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Hou L, Ye M, Wang X, Zhu Y, Sun X, Gu R, Chen L, Fang B. Synergism with Shikimic Acid Restores β-Lactam Antibiotic Activity against Methicillin-Resistant Staphylococcus aureus. Molecules 2024; 29:1528. [PMID: 38611807 PMCID: PMC11013880 DOI: 10.3390/molecules29071528] [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: 02/26/2024] [Revised: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has evolved into a dangerous pathogen resistant to beta-lactam antibiotics (BLAs) and has become a worrisome superbug. In this study, a strategy in which shikimic acid (SA), which has anti-inflammatory and antibacterial activity, is combined with BLAs to restart BLA activity was proposed for MRSA treatment. The synergistic effects of oxacillin combined with SA against oxacillin resistance in vitro and in vivo were investigated. The excellent synergistic effect of the oxacillin and SA combination was confirmed by performing the checkerboard assay, time-killing assay, live/dead bacterial cell viability assay, and assessing protein leakage. SEM showed that the cells in the control group had a regular, smooth, and intact surface. In contrast, oxacillin and SA or the combination treatment group exhibited different degrees of surface collapse. q-PCR indicated that the combination treatment group significantly inhibited the expression of the mecA gene. In vivo, we showed that the combination treatment increased the survival rate and decreased the bacterial load in mice. These results suggest that the combination of oxacillin with SA is considered an effective treatment option for MRSA, and the combination of SA with oxacillin in the treatment of MRSA is a novel strategy.
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Affiliation(s)
- Limin Hou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Minqi Ye
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoyu Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yifan Zhu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xueyan Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Ruiheng Gu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Liangzhu Chen
- Guangdong Wenshi Dahuanong Biotechnology Co., Ltd., Yunfu 510610, China
| | - Binghu Fang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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He Z, Hou J, Li Y, Li Y, Zeng W, Liu W. Analysis of clinical outcomes and prognosis of patients with early bronchogenic lung cancer after treatment of rigid bronchoscopy combining fiberoptic bronchoscopy: a single-center retrospective study. Expert Rev Med Devices 2024; 21:257-263. [PMID: 38131192 DOI: 10.1080/17434440.2023.2298711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVES To investigate the clinical value of rigid bronchoscopy combined with fiberoptic bronchoscopy in patients with early bronchogenic lung cancer who underwent sleeve lobectomy. METHODS A retrospective study was performed on 76 patients with early bronchogenic lung cancer admitted to our center from March 2016 to March 2017. Patients in the control group received conventional sleeve lobectomy (n = 38), while patients in the observation group underwent sleeve lobectomy by using rigid bronchoscopy combining fiberoptic bronchoscopy (n = 38). We compared perioperative period indicators and the recovery of pulmonary function indexes one month after the operation were compared in two groups. The prognosis of the patients were also analyzed. RESULTS Compared with the control group, the intraoperative blood loss, operation duration and airway reconstruction duration in the observation group were significantly reduced. The total incidence of perioperative complications was markedly lower in the observation group than in the control group. The percentage of DLCO% was significantly improved in the observation group. The relapse-free survival (RFS) in the observation group was remarkably longer than in the control group. CONCLUSION Rigid bronchoscopy combined with fiberoptic bronchoscopy is beneficial to improve the clinical outcome and prognosis of patients with early bronchogenic lung cancer more effectively.
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Affiliation(s)
- Zhengbing He
- Department of Pulmonary and Critical Care Medicine, Yiyang Central Hospital, Yiyang, China
| | - Juhua Hou
- Department of School of Clinical Medicine, Yiyang Medical College, Yiyang, China
| | - Yong Li
- Department of Pulmonary and Critical Care Medicine, Yiyang Central Hospital, Yiyang, China
| | - Yu Li
- Department of Pulmonary and Critical Care Medicine, Yiyang Central Hospital, Yiyang, China
| | - Wei Zeng
- Department of General Practice, Yiyang Medical College Affiliated Hospital, Yiyang, China
| | - Wenguang Liu
- Department of Pulmonary and Critical Care Medicine, Yiyang Central Hospital, Yiyang, China
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3
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Jiang J, Chen S, Yu T, Chang C, Liu J, Ren X, Niu H, Huang K, Li B, Wang C, Yang T. Dynamic analysis of gene signatures in the progression of COPD. ERJ Open Res 2023; 9:00343-2022. [PMID: 36891078 PMCID: PMC9986750 DOI: 10.1183/23120541.00343-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/06/2022] [Indexed: 11/12/2022] Open
Abstract
Aims Oxidative stress is an important amplifying mechanism in COPD; however, it is unclear how oxidative stress changes and what its exact amplification mechanism is in the pathological process. We aimed to dynamically analyse the progression of COPD and further elucidate the characteristics of each developmental stage and unveil the underlying mechanisms. Methods We performed a holistic analysis by integrating Gene Expression Omnibus microarray datasets related to smoking, emphysema and Global Initiative for Chronic Obstructive Lung Disease (GOLD) classification based on the concept of gene, environment and time (GET). Gene ontology (GO), protein-protein interaction (PPI) networks and gene set enrichment analysis (GSEA) were used to explore the changing characteristics and potential mechanisms. Lentivirus was used to promote HIF3A overexpression. Results In smokers versus nonsmokers, the GO term mainly enriched in "negative regulation of apoptotic process". In later transitions between stages, the main enriched terms were continuous progression of "oxidation-reduction process" and "cellular response to hydrogen peroxide". Logistic regression showed that these core differentially expressed genes (DEGs) had diagnostic accuracy in test (area under the curve (AUC)=0.828) and validation (AUC=0.750) sets. GSEA and PPI networks showed that one of the core DEGs, HIF3A, strongly interacted with the ubiquitin-mediated proteolysis pathway. Overexpression of HIF3A restored superoxide dismutase levels and alleviated the reactive oxygen species accumulation caused by cigarette smoke extract treatment. Conclusion Oxidative stress was continuously intensified from mild emphysema to GOLD 4; thus, special attention should be paid to the identification of emphysema. Furthermore, the downregulated HIF3A may play an important role in the intensified oxidative stress in COPD.
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Affiliation(s)
- Junchao Jiang
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,National Center for Respiratory Medicine, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Shengsong Chen
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,National Center for Respiratory Medicine, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Tao Yu
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,National Center for Respiratory Medicine, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Chenli Chang
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,National Center for Respiratory Medicine, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Jixiang Liu
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,National Center for Respiratory Medicine, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Xiaoxia Ren
- National Center for Respiratory Medicine, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Hongtao Niu
- National Center for Respiratory Medicine, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Ke Huang
- National Center for Respiratory Medicine, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Baicun Li
- National Center for Respiratory Medicine, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Chen Wang
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,National Center for Respiratory Medicine, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China.,These authors contributed equally
| | - Ting Yang
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,National Center for Respiratory Medicine, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China.,National Clinical Research Center for Respiratory Diseases, Beijing, China.,These authors contributed equally
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Mumby S, Adcock IM. Recent evidence from omic analysis for redox signalling and mitochondrial oxidative stress in COPD. J Inflamm (Lond) 2022; 19:10. [PMID: 35820851 PMCID: PMC9277949 DOI: 10.1186/s12950-022-00308-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022] Open
Abstract
COPD is driven by exogenous and endogenous oxidative stress derived from inhaled cigarette smoke, air pollution and reactive oxygen species from dysregulated mitochondria in activated inflammatory cells within the airway and lung. This is compounded by the loss in antioxidant defences including FOXO and NRF2 and other antioxidant transcription factors together with various key enzymes that attenuate oxidant effects. Oxidative stress enhances inflammation; airway remodelling including fibrosis and emphysema; post-translational protein modifications leading to autoantibody generation; DNA damage and cellular senescence. Recent studies using various omics technologies in the airways, lungs and blood of COPD patients has emphasised the importance of oxidative stress, particularly that derived from dysfunctional mitochondria in COPD and its role in immunity, inflammation, mucosal barrier function and infection. Therapeutic interventions targeting oxidative stress should overcome the deleterious pathologic effects of COPD if targeted to the lung. We require novel, more efficacious antioxidant COPD treatments among which mitochondria-targeted antioxidants and Nrf2 activators are promising.
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Su X, Wu W, Zhu Z, Lin X, Zeng Y. The effects of epithelial-mesenchymal transitions in COPD induced by cigarette smoke: an update. Respir Res 2022; 23:225. [PMID: 36045410 PMCID: PMC9429334 DOI: 10.1186/s12931-022-02153-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/25/2022] [Indexed: 12/15/2022] Open
Abstract
Cigarette smoke is a complex aerosol containing a large number of compounds with a variety of toxicity and carcinogenicity. Long-term exposure to cigarette smoke significantly increases the risk of a variety of diseases, including chronic obstructive pulmonary disease (COPD) and lung cancer. Epithelial–mesenchymal transition (EMT) is a unique biological process, that refers to epithelial cells losing their polarity and transforming into mobile mesenchymal cells, playing a crucial role in organ development, fibrosis, and cancer progression. Numerous recent studies have shown that EMT is an important pathophysiological process involved in airway fibrosis, airway remodeling, and malignant transformation of COPD. In this review, we summarized the effects of cigarette smoke on the development and progression of COPD and focus on the specific changes and underlying mechanisms of EMT in COPD induced by cigarette smoke. We spotlighted the signaling pathways involved in EMT induced by cigarette smoke and summarize the current research and treatment approaches for EMT in COPD, aiming to provide ideas for potential new treatment and research directions.
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Affiliation(s)
- Xiaoshan Su
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
| | - Weijing Wu
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
| | - Zhixing Zhu
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
| | - Xiaoping Lin
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
| | - Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China.
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Wang H, Huang L, Chen L, Ji J, Zheng Y, Wang Z. Identification of Novel Biomarkers Related to Lung Squamous Cell Carcinoma Using Integrated Bioinformatics Analysis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:9059116. [PMID: 34659450 PMCID: PMC8519687 DOI: 10.1155/2021/9059116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/18/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Lung squamous cell carcinoma (LUSC) is one of the most common types of lung carcinoma and has specific clinicopathologic characteristics. In this study, we screened novel molecular biomarkers relevant to the prognosis of LUSC to explore new diagnostic and treatment approaches for this disease. METHODS We downloaded GSE73402 from the Gene Expression Omnibus (GEO) database. GSE73402 contains 62 samples, which could be classified as four subtypes according to their pathology and stages. Via weighted gene coexpression network analysis (WGCNA), the main module was identified and was further analyzed using differentially expressed genes (DEGs) analysis. Then, by protein-protein interaction (PPI) network and Gene Expression Profiling Interactive Analysis (GEPIA), hub genes were screened for potential biomarkers of LUSC. RESULTS Via WGCNA, the yellow module containing 349 genes was identified, and it is strongly related to the subtype of CIS (carcinoma in situ). DEGs analysis detected 180 genes that expressed differentially between the subtype of CIS and subtype of early-stage carcinoma (Stage I and Stage II). A PPI network of DEGs was constructed, and the top 20 genes with the highest correlations were selected for GEPIA database to explore their effect on LUSC survival prognosis. Finally, ITGA5, TUBB3, SCNN1B, and SERPINE1 were screened as hub genes in LUSC. CONCLUSIONS ITGA5, TUBB3, SCNN1B, and SERPINE1 may have great diagnostic and prognostic significance for LUSC and have great potential to be new treatment targets for LUSC.
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Affiliation(s)
- Haiyan Wang
- Department of Ultrasonography Center, Tai'an City Central Hospital, Tai'an, China
| | - Lizhi Huang
- Department of Thoracic Surgery, Shenzhen Bao'an People's Hospital (Group), Shenzhen, China
| | - Li Chen
- Department of Vascular, Tai'an City Central Hospital, Tai'an, China
| | - Jing Ji
- Department of Geriatrics, Tai'an City Central Hospital, Tai'an, China
| | - Yuanyuan Zheng
- Department of Radiotherapy, Tai'an City Central Hospital, Tai'an, China
| | - Zhen Wang
- Department of Thoracic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
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7
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Chen T, Yasen Y, Wu J, Cheng H. Factors influencing lower respiratory tract infection in older patients after general anesthesia. J Int Med Res 2021; 49:3000605211043245. [PMID: 34521241 PMCID: PMC8447098 DOI: 10.1177/03000605211043245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Objective Pulmonary complication is common in older patients after surgery. We analyzed
risk factors of lower respiratory tract infection after general anesthesia
among older patients. Methods In this retrospective investigation, we included older patients who underwent
surgery with general anesthesia. Logistic regression analyses were performed
to determine risk factors of lower respiratory tract infection. Results A total 418 postoperative patients with general anesthesia were included; the
incidence of lower respiratory tract infection was 9.33%. Ten cases were
caused by gram-positive bacteria, 26 cases by gram-negative bacteria, and 2
cases by fungus. We found significant differences in age, smoking, diabetes,
oral/nasal tracheal intubation, and surgery duration. Logistic regression
analysis indicated that age ≥70 years (odds ratio [OR] 2.028, 95% confidence
interval [CI] 1.115–3.646), smoking (OR 2.314, 95% CI 1.073–4.229), diabetes
(OR 2.185, 95% CI 1.166–4.435), nasotracheal intubation (OR 3.528, 95% CI
1.104–5.074), and duration of surgery ≥180 minutes (OR 1.334, 95% CI
1.015–1.923) were independent risk factors of lower respiratory tract
infections. Conclusions Older patients undergoing general anesthesia after tracheal intubation have a
high risk of lower respiratory tract infections. Clinical interventions
should be provided to prevent pulmonary infections in patients with relevant
risk factors.
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Affiliation(s)
- Tingting Chen
- Department of Anesthesiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yali Yasen
- Department of Anesthesiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Jianjiang Wu
- Department of Anesthesiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Hu Cheng
- Department of Anesthesiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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Luo C, Huang B, Wu Y, Xu Y, Ou W, Chen J, Chen L. Identification of Lymph Node Metastasis-Related Key Genes and Prognostic Risk Model in Bladder Cancer by Co-Expression Analysis. Front Mol Biosci 2021; 8:633299. [PMID: 34368222 PMCID: PMC8339436 DOI: 10.3389/fmolb.2021.633299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Lymph node metastasis (LNM) is an important pathological characteristic of bladder cancer (BCa). However, the molecular mechanism underlying LNM was not thoroughly elaborated. Identification for LNM-related biomarkers may contribute to making suitable therapies. So, the current study was aimed to identify key genes and construct a prognostic signature. Methods: Based on the Cancer Genome Atlas (TCGA) database, gene expression and clinical information were obtained. Then, the weighted gene co-expression network analysis (WGCNA) was performed to identify the key modules and hub genes. A function analysis and a gene set enrichment analysis were applied to explore biological functions and pathways of interested genes. Furthermore, a prognostic model based on LNM-related genes was constructed by using the least absolute shrinkage and selection operator (LASSO) Cox regression analysis. Results: Finally, nine co-expression modules were constructed, and two modules (turquoise and green) were significantly associated with LNM. Three hub genes were identified as DACT3, TNS1, and MSRB3, which were annotated in actin binding, actin cytoskeleton, adaptive immune response, and cell adhesion molecular binding by the GSEA method. Further analysis demonstrated that three hub genes were associated with the overall survival of BCa patients. In addition, we built a prognostic signature based on the genes from LNM-related modules and evaluated the prognostic value of this signature. Conclusion: In general, this study revealed the key genes related to LNM and prognostic signature, which might provide new insights into therapeutic target of BCa.
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Affiliation(s)
- Cheng Luo
- Department of Urology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Bin Huang
- Department of Urology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yukun Wu
- Department of Urology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yadong Xu
- Department of Urology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wei Ou
- Department of Urology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Junxing Chen
- Department of Urology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Lingwu Chen
- Department of Urology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
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Zhu M, Ye M, Wang J, Ye L, Jin M. Construction of Potential miRNA-mRNA Regulatory Network in COPD Plasma by Bioinformatics Analysis. Int J Chron Obstruct Pulmon Dis 2020; 15:2135-2145. [PMID: 32982206 PMCID: PMC7490070 DOI: 10.2147/copd.s255262] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/18/2020] [Indexed: 12/14/2022] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) has become a major cause of morbidity and mortality worldwide. Increasing evidence indicates that aberrantly expressed microRNAs (miRNAs) are involved in the pathogenesis of COPD. However, an integrative exploration of miRNA–mRNA regulatory network in COPD plasma remains lacking. Methods The microarray datasets GSE24709, GSE61741, and GSE31568 were downloaded from the GEO database and analyzed using GEO2R tool to identify differentially expressed miRNAs (DEMs) between COPD and normal plasma. The consistently changing miRNAs in the three datasets were screened out as candidate DEMs. Potential upstream transcription factors and downstream target genes of candidate DEMs were predicted by FunRich and miRNet, respectively. Next, GO annotation and KEGG pathway enrichment analysis for target genes were performed using DAVID. Then, PPI and DEM-hub gene network were constructed using the STRING database and Cytoscape software. Finally, GSE56768 was used to evaluate the hub gene expressions. Results A total of nine (six upregulated and three downregulated) DEMs were screened out in the above three datasets. SP1 was predicted to potentially regulate most of the downregulated DEMs, while YY1 and E2F1 could regulate both upregulated and downregulated DEMs. 1139 target genes were then predicted, including 596 upregulated DEM target genes and 543 downregulated DEM target genes. Target genes of DEMs were mainly enriched in PI3K/Akt signaling pathway, mTOR signaling pathway, and autophagy. Through the DEM-hub gene network construction, most of the hub genes were found to be potentially modulated by miR-497-5p, miR-130b-5p, and miR-126-5p. Among the top 12 hub genes, MYC and FOXO1 expressions were consistent with that in the GSE56768 dataset. Conclusion In the study, potential miRNA–mRNA regulatory network was firstly constructed in COPD plasma, which may provide a new insight into the pathogenesis and treatment of COPD.
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Affiliation(s)
- Mengchan Zhu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Maosong Ye
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Jian Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Ling Ye
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Meiling Jin
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
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GPNMB contributes to a vicious circle for chronic obstructive pulmonary disease. Biosci Rep 2020; 40:225097. [PMID: 32478378 PMCID: PMC7308735 DOI: 10.1042/bsr20194459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 05/15/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022] Open
Abstract
Osteoporosis (OP) is significant and debilitating comorbidity of chronic obstructive pulmonary disease (COPD). We hypothesize that genetic variance identified with OP may also play roles in COPD. We have conducted a large-scale relation data analysis to explore the genes implicated with either OP or COPD, or both. Each gene linked to OP but not to COPD was further explored in a mega-analysis and partial mega-analysis of 15 independently collected COPD RNA expression datasets, followed by gene set enrichment analysis (GSEA) and literature-based pathway analysis to explore their functional linked to COPD. A multiple linear regression (MLR) model was built to study the possible influence of sample size, population region, and study date on the gene expression data in COPD. At the first step of the analysis, we have identified 918 genes associated with COPD, 581 with OP, and a significant overlap (P<2.30e-140; 210 overlapped genes). Partial mega-analysis showed that, one OP gene, GPNMB presented significantly increased expression in COPD patients (P-value = 0.0018; log fold change = 0.83). GPNMB was enriched in multiple COPD pathways and plays roles as a gene hub formulating multiple vicious COPD pathways included gene MMP9 and MYC. GPNMB could be a novel gene that plays roles in both COPD and OP. Partial mega-analysis is valuable in identify case-specific genes for COPD.
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Sun X, Shang J, Wu A, Xia J, Xu F. Identification of dynamic signatures associated with smoking-related squamous cell lung cancer and chronic obstructive pulmonary disease. J Cell Mol Med 2019; 24:1614-1625. [PMID: 31829519 PMCID: PMC6991676 DOI: 10.1111/jcmm.14852] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 08/27/2019] [Accepted: 09/05/2019] [Indexed: 01/09/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a risk factor for the development of lung cancer. The aim of this study was to identify early diagnosis biomarkers for lung squamous cell carcinoma (SQCC) in COPD patients and to determine the potential pathogenetic mechanisms. The GSE12472 data set was downloaded from the Gene Expression Omnibus database. Differentially co‐expressed links (DLs) and differentially expressed genes (DEGs) in both COPD and normal tissues, or in both SQCC + COPD and COPD samples were used to construct a dynamic network associated with high‐risk genes for the SQCC pathogenetic process. Enrichment analysis was performed based on Gene Ontology annotations and Kyoto Encyclopedia of Genes and Genomes pathway analysis. We used the gene expression data and the clinical information to identify the co‐expression modules based on weighted gene co‐expression network analysis (WGCNA). In total, 205 dynamic DEGs, 5034 DLs and one pathway including CDKN1A, TP53, RB1 and MYC were found to have correlations with the pathogenetic progress. The pathogenetic mechanisms shared by both SQCC and COPD are closely related to oxidative stress, the immune response and infection. WGCNA identified 11 co‐expression modules, where magenta and black were correlated with the “time to distant metastasis.” And the “surgery due to” was closely related to the brown and blue modules. In conclusion, a pathway that includes TP53, CDKN1A, RB1 and MYC may play a vital role in driving COPD towards SQCC. Inflammatory processes and the immune response participate in COPD‐related carcinogenesis.
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Affiliation(s)
- Xiaoru Sun
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingzhe Shang
- Center of Systems Medicine, Chinese Academy of Medical Science (CAMS), Suzhou Institute of System Medicine, Suzhou, China
| | - Aiping Wu
- Center of Systems Medicine, Chinese Academy of Medical Science (CAMS), Suzhou Institute of System Medicine, Suzhou, China
| | - Jingyan Xia
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Feng Xu
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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