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Luo X, Zhao M, Chen C, Lin F, Li X, Huang H, Dou L, Feng J, Xiao S, Liu D, He J, Yu J. Identification of genetic susceptibility in preterm newborns with bronchopulmonary dysplasia by whole-exome sequencing: BIVM gene may play a role. Eur J Pediatr 2023; 182:1707-1718. [PMID: 36757497 PMCID: PMC10167099 DOI: 10.1007/s00431-022-04779-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/08/2022] [Accepted: 12/21/2022] [Indexed: 02/10/2023]
Abstract
UNLABELLED Bronchopulmonary dysplasia (BPD) is a common chronic respiratory disease in preterm infants caused by multifactorial etiology. Genetic factors are involved in the occurrence of BPD, but studies have found that candidate genes have poor reproducibility and are influenced by ethnic heterogeneity; therefore, more exploration is still needed. We performed whole-exon sequencing in 34 preterm infants with BPD and 32 non-BPD control neonates. The data were analyzed and interpreted by Fisher difference comparison, PLINK and eQTL association analysis, KEGG and GO enrichment analysis, STRING tool, Cytoscape software, ProtParam tool, HOPE online software, and GEOR2 analysis on NCBI GEO dataset. BPD has a highly heterogeneity in different populations, and we found 35 genes overlapped with previous whole-exon sequencing studies, such as APOB gene. Arterial and epithelial cell development and energy metabolism pathways affect BPD. In this study, 24 key genes were identified, and BIVM rs3825519 mutation leads to prolonged assisted ventilation in patients with BPD. A novel DDAH1 mutation site (NM_012137: exon1: c.89 T > G: p.L30R) was found in 9 BPD patients. CONCLUSION BIVM gene rs3825519 mutation may play a role in the pathogenesis of BPD by affecting cilia movement, and the DDAH1 and APOB genes mutations may have a pathogenic role in BPD. WHAT IS KNOWN • Genetic factors are involved in the occurrence of bronchopulmonary dysplasia. • The candidate genes have poor reproducibility and are influenced by ethnic heterogeneity, therefore, more exploration is still needed. WHAT IS NEW • We identified the role of susceptible SNPs in BPD in Shenzhen, China, and identified 24 key genes that influence the pathogenesis of BPD, and also found 35 genes overlapped with previous whole exon sequencing studies, such as APOB gene. • We found that BIVM and DDAH1 genes may play a pathogenic role in the pathogenesis of BPD.
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Affiliation(s)
- Xi Luo
- Department of Neonatology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, 136 Zhongshan 2nd Road, Yuzhong District, Chongqing, 40014, China
| | - Min Zhao
- Department of Neonatology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, 136 Zhongshan 2nd Road, Yuzhong District, Chongqing, 40014, China
| | - Cheng Chen
- Department of Neonatology, Shenzhen Longgang District Maternity & Child Healthcare Hospital, Shenzhen, 518172, China
| | - Fengji Lin
- Department of Neonatology, Shenzhen Longgang District Maternity & Child Healthcare Hospital, Shenzhen, 518172, China
| | - Xiaodong Li
- Department of Neonatology, Huazhong University of Science and Technology Union Shenzhen Hospital (NanShan Hospital), Shenzhen, 518052, China
| | - Haiyun Huang
- Department of Neonatology, Huazhong University of Science and Technology Union Shenzhen Hospital (NanShan Hospital), Shenzhen, 518052, China
| | - Lei Dou
- Department of Neonatology, Southern University of Science and Technology Hospital, No. 6019 Liuxian Avenue, Xili Street, Nanshan District, Shenzhen, 518055, China
| | - Jinxing Feng
- Department of Neonatology, Shenzhen Children's Hospital, Shenzhen, 518031, China
| | - Shanqiu Xiao
- Department of Neonatology, Shenzhen Baoan Women's and Children's Hospital, Shenzhen, 518133, China
| | - Dong Liu
- Department of Neonatology, Shenzhen People's Hospital, Shenzhen, 518020, China
| | - Junli He
- Department of Neonatology, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Jialin Yu
- Department of Neonatology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, 136 Zhongshan 2nd Road, Yuzhong District, Chongqing, 40014, China. .,Department of Neonatology, Southern University of Science and Technology Hospital, No. 6019 Liuxian Avenue, Xili Street, Nanshan District, Shenzhen, 518055, China.
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Dai D, Chen H, Dong X, Chen J, Mei M, Lu Y, Yang L, Wu B, Cao Y, Wang J, Zhou W, Qian L. Bronchopulmonary Dysplasia Predicted by Developing a Machine Learning Model of Genetic and Clinical Information. Front Genet 2021; 12:689071. [PMID: 34276789 PMCID: PMC8283015 DOI: 10.3389/fgene.2021.689071] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Background An early and accurate evaluation of the risk of bronchopulmonary dysplasia (BPD) in premature infants is pivotal in implementing preventive strategies. The risk prediction models nowadays for BPD risk that included only clinical factors but without genetic factors are either too complex without practicability or provide poor-to-moderate discrimination. We aim to identify the role of genetic factors in BPD risk prediction early and accurately. Methods Exome sequencing was performed in a cohort of 245 premature infants (gestational age <32 weeks), with 131 BPD infants and 114 infants without BPD as controls. A gene burden test was performed to find risk genes with loss-of-function mutations or missense mutations over-represented in BPD and severe BPD (sBPD) patients, with risk gene sets (RGS) defined as BPD-RGS and sBPD-RGS, respectively. We then developed two predictive models for the risk of BPD and sBPD by integrating patient clinical and genetic features. The performance of the models was evaluated using the area under the receiver operating characteristic curve (AUROC). Results Thirty and 21 genes were included in BPD-RGS and sBPD-RGS, respectively. The predictive model for BPD, which combined the BPD-RGS and basic clinical risk factors, showed better discrimination than the model that was only based on basic clinical features (AUROC, 0.915 vs. AUROC, 0.814, P = 0.013, respectively) in the independent testing dataset. The same was observed in the predictive model for sBPD (AUROC, 0.907 vs. AUROC, 0.826; P = 0.016). Conclusion This study suggests that genetic information contributes to susceptibility to BPD. The predictive model in this study, which combined BPD-RGS with basic clinical risk factors, can thus accurately stratify BPD risk in premature infants.
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Affiliation(s)
- Dan Dai
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Huiyao Chen
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Xinran Dong
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Jinglong Chen
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Mei Mei
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Yulan Lu
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Lin Yang
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China
| | - Bingbing Wu
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yun Cao
- Department of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Jin Wang
- Department of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Wenhao Zhou
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China.,Department of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Liling Qian
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China
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