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ORIGINAL RESEARCH

Investigation of the miRNA-mRNA Regulatory Circuits and Immune Signatures Associated with Bronchopulmonary Dysplasia

, , , , , , & ORCID Icon show all
Pages 1467-1480 | Received 06 Nov 2023, Accepted 29 Feb 2024, Published online: 05 Mar 2024

References

  • Higgins RD, Jobe AH, Koso-Thomas M, et al. Bronchopulmonary dysplasia: executive summary of a workshop. J Pediatr. 2018;197:300–308. doi:10.1016/j.jpeds.2018.01.043
  • Walsh MC, Szefler S, Davis J, et al. Summary proceedings from the bronchopulmonary dysplasia group. Pediatrics. 2006;117(3):S52–6. doi:10.1542/peds.2005-0620I
  • Islam JY, Keller RL, Aschner JL, et al. Understanding the short- and long-term respiratory outcomes of prematurity and bronchopulmonary dysplasia. Am J Respir Crit Care Med. 2015;192(2):134–156. doi:10.1164/rccm.201412-2142PP
  • Principi N, Di Pietro GM, Esposito S. Bronchopulmonary dysplasia: clinical aspects and preventive and therapeutic strategies. J Transl Med. 2018;16(1):36. doi:10.1186/s12967-018-1417-7
  • Thomas JM, Sudhadevi T, Basa P, et al. The role of sphingolipid signaling in oxidative lung injury and pathogenesis of bronchopulmonary dysplasia. Int J Mol Sci. 2022;23(3). doi:10.3390/ijms23031254
  • Zaramella P, Munari F, Stocchero M, et al. Innate immunity ascertained from blood and tracheal aspirates of preterm newborn provides new clues for assessing bronchopulmonary dysplasia. PLoS One. 2019;14(9):e0221206. doi:10.1371/journal.pone.0221206
  • Berger J, Bhandari V. Animal models of bronchopulmonary dysplasia. The term mouse models. Am J Physiol Lung Cell Mol Physiol. 2014;307(12):L936–47. doi:10.1152/ajplung.00159.2014
  • Xu J, Mao X, Jin R, et al. Neutrophil extracellular traps degrade fibronectin in a rat model of bronchopulmonary dysplasia induced by perinatal exposure to lipopolysaccharide. J Cell Mol Med. 2020;24(24):14645–14649. doi:10.1111/jcmm.15842
  • Windhorst AC, Heydarian M, Schwarz M, et al. Monocyte signature as a predictor of chronic lung disease in the preterm infant. Front Immunol. 2023;14:1112608. doi:10.3389/fimmu.2023.1112608
  • Eldredge LC, Creasy RS, Presnell S, et al. Infants with evolving bronchopulmonary dysplasia demonstrate monocyte-specific expression of IL-1 in tracheal aspirates. Am J Physiol Lung Cell Mol Physiol. 2019;317(1):L49–l56. doi:10.1152/ajplung.00060.2019
  • Sahoo D, Zaramela LS, Hernandez GE, et al. Transcriptional profiling of lung macrophages identifies a predictive signature for inflammatory lung disease in preterm infants. Commun Biol. 2020;3(1):259. doi:10.1038/s42003-020-0985-2
  • Hu Y, Xie L, Yu J, et al. Inhibition of microRNA-29a alleviates hyperoxia-induced bronchopulmonary dysplasia in neonatal mice via upregulation of GAB1. Mol Med. 2019;26(1):3. doi:10.1186/s10020-019-0127-9
  • Syed M, Das P, Pawar A, et al. Hyperoxia causes miR-34a-mediated injury via angiopoietin-1 in neonatal lungs. Nat Commun. 2017;8(1):1173. doi:10.1038/s41467-017-01349-y
  • Durrani-Kolarik S, Pool CA, Gray A, et al. miR-29b supplementation decreases expression of matrix proteins and improves alveolarization in mice exposed to maternal inflammation and neonatal hyperoxia. Am J Physiol Lung Cell Mol Physiol. 2017;313(2):L339–l49. doi:10.1152/ajplung.00273.2016
  • Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. doi:10.1093/nar/gkv007
  • Ito K, Murphy D. Application of ggplot2 to pharmacometric graphics. CPT Pharmacometrics Syst Pharmacol. 2013;2(10):e79. doi:10.1038/psp.2013.56
  • Chen Y, Wang X. miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Res. 2020;48(D1):D127–d31. doi:10.1093/nar/gkz757
  • Fan Y, Siklenka K, Arora SK, et al. miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis. Nucleic Acids Res. 2016;44(W1):W135–41. doi:10.1093/nar/gkw288
  • Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005;120(1):15–20. doi:10.1016/j.cell.2004.12.035
  • Sticht C, De La Torre C, Parveen A, et al. miRWalk: an online resource for prediction of microRNA binding sites. PLoS One. 2018;13(10):e0206239. doi:10.1371/journal.pone.0206239
  • Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504. doi:10.1101/gr.1239303
  • Szklarczyk D, Gable AL, Lyon D, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47(D1):D607–d13. doi:10.1093/nar/gky1131
  • Chin CH, Chen SH, Wu HH, et al. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014;8(4):S11. doi:10.1186/1752-0509-8-s4-s11
  • Keenan AB, Torre D, Lachmann A, et al. ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Res. 2019;47(W1):W212–w24. doi:10.1093/nar/gkz446
  • Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453–457. doi:10.1038/nmeth.3337
  • Lingappan K, Savani RC. The wnt signaling pathway and the development of bronchopulmonary dysplasia. Am J Respir Crit Care Med. 2020;201(10):1174–1176. doi:10.1164/rccm.202002-0277ED
  • Hu Z, Liu C, Mao Y, et al. Integration of transcriptomics reveals ferroptosis-related signatures and immune cell infiltration in bronchopulmonary dysplasia. Heliyon. 2023;9(10):e21093. doi:10.1016/j.heliyon.2023.e21093
  • Song N, Wang W, Wang Y, et al. Hydrogen sulfide of air induces macrophage extracellular traps to aggravate inflammatory injury via the regulation of miR-15b-5p on MAPK and insulin signals in trachea of chickens. Sci Total Environ. 2021;771:145407. doi:10.1016/j.scitotenv.2021.145407
  • Li H, Lei Y, Li S, et al. MicroRNA-20a-5p inhibits the autophagy and cisplatin resistance in ovarian cancer via regulating DNMT3B-mediated DNA methylation of RBP1. Reprod Toxicol. 2022;109:93–100. doi:10.1016/j.reprotox.2021.12.011
  • Müller UC, Zheng H. Physiological functions of APP family proteins. Cold Spring Harb Perspect Med. 2012;2(2):a006288. doi:10.1101/cshperspect.a006288
  • Sharma C, Kim S, Nam Y, et al. Mitochondrial dysfunction as a driver of cognitive impairment in alzheimer’s disease. Int J Mol Sci. 2021;22(9):4850. doi:10.3390/ijms22094850
  • Sobol A, Galluzzo P, Liang S, et al. Amyloid precursor protein (APP) affects global protein synthesis in dividing human cells. J Cell Physiol. 2015;230(5):1064–1074. doi:10.1002/jcp.24835
  • Sobol A, Galluzzo P, Weber MJ, et al. Depletion of amyloid precursor protein (APP) causes G0 arrest in non-small cell lung cancer (NSCLC) cells. J Cell Physiol. 2015;230(6):1332–1341. doi:10.1002/jcp.24875
  • d’Uscio LV, He T, Santhanam AV, et al. Endothelium-specific amyloid precursor protein deficiency causes endothelial dysfunction in cerebral arteries. J Cereb Blood Flow Metab. 2018;38(10):1715–1726. doi:10.1177/0271678x17735418
  • Ristori E, Cicaloni V, Salvini L, et al. Amyloid-β precursor protein APP down-regulation alters actin cytoskeleton-interacting proteins in endothelial cells. Cells. 2020;9(11):2506. doi:10.3390/cells9112506
  • Abman SH. Bronchopulmonary dysplasia “a vascular hypothesis”. Am J Respir Crit Care Med. 2001;164(10 Pt 1):1755–1756. doi:10.1164/ajrccm.164.10.2109111c
  • Seedorf G, Metoxen AJ, Rock R, et al. Hepatocyte growth factor as a downstream mediator of vascular endothelial growth factor-dependent preservation of growth in the developing lung. Am J Physiol Lung Cell Mol Physiol. 2016;310(11):L1098–110. doi:10.1152/ajplung.00423.2015
  • Xia F, Deng C, Jiang Y, et al. IL4 (interleukin 4) induces autophagy in B cells leading to exacerbated asthma. Autophagy. 2018;14(3):450–464. doi:10.1080/15548627.2017.1421884
  • Zhang F, Ma H, Wang ZL, et al. The PI3K/AKT/mTOR pathway regulates autophagy to induce apoptosis of alveolar epithelial cells in chronic obstructive pulmonary disease caused by PM2.5 particulate matter. J Int Med Res. 2020;48(7):300060520927919. doi:10.1177/0300060520927919
  • Salimi U, Dummula K, Tucker MH, et al. Postnatal sepsis and bronchopulmonary dysplasia in premature infants: mechanistic insights into “New BPD”. Am J Respir Cell Mol Biol. 2022;66(2):137–145. doi:10.1165/rcmb.2021-0353PS
  • Voynow JA, Shinbashi M. Neutrophil elastase and chronic lung disease. Biomolecules. 2021;11(8):1065. doi:10.3390/biom11081065
  • Li X, Wang Q, Luo T, et al. Decreased neutrophil levels in bronchopulmonary dysplasia infants. Pediatr Neonatol. 2020;61(6):637–644. doi:10.1016/j.pedneo.2020.08.013
  • Palta M, Sadek-Badawi M, Carlton DP. Association of BPD and IVH with early neutrophil and white counts in VLBW neonates with gestational age <32 weeks. J Perinatol. 2008;28(9):604–610. doi:10.1038/jp.2008.65
  • Sun Y, Chen C, Zhang X, et al. High neutrophil-to-lymphocyte ratio is an early predictor of bronchopulmonary dysplasia. Front Pediatr. 2019;7:464. doi:10.3389/fped.2019.00464
  • Potera RM, Cao M, Jordan LF, et al. Alveolar macrophage chemokine secretion mediates neutrophilic lung injury in Nox2-deficient mice. Inflammation. 2019;42(1):185–198. doi:10.1007/s10753-018-0883-7
  • Geng S, Zhang Y, Lee C, et al. Novel reprogramming of neutrophils modulates inflammation resolution during atherosclerosis. Sci Adv. 2019;5(2):eaav2309. doi:10.1126/sciadv.aav2309
  • Tak T, Wijten P, Heeres M, et al. Human CD62L(dim) neutrophils identified as a separate subset by proteome profiling and in vivo pulse-chase labeling. Blood. 2017;129(26):3476–3485. doi:10.1182/blood-2016-07-727669
  • Juss JK, House D, Amour A, et al. Acute respiratory distress syndrome neutrophils have a distinct phenotype and are resistant to phosphoinositide 3-kinase inhibition. Am J Respir Crit Care Med. 2016;194(8):961–973. doi:10.1164/rccm.201509-1818OC
  • Sun L, Zhang M, Jiang J, et al. Neutrophil extracellular traps promote bronchopulmonary dysplasia-like injury in neonatal mice via the WNT/β-catenin pathway. Front Cell Infect Microbiol. 2023;13:1126516. doi:10.3389/fcimb.2023.1126516