomal miRNA Profiling in Pediatric Plasma and Saliva
2.4. Exosomal miRNAs and Their Gene Targets in Plasma and Saliva
2.5. KEGG Pathway Analysis of miRNA Targets in Plasma and Saliva
2.6. KEGG Pathways of Exosomal miRNAs in Shared Plasma and Saliva
2.7. KEGG Pathway Analysis Specific to miRNAs-Plasma and Saliva
2.8. Comparative Analysis of lncRNA Expression in Plasma and Saliva
2.9. KEGG Pathways for lncRNAs in Plasma and Asthma
3. Discussion
3.1. miRNA Profiling and KEGG Pathways
3.2. KEGG Pathways for miRNAs’ Target Genes
3.3. lncRNAs Profiling and KEGG Pathways
4. Materials and Methods
4.1. Subjects
4.2. Saliva and Blood Collection
4.3. Exosome Isolations and Characterization
4.4. Small RNA-Sequencing for Plasma and Saliva
4.5. Small RNA-Seq Data Processing and Analysis
4.6. Illumina RNA Library Preparation and Sequencing
4.7. Differential Gene Expression Analysis (DGEA)
4.8. Protein–Protein Interaction (PPI) Analysis
4.9. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Items | Normal Lung Function (NLF) | Severe Airflow Obstruction (SAO) | p-Value |
---|---|---|---|
Age | 10.71 ± 1.33 | 13.81 ± 2.67 | 0.006 |
FVC | 2.58 ± 0.43 | 3.93 ± 1.51 | 0.01973155 |
FVC% Pred | 112.51 ± 10.48 | 108.91 ± 16.01 | 0.579436397 |
FEV1 | 2.23 ± 0.37 | 2.53 ± 1.05 | 0.427157081 |
FEV1% Pred | 112.51 ± 9.81 | 82.11 ± 17.81 | 0.000287177 |
FEV1/FVC Ratio | 86.52 ± 1.63 | 64.52 ± 7.77 | 1.42353 × 10−7 |
FEF75% Pred | 124.74 ± 19.09 | 39.72 ± 10.61 | 7.83717 × 10−10 |
IgE | 72.11 ± 62.54 | 288.12 ± 223.19 | 0.01 |
Name | Log2 Fold Change | p-Value | Adjusted p-Value |
---|---|---|---|
hsa-miR-451b-5p | 6.873 | <0.0001 | <0.0001 |
hsa-miR-7706 | 5.907 | 0.003 | 0.02 |
hsa-miR-195-3p | 5.825 | <0.0001 | 0.0004 |
hsa-miR-141-3p | 5.218 | 0.004 | 0.03 |
hsa-miR-3158-5p | 4.886 | <0.0001 | <0.0001 |
hsa-miR-3158-3p | 4.584 | <0.0001 | <0.0001 |
hsa-miR-375-3p | 4.126 | <0.0001 | <0.0001 |
hsa-miR-501-3p | 3.835 | <0.0001 | <0.0001 |
hsa-miR-200a-3p | 3.760 | <0.0001 | <0.0001 |
hsa-miR-451a | 2.626 | <0.0001 | <0.0001 |
hsa-miR-122-5p | 1.985 | <0.0001 | <0.0001 |
hsa-miR-192-5p | 1.961 | <0.0001 | <0.0001 |
hsa-miR-122b-3p | 1.925 | <0.0001 | <0.0001 |
hsa-miR-16-2-3p | 1.851 | <0.0001 | <0.0001 |
hsa-miR-194-5p | 1.653 | 0.0001 | 0.001 |
hsa-miR-486-3p | 1.627 | <0.0001 | 0.0001 |
hsa-miR-16-5p | 1.601 | <0.0001 | <0.0001 |
hsa-miR-25-3p | 1.594 | <0.0001 | <0.0001 |
hsa-miR-486-5p | 1.525 | <0.0001 | 0.0002 |
hsa-miR-92a-3p | 1.068 | <0.0001 | <0.0001 |
hsa-miR-27a-5p | −1.131 | 0.001 | 0.01 |
hsa-miR-125a-5p | −1.168 | <0.0001 | 0.0006 |
hsa-miR-203a-3p | −1.384 | 0.0006 | 0.006 |
hsa-miR-4433a-3p | −1.662 | 0.003 | 0.02 |
hsa-miR-203b-5p | −1.705 | <0.0001 | 0.0006 |
hsa-miR-203b-5p | −1.705 | <0.0001 | 0.0006 |
hsa-miR-1246 | −1.746 | 0.0001 | 0.001 |
hsa-miR-4665-5p | −7.627 | 0.003 | 0.02 |
MiRNA | Log2 Fold Change | p-Value | Adjusted p-Value |
---|---|---|---|
hsa-miR-550a-3-5p | 3.063 | 0.009 | 0.04 |
hsa-miR-486-3p | 2.363 | 0.0009 | 0.007 |
hsa-miR-3615-3p | 2.261 | <0.0001 | 0.0003 |
hsa-miR-106b-3p | 2.234 | 0.0007 | 0.0055 |
hsa-miR-25-3p | 2.084 | <0.0001 | 0.0001 |
hsa-miR-140-3p | 2.004 | <0.0001 | 0.0001 |
hsa-miR-423-3p | 1.977 | <0.0001 | 0.0003 |
hsa-miR-3184-5p | 1.963 | <0.0001 | 0.0003 |
hsa-miR-629-5p | 1.909 | <0.0001 | 0.0001 |
hsa-miR-223-3p | 1.880 | 0.0001 | 0.001 |
hsa-miR-92a-3p | 1.837 | <0.0001 | 0.0001 |
hsa-miR-142-5p | 1.818 | <0.0001 | 0.0001 |
hsa-miR-345-5p | 1.812 | <0.0001 | 0.0001 |
hsa-miR-501-3p | 1.794 | 0.006 | 0.03 |
hsa-miR-425-5p | 1.751 | <0.0001 | 0.0001 |
hsa-miR-223-5p | 1.629 | <0.0001 | 0.0002 |
hsa-miR-146b-5p | 1.624 | <0.0001 | 0.0007 |
hsa-let-7d-3p | 1.618 | <0.0001 | 0.0004 |
hsa-miR-24-3p | 1.609 | <0.0001 | 0.0001 |
hsa-miR-140-5p | 1.578 | 0.0008 | 0.006 |
hsa-miR-199a-3p | 1.559 | 0.0003 | 0.003 |
hsa-miR-744-5p | 1.552 | 0.002 | 0.01 |
hsa-miR-221-3p | 1.541 | <0.0001 | 0.0002 |
hsa-miR-145-5p | 1.528 | 0.004 | 0.02 |
hsa-miR-3074-5p | 1.512 | <0.0001 | 0.0001 |
hsa-miR-23a-3p | 1.483 | 0.0002 | 0.002 |
hsa-miR-143-3p | 1.478 | 0.0004 | 0.003 |
hsa-miR-193a-5p | 1.447 | 0.0001 | 0.001 |
hsa-miR-941 | 1.373 | 0.001 | 0.01 |
hsa-miR-378a-3p | 1.340 | <0.0001 | 0.0003 |
hsa-miR-1307-3p | 1.298 | 0.0007 | 0.005 |
hsa-miR-320a-3p | 1.279 | 0.004 | 0.02 |
hsa-miR-652-3p | 1.273 | 0.002 | 0.01 |
hsa-miR-191-5p | 1.248 | 0.003 | 0.02 |
hsa-miR-185-5p | 1.235 | 0.002 | 0.01 |
hsa-miR-16-5p | 1.197 | 0.004 | 0.02 |
hsa-miR-27a-3p | 1.150 | 0.001 | 0.007 |
hsa-miR-22-3p | 1.084 | 0.0001 | 0.001 |
hsa-miR-30d-5p | 1.025 | 0.003 | 0.01 |
hsa-miR-103b | 1.015 | 0.01 | 0.04 |
Plasma | Saliva | ||
---|---|---|---|
Name | Log2 Fold Change | Adjusted p-Value | Log2 Fold Change |
hsa-miR-501-3p | 3.83 | 1.57 × 10−5 | 1.79 |
hsa-miR-486-3p | 1.62 | 0.0001 | 2.36 |
hsa-miR-16-5p | 1.60 | 1.83 × 10−15 | 1.19 |
hsa-miR-25-3p | 1.59 | 9.64 × 10−18 | 2.08 |
hsa-miR-92a-3p | 1.067 | 3.15 × 10−7 | 1.83 |
KEGG Pathway | KEGG IDs | p-Value | #Genes | #miRNAs |
---|---|---|---|---|
PI3K-Akt signaling pathway | hsa04151 | 2.11 × 10−12 | 61 | 5 |
Focal adhesion | hsa04510 | 4.44 × 10−12 | 43 | 5 |
Wnt signaling pathway | hsa04310 | 2.27 × 10−9 | 35 | 5 |
Non-small cell lung cancer | hsa05223 | 7.41 × 10−8 | 15 | 5 |
Regulation of actin cytoskeleton | hsa04810 | 1.36 × 10−7 | 39 | 5 |
B cell receptor signaling pathway | hsa04662 | 1.48 × 10−7 | 19 | 5 |
Small cell lung cancer | hsa05222 | 6.48 × 10−7 | 19 | 5 |
Insulin signaling pathway | hsa04910 | 8.42 × 10−7 | 27 | 5 |
Neurotrophin signaling pathway | hsa04722 | 9.18 × 10−7 | 25 | 5 |
T cell receptor signaling pathway | hsa04660 | 9.23 × 10−7 | 23 | 5 |
MAPK signaling pathway | hsa04010 | 2.31 × 10−6 | 44 | 5 |
Acute myeloid leukemia | hsa05221 | 3.98 × 10−6 | 15 | 5 |
Long-term potentiation | hsa04720 | 5.06 × 10−6 | 16 | 5 |
Dopaminergic synapse | hsa04728 | 9.10 × 10−6 | 26 | 5 |
Ubiquitin mediated proteolysis | hsa04120 | 9.52 × 10−6 | 26 | 5 |
Glioma | hsa05214 | 1.19 × 10−5 | 16 | 5 |
VEGF signaling pathway | hsa04370 | 1.59 × 10−5 | 15 | 5 |
Chronic myeloid leukemia | hsa05220 | 0.00017042 | 16 | 5 |
Type II diabetes mellitus | hsa04930 | 0.000395913 | 11 | 5 |
Renal cell carcinoma | hsa05211 | 0.000395913 | 16 | 5 |
Endocytosis | hsa04144 | 0.000453408 | 32 | 5 |
ErbB signaling pathway | hsa04012 | 0.000758374 | 16 | 5 |
Fc gamma R-mediated phagocytosis | hsa04666 | 0.001040455 | 17 | 5 |
Axon guidance | hsa04360 | 0.001191295 | 24 | 5 |
HIF-1 signaling pathway | hsa04066 | 0.002165998 | 19 | 5 |
Cholinergic synapse | hsa04725 | 0.002246121 | 21 | 5 |
Bacterial invasion of epithelial cells | hsa05100 | 0.004172215 | 13 | 5 |
Calcium signaling pathway | hsa04020 | 0.00556725 | 27 | 5 |
Gap junction | hsa04540 | 0.00633416 | 16 | 5 |
Glutamatergic synapse | hsa04724 | 0.007451913 | 19 | 5 |
Phosphatidylinositol signaling system | hsa04070 | 0.008247675 | 14 | 5 |
GnRH signaling pathway | hsa04912 | 0.009589913 | 15 | 5 |
Viral carcinogenesis | hsa05203 | 0.01249035 | 25 | 5 |
Gastric acid secretion | hsa04971 | 0.02177694 | 12 | 5 |
Adherens junction | hsa04520 | 0.02235759 | 14 | 5 |
Melanogenesis | hsa04916 | 0.02235759 | 16 | 5 |
Osteoclast differentiation | hsa04380 | 0.02479279 | 19 | 5 |
Cell cycle | hsa04110 | 0.03556233 | 21 | 5 |
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Khalyfa, A.; Verma, M.; Alexander, M.M.; Qiao, Z.; Rood, T.; Kapoor, R.; Joshi, T.; Gozal, D.; Francisco, B.D. Childhood Asthma Biomarkers Derived from Plasma and Saliva Exosomal miRNAs. Int. J. Mol. Sci. 2025, 26, 7043. https://doi.org/10.3390/ijms26157043
Khalyfa A, Verma M, Alexander MM, Qiao Z, Rood T, Kapoor R, Joshi T, Gozal D, Francisco BD. Childhood Asthma Biomarkers Derived from Plasma and Saliva Exosomal miRNAs. International Journal of Molecular Sciences. 2025; 26(15):7043. https://doi.org/10.3390/ijms26157043
Chicago/Turabian StyleKhalyfa, Abdelnaby, Mohit Verma, Meghan M. Alexander, Zhuanhong Qiao, Tammy Rood, Ragini Kapoor, Trupti Joshi, David Gozal, and Benjamin D. Francisco. 2025. "Childhood Asthma Biomarkers Derived from Plasma and Saliva Exosomal miRNAs" International Journal of Molecular Sciences 26, no. 15: 7043. https://doi.org/10.3390/ijms26157043
APA StyleKhalyfa, A., Verma, M., Alexander, M. M., Qiao, Z., Rood, T., Kapoor, R., Joshi, T., Gozal, D., & Francisco, B. D. (2025). Childhood Asthma Biomarkers Derived from Plasma and Saliva Exosomal miRNAs. International Journal of Molecular Sciences, 26(15), 7043. https://doi.org/10.3390/ijms26157043