Exploratory analysis of the key role of immune function changes in BPD

Abstract

Bronchopulmonary dysplasia (BPD) is one of the most prevalent and severe chronic lung diseases in premature infants. The objective of the current study was to screen for key BPD-associated genes and pathways by transcriptomic analysis from clinical patients and animal models. In our study, the differentially expressed genes were screened from 58 children with 14-day BPD and 40 normal children in the GSE32472 dataset of the Gene Expression Omnibus database. Then, we identified four hub genes (Cd3e, Cd3g, Cd247, and Itk) and a signaling pathway (T cell receptor signaling pathway) by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis and protein-protein interaction analysis. The differential expression of the relevant pathways and gene sets among the groups was verified via GSEA analysis. Subsequently, a rat model of BPD with hyperoxiainduced lung injury was established, and the transcriptome sequencing of the whole lung tissue was performed. A similar analysis was done on the sequencing data of the hub genes and associated pathway screening to verify the accuracy. Ultimately, quantitative polymerase chain reaction was performed to validate the transcriptomics data of core gene expression in the rat model. Our study revealed that the downregulation of the expression of the above four key genes in the course of BPD leads to a decrease in the function of T cell receptor signaling pathways, it causes immune dysfunction and increases the severity of lung inflammation as well as susceptibility to other respiratory infectious diseases.

Keywords

BPD / differential gene analysis / enrichment analysis / GSEA analysis / immune function

References

[1] AgsP. Chronic lung disease of prematurity: a short history. Semin Fetal Neonatal Med. 2009; 14(6):333-338.

[2] MorrowLA, WagnerBD, IngramDA, et al. Antenatal determinants of bronchopulmonary dysplasia and late respiratory disease in preterm infants. Am J Respir Crit Care Med. 2017; 196(3):364-374.

[3] YouJ.-Y, ShuC, GongC.-H, Liu S, FuZ. Readmission of children with bronchopulmonary dysplasia in the first 2 years of life: a clinical analysis of 121 cases. Chin J Contemp Pediatr 2017; 19(10):1056-1060.

[4] McGrath-MorrowSA, Collaco JM. Bronchopulmonary dysplasia: what are its links to COPD? Ther Adv Respir Dis. 2019; 13:1753466619892492.

[5] PrincipiN, Di Pietro GM, EspositoS. Bronchopulmonary dysplasia: clinical aspects and preventive and therapeutic strategies. J Transl Med. 2018; 16(1):36.

[6] CaiY, MaF, QuL.-H, et al. Weighted gene co-expression network analysis of key biomarkers associated with bronchopulmonary dysplasia. Front Genet. 2020; 11:539292.

[7] ShahzadT, Radajewski S, ChaoCM, BellusciS, Ehrhardt H. Pathogenesis of bronchopulmonary dysplasia: when inflammation meets organ development. Mol Cell Pediatr. 2016; 3(1):23.

[8] WangSH, TsaoPN. Phenotypes of bronchopulmonary dysplasia. Int J Mol Sci. 2020; 21(17):6112.

[9] GaoJ.-Y, WuM.-F, WangF.-D, et al. CD74, a novel predictor for bronchopulmonary dysplasia in preterm infants. Medicine (Baltimore). 2020; 99(48):e23477.

[10] ShresthaD, YeGX, StableyD, et al. Pulmonary immune cell transcriptome changes in double-hit model of BPD induced by chorioamnionitis and postnatal hyperoxia. Pediatr Res. 2021; 90(3):565-575.

[11] TaoX.-W, MoL.-X, ZengL.-K. Hyperoxia induced bronchopulmonary dysplasia-like inflammation via miR34a-TNIP2-IL-1β pathway. Front Pediatr. 2022; 10:805860.

[12] LiJ.-J, YuKH, OehlertJ, et al. Exome sequencing of neonatal blood spots and the identification of genes implicated in bronchopulmonary dysplasia. Am J Respir Crit Care Med. 2015; 192(5):589-596.

[13] CollacoJM, McGrath-Morrow SA. Respiratory phenotypes for preterm infants, children, and adults: bronchopulmonary dysplasia and more. Ann Am Thorac Soc. 2018; 15(5):530-538.

[14] SpeerCP. Inflammation and bronchopulmonary dysplasia: a continuing story. Semin Fetal Neonatal Med. 2006; 11(5):354-362.

[15] SpeerCP. Pulmonary inflammation and bronchopulmonary dysplasia. J Perinatol. 2006; 26(suppl 1): S57-S62.Discussion S63–4.

[16] HwangJS, RehanVK. Recent advances in bronchopulmonary dysplasia: pathophysiology, prevention, and treatment. Lung. 2018; 196(2):129-138.

[17] ShahK, Al-Haidari A, SunJ.-M, KaziJU. T cell receptor (TCR) signaling in health and disease. Signal Transduct Targeted Ther. 2021; 6(1):412.

[18] WucherpfennigKW, GagnonE, CallMJ, Huseby ES, CallME. Structural biology of the T-cell receptor: insights into receptor assembly, ligand recognition, and initiation of signaling. Cold Spring Harb Perspect Biol. 2010; 2(4):a005140.

[19] MariuzzaRA, Agnihotri P, OrbanJ. The structural basis of T-cell receptor (TCR) activation: an enduring Enigma. J Biol Chem. 2020; 295(4):914-925.

[20] LiY.-P, ChenS.-B, LiX.-C, et al. CD247, a potential T cell-derived disease severity and prognostic biomarker in patients with idiopathic pulmonary fibrosis. Front Immunol. 2021; 12:762594.

[21] PanB.-H, YangM.-D, WeiX.-Y, et al. Interleukin-2 inducible T-cell kinase: a potential prognostic biomarker and tumor microenvironment remodeling indicator for hepatocellular carcinoma. Aging (Albany NY). 2021; 13(14):18620-18644.

[22] AndreottiAH, Schwartzberg PL, JosephRE, BergLJ. T-cell signaling regulated by the Tec family kinase, Itk. Cold Spring Harb Perspect Biol. 2010; 2(7):a002287.

[23] HuangL, YeK.-X, McGeeMC, et al. Interleukin-2-inducible T-cell kinase deficiency impairs early pulmonary protection against Mycobacterium tuberculosis infection. Front Immunol. 2020; 10:3103.

[24] GhoshS, Drexler I, BhatiaS, AdlerH, Gennery AR, BorkhardtA. Corrigendum: interleukin-2-inducible T-cell kinase deficiency-new patients, new insight? Front Immunol. 2018; 9:2197.

[25] PrinceAL, KrausZ, CartySA, et al. Development of innate CD4⁺ and CD8⁺ T cells in Itk-deficient mice is regulated by distinct pathways. J Immunol. 2014; 193(2):688-699.

[26] LiaoXC, Littman DR. Altered T cell receptor signaling and disrupted T cell development in mice lacking Itk. Immunity. 1995; 3(6):757-769.

[27] ElmoreJ, CarterC, RedkoA, et al. ITK independent development of Th17 responses during hypersensitivity pneumonitis driven lung inflammation. Commun Biol. 2022; 5(1):162.

[28] Al-Akioui-SanzK, MoraruM, VilchesC. A simple genotyping method for CD247 3’-untranslated region polymorphism rs1052231 and characterization of a reference cell panel. HLA. 2021; 98(3):218-222.

[29] BallabhP, SimmM, KumariJ, et al. Lymphocyte subpopulations in bronchopulmonary dysplasia. Am J Perinatol. 2003; 20(8):465-475.

[30] XuM.-Y, HuangS, ChenJ.-H, et al. Cytotoxic lymphocytes-related gene ITK from a systematic CRISPR screen could predict prognosis of ovarian cancer patients with distant metastasis. J Transl Med. 2021; 19(1):447.

[31] ChawPS, HuaL, CunninghamS, et al. Respiratory syncytial virus-associated acute lower respiratory infections in children with bronchopulmonary dysplasia: systematic review and meta-analysis. J Infect Dis. 2020; 222(Suppl 7): S620-S627.

[32] LloydCM, Marsland BJ. Lung homeostasis: influence of age, microbes, and the immune system. Immunity. 2017; 46(4):549-561.

[33] PietrzykJJ, KwintaP, WollenEJ, et al. Gene expression profiling in preterm infants: new aspects of bronchopulmonary dysplasia development. PLoS One. 2013; 8(10):e78585.

RIGHTS & PERMISSIONS

2024 The Author(s). Pediatric Discovery published by John Wiley & Sons Australia, Ltd on behalf of Children’s Hospital of Chongqing Medical University.