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Li F, Tan Z, Chen H, Gao Y, Xia J, Huang T, Liang L, Zhang J, Zhang X, Shi X, Chen Q, Shu Q, Yu L. Integrative analysis of bulk and single-cell RNA sequencing reveals the gene expression profile and the critical signaling pathways of type II CPAM. Cell Biosci 2024; 14:94. [PMID: 39026356 PMCID: PMC11264590 DOI: 10.1186/s13578-024-01276-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUD Type II congenital pulmonary airway malformation (CPAM) is a rare pulmonary microcystic developmental malformation. Surgical excision is the primary treatment for CPAM, although maternal steroids and betamethasone have proven effective in reducing microcystic CPAM. Disturbed intercellular communication may contribute to the development of CPAM. This study aims to investigate the expression profile and analyze intercellular communication networks to identify genes potentially associated with type II CPAM pathogenesis and therapeutic targets. METHODS RNA sequencing (RNA-seq) was performed on samples extracted from both the cystic area and the adjacent normal tissue post-surgery in CPAM patients. Iterative weighted gene correlation network analysis (iWGCNA) was used to identify genes specifically expressed in type II CPAM. Single-cell RNA-seq (scRNA-seq) was integrated to unveil the heterogeneity in cell populations and analyze the communication and interaction within epithelial cell sub-populations. RESULTS A total of 2,618 differentially expressed genes were identified, primarily enriched in cilium-related biological process and inflammatory response process. Key genes such as EDN1, GPR17, FPR2, and CHRM1, involved in the G protein-coupled receptor (GPCR) signaling pathway and playing roles in cell differentiation, apoptosis, calcium homeostasis, and the immune response, were highlighted based on the protein-protein interaction network. Type II CPAM-associated modules, including ciliary function-related genes, were identified using iWGCNA. By integrating scRNA-seq data, AGR3 (related to calcium homeostasis) and SLC11A1 (immune related) were identified as the only two differently expressed genes in epithelial cells of CPAM. Cell communication analysis revealed that alveolar type 1 (AT1) and alveolar type 2 (AT2) cells were the predominant communication cells for outgoing and incoming signals in epithelial cells. The ligands and receptors between epithelial cell subtypes included COLLAGEN genes enriched in PI3K-AKT singaling and involved in epithelial to mesenchymal transition. CONCLUSIONS In summary, by integrating bulk RNA-seq data of type II CPAM with scRNA-seq data, the gene expression profile and critical signaling pathways such as GPCR signaling and PI3K-AKT signaling pathways were revealed. Abnormally expressed genes in these pathways may disrupt epithelial-mesenchymal transition and contribute to the development of CPAM. Given the effectiveness of prenatal treatments of microcystic CPAM using maternal steroids and maternal betamethasone administration, targeting the genes and signaling pathways involved in the development of CPAM presents a promising therapeutic strategy.
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Affiliation(s)
- Fengxia Li
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Zheng Tan
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Hongyu Chen
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Yue Gao
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Jie Xia
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Ting Huang
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Liang Liang
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Jian Zhang
- Department of Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Xianghong Zhang
- Department of Cardiac Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Xucong Shi
- Department of Cardiac Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Qiang Chen
- Department of General Surgery, Jiangxi Provincial Children's Hospital, Jiangxi, China.
| | - Qiang Shu
- Department of Cardiac Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Lan Yu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China.
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Tan Z, Li F, Chen Q, Chen H, Xue Z, Zhang J, Gao Y, Liang L, Huang T, Zhang S, Li J, Shu Q, Yu L. Integrated bulk and single-cell RNA-sequencing reveals SPOCK2 as a novel biomarker gene in the development of congenital pulmonary airway malformation. Respir Res 2023; 24:127. [PMID: 37165378 PMCID: PMC10170809 DOI: 10.1186/s12931-023-02436-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 04/26/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Congenital pulmonary airway malformation (CPAM) is the most frequent pulmonary developmental malformation and the pathophysiology remains poorly understood. This study aimed to identify the characteristic gene expression patterns and the marker genes essential to CPAM. METHODS Tissues from the cystic area displaying CPAM and the area of normal appearance were obtained during surgery. Bulk RNA sequencing (RNA-seq) and single-cell RNA sequencing (scRNA-seq) were performed for integrating analysis. Iterative weighted gene correlation network analysis (iWGCNA) was used to identify specifically expressed genes to CPAM. RESULTS In total, 2074 genes were significantly differentially expressed between the CPAM and control areas. Of these differentially expressed genes (DEGs), 1675 genes were up-regulated and 399 genes were down-regulated. Gene ontology analysis revealed these DEGs were specifically enriched in ciliated epithelium and involved in immune response. We also identified several CPAM-related modules by iWGCNA, among them, P15_I4_M3 module was the most influential module for distinguishing CPAMs from controls. By combining the analysis of the expression dataset from RNA-seq and scRNA-seq, SPOCK2, STX11, and ZNF331 were highlighted in CPAM. CONCLUSIONS Through our analysis of expression datasets from both scRNA-seq and bulk RNA-seq of tissues obtained from patients with CPAM, we identified the characteristic gene expression patterns associated with the condition. Our findings suggest that SPOCK2 could be a potential biomarker gene for the diagnosis and therapeutic target in the development of CPAM, whereas STX11 and ZNF331 might serve as prognostic markers for this condition. Further investigations with larger samples and function studies are necessary to confirm the involvement of these genes in CPAM.
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Affiliation(s)
- Zheng Tan
- Department of Paediatric Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Fengxia Li
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Qiang Chen
- Department of Pediatrics, Jiangxi Provincial Children's Hospital, Jiangxi, China
| | - Hongyu Chen
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Ziru Xue
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Jian Zhang
- Department of Paediatric Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Yue Gao
- Department of Paediatric Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Liang Liang
- Department of Paediatric Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Ting Huang
- Department of Paediatric Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Shouhua Zhang
- Department of Pediatrics, Jiangxi Provincial Children's Hospital, Jiangxi, China
- Department of General Surgery, Jiangxi Provincial Children's Hospital, Jiangxi, China
| | - Jianhua Li
- Department of Paediatric Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Qiang Shu
- Department of Paediatric Thoracic Surgery, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China.
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Lan Yu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China.
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Congenital lung malformations: Dysregulated lung developmental processes and altered signaling pathways. Semin Pediatr Surg 2022; 31:151228. [PMID: 36442455 DOI: 10.1016/j.sempedsurg.2022.151228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Congenital lung malformations comprise a diverse group of anomalies including congenital pulmonary airway malformation (CPAM, previously known as congenital cystic adenomatoid malformation or CCAM), bronchopulmonary sequestration (BPS), congenital lobar emphysema (CLE), bronchogenic cysts, and hybrid lesions. Little is known about the signaling pathways that underlie the pathophysiology of these lesions and the processes that may promote their malignant transformation. In the last decade, the use of transgenic/knockout animal models and the implementation of next generation sequencing on surgical lung specimens have increased our knowledge on the pathophysiology of these lesions. Herein, we provide an overview of normal lung development in humans and rodents, and we discuss the current state of knowledge on the pathophysiology and molecular pathways that are altered in each congenital lung malformation.
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Yang W, Zhao P, Cao P, Miao C, Ji X, Gao Y, Li P, Cheng J. Global interpretation of novel alternative splicing events in human congenital pulmonary airway malformations: A pilot study. J Cell Biochem 2022; 123:736-745. [PMID: 35064685 DOI: 10.1002/jcb.30216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Weili Yang
- Department of Pediatric Surgery The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi China
| | - Pu Zhao
- Department of Neonatology Shaanxi Provincial People's Hospital Xi'an Shaanxi China
| | - Ping Cao
- Department of Pediatric Surgery The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi China
| | - Chunlin Miao
- Department of Pediatric Surgery The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi China
| | - Xiang Ji
- Department of Pediatric Surgery The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi China
| | - Ya Gao
- Department of Pediatric Surgery The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi China
| | - Peng Li
- Department of Pediatric Surgery The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi China
| | - Jiwen Cheng
- Department of Pediatric Surgery The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi China
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Landry-Truchon K, Houde N, Lhuillier M, Charron L, Hadchouel A, Delacourt C, Foulkes WD, Galmiche-Rolland L, Jeannotte L. Deletion of Yy1 in mouse lung epithelium unveils molecular mechanisms governing pleuropulmonary blastoma pathogenesis. Dis Model Mech 2020; 13:dmm045989. [PMID: 33158935 PMCID: PMC7790197 DOI: 10.1242/dmm.045989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022] Open
Abstract
Pleuropulmonary blastoma (PPB) is a very rare pediatric lung disease. It can progress from abnormal epithelial cysts to an aggressive sarcoma with poor survival. PPB is difficult to diagnose as it can be confounded with other cystic lung disorders, such as congenital pulmonary airway malformation (CPAM). PPB is associated with mutations in DICER1 that perturb the microRNA (miRNA) profile in lung. How DICER1 and miRNAs act during PPB pathogenesis remains unsolved. Lung epithelial deletion of the Yin Yang1 (Yy1) gene in mice causes a phenotype mimicking the cystic form of PPB and affects the expression of key regulators of lung development. Similar changes in expression were observed in PPB but not in CPAM lung biopsies, revealing a distinctive PPB molecular signature. Deregulation of molecules promoting epithelial-mesenchymal transition (EMT) was detected in PPB specimens, suggesting that EMT might participate in tumor progression. Changes in miRNA expression also occurred in PPB lung biopsies. miR-125a-3p, a candidate to regulate YY1 expression and lung branching, was abnormally highly expressed in PPB samples. Together, these findings support the concept that reduced expression of YY1, due to the abnormal miRNA profile resulting from DICER1 mutations, contributes to PPB development via its impact on the expression of key lung developmental genes.This article has an associated First Person interview with the joint first authors of the paper.
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Affiliation(s)
- Kim Landry-Truchon
- Centre de recherche sur le cancer de l'Université Laval, Centre de recherche du CHU de Québec-Université Laval (Oncology Axis), Québec, Canada G1R 3S3
| | - Nicolas Houde
- Centre de recherche sur le cancer de l'Université Laval, Centre de recherche du CHU de Québec-Université Laval (Oncology Axis), Québec, Canada G1R 3S3
| | - Mickaël Lhuillier
- Inserm U1151, Institut Necker-Enfants Malades, Université de Paris, 75743 Paris, Cedex15, France
| | - Louis Charron
- Centre de recherche sur le cancer de l'Université Laval, Centre de recherche du CHU de Québec-Université Laval (Oncology Axis), Québec, Canada G1R 3S3
| | - Alice Hadchouel
- Inserm U1151, Institut Necker-Enfants Malades, Université de Paris, 75743 Paris, Cedex15, France
- AP-HP, Hôpital Necker-Enfants Malades, 75743 Paris, Cedex15, France
| | - Christophe Delacourt
- Inserm U1151, Institut Necker-Enfants Malades, Université de Paris, 75743 Paris, Cedex15, France
- AP-HP, Hôpital Necker-Enfants Malades, 75743 Paris, Cedex15, France
| | - William D Foulkes
- Department of Medical Genetics, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montréal, Canada H3T 1E2
| | | | - Lucie Jeannotte
- Centre de recherche sur le cancer de l'Université Laval, Centre de recherche du CHU de Québec-Université Laval (Oncology Axis), Québec, Canada G1R 3S3
- Department of Molecular Biology, Medical Biochemistry & Pathology, Université Laval, Québec, Canada G1V 0A6
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