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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 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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Osei-Wusu S, Tetteh JKA, Musah AB, Ntiamoah DO, Arthur N, Adjei A, Arbues A, Ofori EA, Mensah KA, Galevo SEA, Frempong AF, Asare P, Asante-Poku A, Otchere ID, Kusi KA, Lenz TL, Gagneux S, Portevin D, Yeboah-Manu D. Macrophage susceptibility to infection by Ghanaian Mycobacterium tuberculosis complex lineages 4 and 5 varies with self-reported ethnicity. Front Cell Infect Microbiol 2023; 13:1163993. [PMID: 37645380 PMCID: PMC10461633 DOI: 10.3389/fcimb.2023.1163993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Background The epidemiology of Mycobacterium tuberculosis complex (MTBC) lineage 5 (L5) infections in Ghana revealed a significantly increased prevalence in Ewes compared to other self-reported ethnic groups. In that context, we sought to investigate the early phase of tuberculosis (TB) infection using ex vivo infection of macrophages derived from the blood of Ewe and Akan ethnic group volunteers with MTBC L4 and L5 strains. Methods The study participants consisted of 16 controls, among which self-reported Akan and Ewe ethnicity was equally represented, as well as 20 cured TB cases consisting of 11 Akans and 9 Ewes. Peripheral blood mononuclear cells were isolated from both healthy controls and cured TB cases. CD14+ monocytes were isolated and differentiated into monocyte-derived macrophages (MDMs) before infection with L4 or L5 endemic strains. The bacterial load was assessed after 2 hours (uptake) as well as 3 and 7 days post-infection. Results We observed a higher capacity of MDMs from Ewes to phagocytose L4 strains (p < 0.001), translating into a higher bacillary load on day 7 (p < 0.001) compared to L5, despite the higher replication rate of L5 in Ewe MDMs (fold change: 1.4 vs. 1.2, p = 0.03) among the controls. On the contrary, within macrophages from Akans, we observed a significantly higher phagocytic uptake of L5 (p < 0.001) compared to L4, also translating into a higher load on day 7 (p = 0.04). However, the replication rate of L4 in Akan MDMs was higher than that of L5 (fold change: L4 = 1.2, L4 = 1.1, p = 0.04). Although there was no significant difference in the uptake of L4 and L5 among cured TB cases, there was a higher bacterial load of both L4 (p = 0.02) and L5 (p = 0.02) on day 7 in Ewe MDMs. Conclusion Our results suggest that host ethnicity (driven by host genetic diversity), MTBC genetic diversity, and individual TB infection history are all acting together to modulate the outcome of macrophage infections by MTBC.
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Affiliation(s)
- Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - John K. A. Tetteh
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Abdul Basit Musah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Nelly Arthur
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Abraham Adjei
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Ainhoa Arbues
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Ebenezer Addo Ofori
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Kwadwo Akyea Mensah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Abena Frema Frempong
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Kwadwo Asamoah Kusi
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Tobias L. Lenz
- Research Group for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Damien Portevin
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
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Hu B, Wang Y, Wang Z, He X, Wang L, Yuan D, He Y, Jin T, He S. Association of SLC11A1 Polymorphisms With Tuberculosis Susceptibility in the Chinese Han Population. Front Genet 2022; 13:899124. [PMID: 35938025 PMCID: PMC9352942 DOI: 10.3389/fgene.2022.899124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/02/2022] [Indexed: 11/30/2022] Open
Abstract
Tuberculosis (TB) is an important health issue in the world. Although the relation of SLC11A1 polymorphisms with TB risk has been extensively studied, it has not been reported in the northwest Chinese Han population. Therefore, this study aimed to investigate the relationships between five polymorphisms in or near the SLC11A1 gene and susceptibility to TB. The Agena MassARRAY platform was conducted for genotyping from 510 TB patients and 508 healthy controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were analyzed through logistic regression adjustment age and gender to assess the relationships between polymorphisms and TB risk. Our results identified that rs7608307 was related to increased TB risk in males (CT vs. CC: OR = 1.69, 95%CI: 1.12–2.56, p = 0.013; CT-TT vs. CC: OR = 1.61, 95%CI: 1.08–2.41, p = 0.020) and age ≤41 group (CT vs. CC: OR = 1.66, 95%CI: 1.04–2.65, p = 0.035), respectively. The SNP rs13062 was associated with the TB risk both in males (p = 0.012) and age >41 group (p = 0.021). In addition, we observed that the CC genotype of rs4674301 was correlated with increased TB risk in females (p = 0.043). Our results demonstrated the relationships between polymorphisms (rs7608307, rs4674301, and rs13062) in or near the SLC11A1 gene and age- and sex-specific TB risk in the northwest Chinese Han population.
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Affiliation(s)
- Baoping Hu
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, Xianyang, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, China
- Department of Anesthesiology, The Affiliated Hospital of Xizang Minzu University, Xianyang, China
| | - Yuhe Wang
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, Xianyang, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, China
- Department of Clinical Laboratory, The Affiliated Hospital of Xizang Minzu University, Xianyang, China
| | - Zhongtao Wang
- Department of Infectious Diseases, General Hospital of Tibet Military Command, Lhasa, China
| | - Xue He
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, Xianyang, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Li Wang
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, Xianyang, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Dongya Yuan
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, Xianyang, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Yongjun He
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, Xianyang, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Tianbo Jin
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, Xianyang, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, China
- *Correspondence: Tianbo Jin, , Shumei He,
| | - Shumei He
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, Xianyang, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, China
- *Correspondence: Tianbo Jin, , Shumei He,
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