Identification of Epithelial-mesenchymal Transition-related Genes and Potential Biomarkers for Bronchopulmonary Dysplasia using Bioinformatical Analysis
Keywords:
bronchopulmonary dysplasia, Epithelial-mesenchymal transition, Weighted gene co-expression network analysis, Machine learning, Bioinformatical analysisAbstract
Bronchopulmonary dysplasia (BPD) is a prevalent and serious disease among preterm newborns. Epithelial-mesenchymal transition (EMT) represents the biological process where cells switch from an epithelial to mesenchymal phenotype. Hyperoxia induces EMT in alveolar epithelial cells, which can affect alveolar development. However, the specific molecular mechanism of EMT in BPD remains incompletely unclear. In this study, the GSE108754 and GSE32472 datasets were merged and de-batched, with external validation from GSE188944 and GSE51039. Differentially Expressed Genes (DEGs) were screened, focusing on those associated with EMT using the GeneCards database, resulting in the identification of 213 overlapping genes. Weighted gene co-expression network analysis (WGCNA) revealed that the turquoise module was strongly correlated with BPD, identifying 33 hub genes related to EMT in BPD patients.
Utilizing support vector machine (SVM) and random forest recursive feature elimination (RF-RFE) methods, 17 potential biomarkers were assessed. Risk prediction performance was evaluated through a nomogram model and receiver operating characteristic (ROC) analysis. Notably, FLOT2, AQP9, SEMA4A, and CXCR1 emerged as vital genes, with RT-qPCR validation indicating their mRNA levels significantly increased in BPD. In summary, four biomarkers, FLOT2, AQP9, SEMA4A, and CXCR1, were potentially critical in BPD occurrence and progression, shedding novel light on diagnosing and treating BPD.
References
W. H. Northway, Jr., R. C. Rosan, and D. Y. Porter, "Pulmonary disease following respirator therapy of hyaline-membrane disease. Bronchopulmonary dysplasia," (in eng), N Engl J Med, vol. 276, no. 7, pp. 357-68, Feb 16 1967.
Y. Regin, A. Gie, A. Eerdekens, J. Toelen, and A. Debeer, "Ventilation and respiratory outcome in extremely preterm infants: trends in the new millennium," (in eng), Eur J Pediatr, vol. 181, no. 5, pp. 1899-1907, May 2022.
J. Y. Islam, R. L. Keller, J. L. Aschner, T. V. Hartert, and P. E. Moore, "Understanding the Short- and Long-Term Respiratory Outcomes of Prematurity and Bronchopulmonary Dysplasia," (in eng), Am J Respir Crit Care Med, vol. 192, no. 2, pp. 134-56, Jul 15 2015.
O. D. Saugstad, C. P. Speer, and H. L. Halliday, "Oxygen saturation in immature babies: revisited with updated recommendations," (in eng), Neonatology, vol. 100, no. 3, pp. 217-8, 2011.
L. Fu et al., "Reactive oxygen species-evoked endoplasmic reticulum stress mediates 1-nitropyrene-induced epithelial-mesenchymal transition and pulmonary fibrosis," (in eng), Environ Pollut, vol. 283, p. 117134, Aug 15 2021.
R. Kalluri and R. A. Weinberg, "The basics of epithelial-mesenchymal transition," (in eng), J Clin Invest, vol. 119, no. 6, pp. 1420-8, Jun 2009.
P. Debnath, R. S. Huirem, P. Dutta, and S. Palchaudhuri, "Epithelial-mesenchymal transition and its transcription factors," (in eng), Biosci Rep, vol. 42, no. 1, p. BSR20211754, Jan 28 2022.
K. K. Kim et al., "Alveolar epithelial cell mesenchymal transition develops in vivo during pulmonary fibrosis and is regulated by the extracellular matrix," (in eng), Proc Natl Acad Sci U S A, vol. 103, no. 35, pp. 13180-5, Aug 29 2006.
H. Yang et al., "Epithelial-mesenchymal transitions in bronchopulmonary dysplasia of newborn rats," (in eng), Pediatr Pulmonol, vol. 49, no. 11, pp. 1112-23, Nov 2014.
X. Gong, J. Qiu, G. Qiu, and C. Cai, "Adrenomedullin regulated by miRNA-574-3p protects premature infants with bronchopulmonary dysplasia," (in eng), Biosci Rep, vol. 40, no. 5, pp. BSR20191879,May 29 2020.
J. J. Pietrzyk et al., "Gene expression profiling in preterm infants: new aspects of bronchopulmonary dysplasia development," (in eng), PLoS One, vol. 8, no. 10, p. e78585, 2013.
X. Wang et al., "Epigenome-wide association study of bronchopulmonary dysplasia in preterm infants: results from the discovery-BPD program," (in eng), Clin Epigenetics, vol. 14, no. 1, p. 57, Apr 28 2022.
K. Lingappan, C. Srinivasan, W. Jiang, L. Wang, X. I. Couroucli, and B. Moorthy, "Analysis of the transcriptome in hyperoxic lung injury and sex-specific alterations in gene expression," (in eng), PLoS One, vol. 9, no. 7, p. e101581, 2014.
J. T. Leek, W. E. Johnson, H. S. Parker, A. E. Jaffe, and J. D. Storey, "The sva package for removing batch effects and other unwanted variation in high-throughput experiments," (in eng), Bioinformatics, vol. 28, no. 6, pp. 882-3, Mar 15 2012.
M. E. Ritchie et al., "limma powers differential expression analyses for RNA-sequencing and microarray studies," (in eng), Nucleic Acids Res, vol. 43, no. 7, p. e47, Apr 20 2015.
M. Safran et al., "GeneCards Version 3: the human gene integrator," (in eng), Database (Oxford), vol. 2010, p. baq020, Aug 5 2010.
G. Stelzer et al., "The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses," (in eng), Curr Protoc Bioinformatics, vol. 54, pp. 1.30.1-1.30.33, Jun 20 2016.
A. M. Newman et al., "Robust enumeration of cell subsets from tissue expression profiles," (in eng), Nat Methods, vol. 12, no. 5, pp. 453-7, May 2015.
B. Chen, M. S. Khodadoust, C. L. Liu, A. M. Newman, and A. A. Alizadeh, "Profiling Tumor Infiltrating Immune Cells with CIBERSORT," (in eng), Methods Mol Biol, vol. 1711, pp. 243-259, 2018.
P. Langfelder and S. Horvath, "WGCNA: an R package for weighted correlation network analysis," (in eng), BMC Bioinformatics, vol. 9, p. 559, Dec 29 2008.
B. Zhang and S. Horvath, "A general framework for weighted gene co-expression network analysis," (in eng), Stat Appl Genet Mol Biol, vol. 4, p. Article17, 2005.
Y. Hu, J. Han, S. Ding, S. Liu, and H. Wang, "Identification of ferroptosis-associated biomarkers for the potential diagnosis and treatment of postmenopausal osteoporosis," (in eng), Front Endocrinol (Lausanne), vol. 13, p. 986384, 2022.
G. Karami, M. Giuseppe Orlando, A. Delli Pizzi, M. Caulo, and C. Del Gratta, "Predicting Overall Survival Time in Glioblastoma Patients Using Gradient Boosting Machines Algorithm and Recursive Feature Elimination Technique," (in eng), Cancers (Basel), vol. 13, no. 19, p.4976, Oct 4 2021.
V. N. Vapnik, "An overview of statistical learning theory," (in eng), IEEE Trans Neural Netw, vol. 10, no. 5, pp. 988-99, 1999.
B. T. Sherman et al., "DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis," (in eng), BMC Bioinformatics, vol. 8, p. 426, Nov 2 2007.
D. Otasek, J. H. Morris, J. Bouças, A. R. Pico, and B. Demchak, "Cytoscape Automation: empowering workflow-based network analysis," (in eng), Genome Biol, vol. 20, no. 1, p. 185, Sep 2 2019.
N. Bhattacharyya et al., "CDK1 and HSP90AA1 Appear as the Novel Regulatory Genes in Non-Small Cell Lung Cancer: A Bioinformatics Approach," (in eng), J Pers Med, vol. 12, no. 3, p. 393, Mar 4 2022.
C. Y. Lin, C. H. Chin, H. H. Wu, S. H. Chen, C. W. Ho, and M. T. Ko, "Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology," (in eng), Nucleic Acids Res, vol. 36, no. Web Server issue, pp. W438-43, Jul 1 2008.
M. D. Wilkerson and D. N. Hayes, "ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking," (in eng), Bioinformatics, vol. 26, no. 12, pp. 1572-3, Jun 15 2010.
M. Jia et al., "Identification and validation of cuproptosis related genes and signature markers in bronchopulmonary dysplasia disease using bioinformatics analysis and machine learning," (in eng), BMC Med Inform Decis Mak, vol. 23, no. 1, p. 69, Apr 14 2023.
V. Grollemund et al., "Development and validation of a 1-year survival prognosis estimation model for Amyotrophic Lateral Sclerosis using manifold learning algorithm UMAP," (in eng), Sci Rep, vol. 10, no. 1, p. 13378, Aug 7 2020.
S. H. Wang and P. N. Tsao, "Phenotypes of Bronchopulmonary Dysplasia," (in eng), Int J Mol Sci, vol. 21, no. 17, p.6112,Aug 25 2020.
E. Baraldi et al., "Untargeted Metabolomic Analysis of Amniotic Fluid in the Prediction of Preterm Delivery and Bronchopulmonary Dysplasia," (in eng), PLoS One, vol. 11, no. 10, p. e0164211, 2016.
A. Dongre and R. A. Weinberg, "New insights into the mechanisms of epithelial-mesenchymal transition and implications for cancer," (in eng), Nat Rev Mol Cell Biol, vol. 20, no. 2, pp. 69-84, Feb 2019.
R. Y. Huang, V. Y. Chung, and J. P. Thiery, "Targeting pathways contributing to epithelial-mesenchymal transition (EMT) in epithelial ovarian cancer," (in eng), Curr Drug Targets, vol. 13, no. 13, pp. 1649-53, Dec 2012.
C. Li et al., "Exploration of epithelial-mesenchymal transition-related lncRNA signature and drug sensitivity in breast cancer," (in eng), Front Endocrinol (Lausanne), vol. 14, p. 1154741, 2023.
H. Y. Lu et al., "ILC2 influence the differentiation of alveolar type II epithelial cells in bronchopulmonary dysplasia mice," (in eng), J Leukoc Biol, vol. 114, no. 6, pp. 604-614, Nov 24 2023.
H. Yokoyama, S. Fujii, and I. Matsui, "Crystal structure of a core domain of stomatin from Pyrococcus horikoshii Illustrates a novel trimeric and coiled-coil fold," (in eng), J Mol Biol, vol. 376, no. 3, pp. 868-78, Feb 22 2008.
A. Banning, A. Tomasovic, and R. Tikkanen, "Functional aspects of membrane association of reggie/flotillin proteins," (in eng), Curr Protein Pept Sci, vol. 12, no. 8, pp. 725-35, Dec 2011.
E. A. R. Morris et al., "Flotillins control zebrafish epiboly through their role in cadherin-mediated cell-cell adhesion," (in eng), Biol Cell, vol. 109, no. 5, pp. 210-221, May 2017.
Y. L. Wang, W. J. Yao, L. Guo, H. F. Xi, S. Y. Li, and Z. M. Wang, "Expression of flotillin-2 in human non-small cell lung cancer and its correlation with tumor progression and patient survival," (in eng), Int J Clin Exp Pathol, vol. 8, no. 1, pp. 601-7, 2015.
T. Song, Z. Hu, J. Liu, and W. Huang, "FLOT2 upregulation promotes growth and invasion by interacting and stabilizing EphA2 in gliomas," (in eng), Biochem Biophys Res Commun, vol. 548, pp. 67-73, Apr 9 2021.
X. Deng et al., "Molecular mechanisms of cell death in bronchopulmonary dysplasia," (in eng), Apoptosis, vol. 28, no. 1-2, pp. 39-54, Feb 2023.
S. Wei, H. G. Moon, Y. Zheng, X. Liang, C. H. An, and Y. Jin, "Flotillin-2 modulates fas signaling mediated apoptosis after hyperoxia in lung epithelial cells," (in eng), PLoS One, vol. 8, no. 10, p. e77519, 2013.
Y. Qian et al., "AQP9 suppresses hepatocellular carcinoma cell invasion through inhibition of hypoxia-inducible factor 1? expression under hypoxia," (in eng), J Gastroenterol Hepatol, vol. 35, no. 11, pp. 1990-1997, Nov 2020.
B. Nico and D. Ribatti, "Role of aquaporins in cell migration and edema formation in human brain tumors," (in eng), Exp Cell Res, vol. 317, no. 17, pp. 2391-6, Oct 15 2011.
A. Holm, K. E. Magnusson, and E. Vikström, "Pseudomonas aeruginosa N-3-oxo-dodecanoyl-homoserine Lactone Elicits Changes in Cell Volume, Morphology, and AQP9 Characteristics in Macrophages," (in eng), Front Cell Infect Microbiol, vol. 6, p. 32, 2016.
T. Karlsson, M. Glogauer, R. P. Ellen, V. M. Loitto, K. E. Magnusson, and M. A. Magalhães, "Aquaporin 9 phosphorylation mediates membrane localization and neutrophil polarization," (in eng), J Leukoc Biol, vol. 90, no. 5, pp. 963-73, Nov 2011.
M. Heydarian, C. Schulz, T. Stoeger, and A. Hilgendorff, "Association of immune cell recruitment and BPD development," (in eng), Mol Cell Pediatr, vol. 9, no. 1, p. 16, Aug 2 2022.
U. Yazdani and J. R. Terman, "The semaphorins," (in eng), Genome Biol, vol. 7, no. 3, p. 211, 2006.
E. Nkyimbeng-Takwi and S. P. Chapoval, "Biology and function of neuroimmune semaphorins 4A and 4D," (in eng), Immunol Res, vol. 50, no. 1, pp. 10-21, May 2011.
D. Ito and A. Kumanogoh, "The role of Sema4A in angiogenesis, immune responses, carcinogenesis, and retinal systems," (in eng), Cell Adh Migr, vol. 10, no. 6, pp. 692-699, Nov 2016.
X. Liu et al., "SEMA4A promotes prostate cancer invasion: involvement of tumor microenvironment," (in eng), J Cancer, vol. 14, no. 14, pp. 2633-2643, 2023.
H. Kayama et al., "BATF2 prevents T-cell-mediated intestinal inflammation through regulation of the IL-23/IL-17 pathway," (in eng), Int Immunol, vol. 31, no. 6, pp. 371-383, May 21 2019.
C. Molczyk and R. K. Singh, "CXCR1: A Cancer Stem Cell Marker and Therapeutic Target in Solid Tumors," (in eng), Biomedicines, vol. 11, no. 2, p. 576, Feb 16 2023.
K. H. Susek, M. Karvouni, E. Alici, and A. Lundqvist, "The Role of CXC Chemokine Receptors 1-4 on Immune Cells in the Tumor Microenvironment," (in eng), Front Immunol, vol. 9, p. 2159, 2018.
J. Wang et al., "CXCR1 promotes malignant behavior of gastric cancer cells in vitro and in vivo in AKT and ERK1/2 phosphorylation," (in eng), Int J Oncol, vol. 48, no. 5, pp. 2184-96, May 2016.
N. Shamaladevi, D. A. Lyn, D. O. Escudero, and B. L. Lokeshwar, "CXC receptor-1 silencing inhibits androgen-independent prostate cancer," (in eng), Cancer Res, vol. 69, no. 21, pp. 8265-74, Nov 1 2009.
P. A. Ruffini, "The CXCL8-CXCR1/2 Axis as a Therapeutic Target in Breast Cancer Stem-Like Cells," (in eng), Front Oncol, vol. 9, p. 40, 2019.
H. Ha, B. Debnath, and N. Neamati, "Role of the CXCL8-CXCR1/2 Axis in Cancer and Inflammatory Diseases," (in eng), Theranostics, vol. 7, no. 6, pp. 1543-1588, 2017.
K. Dhayni, K. Zibara, H. Issa, S. Kamel, and Y. Bennis, "Targeting CXCR1 and CXCR2 receptors in cardiovascular diseases," (in eng), Pharmacol Ther, vol. 237, p. 108257, Sep 2022.
H. Qin et al., "Targeting CXCR1 alleviates hyperoxia-induced lung injury through promoting glutamine metabolism," (in eng), Cell Rep, vol. 42, no. 7, p. 112745, Jul 25 2023.
J. D. Jacobson, W. E. Truog, and D. R. Benjamin, "Increased expression of human leukocyte antigen-DR on pulmonary macrophages in bronchopulmonary dysplasia," (in eng), Pediatr Res, vol. 34, no. 3, pp. 341-4, Sep 1993.
G. Toldi, H. Hummler, and T. Pillay, "T Lymphocytes, Multi-Omic Interactions and Bronchopulmonary Dysplasia," (in eng), Front Pediatr, vol. 9, p. 694034, 2021.
K. M. Scheible et al., "T cell developmental arrest in former premature infants increases risk of respiratory morbidity later in infancy," (in eng), JCI Insight, vol. 3, no. 4, p. e96724, Feb 22 2018.
B. I. Kim et al., "Increase in cord blood soluble E-selectin and tracheal aspirate neutrophils at birth and the development of new bronchopulmonary dysplasia," (in eng), J Perinat Med, vol. 32, no. 3, pp. 282-7, 2004.
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