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Yuan M, Hu X, Xing W, Wu X, Pu C, Guo W, Zhu X, Yao M, Ao L, Li Z, Xu X. B2M is a Biomarker Associated With Immune Infiltration In High Altitude Pulmonary Edema. Comb Chem High Throughput Screen 2024; 27:168-185. [PMID: 37165489 PMCID: PMC10804239 DOI: 10.2174/1386207326666230510095840] [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: 01/18/2023] [Revised: 03/15/2023] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND High altitude pulmonary edema (HAPE) is a serious mountain sickness with certain mortality. Its early diagnosis is very important. However, the mechanism of its onset and progression is still controversial. AIM This study aimed to analyze the HAPE occurrence and development mechanism and search for prospective biomarkers in peripheral blood. METHODS The difference genes (DEGs) of the Control group and the HAPE group were enriched by gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and then GSEA analysis was performed. After identifying the immune-related hub genes, QPCR was used to verify and analyze the hub gene function and diagnostic value with single-gene GSEA and ROC curves, and the drugs that acted on the hub gene was found in the CTD database. Immune infiltration and its association with the hub genes were analyzed using CIBERSORT. Finally, WGCNA was employed to investigate immune invasion cells' significantly related gene modules, following enrichment analysis of their GO and KEGG. RESULTS The dataset enrichment analysis, immune invasion analysis and WGCNA analysis showed that the occurrence and early progression of HAPE were unrelated to inflammation. The hub genes associated with immunity obtained with MCODE algorithm of Cytoscape were JAK2 and B2M.. RT-qPCR and ROC curves confirmed that the hub gene B2M was a specific biomarker of HAPE and had diagnostic value, and single-gene GSEA analysis confirmed that it participated in MHC I molecule-mediated antigen presentation ability decreased, resulting in reduced immunity. CONCLUSION Occurrence and early progression of high altitude pulmonary edema may not be related to inflammation. B2M may be a new clinical potential biomarker for HAPE for early diagnosis and therapeutic evaluation as well as therapeutic targets, and its decrease may be related to reduced immunity due to reduced ability of MCH I to participate in antigen submission.
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Affiliation(s)
- Mu Yuan
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Xueting Hu
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Wei Xing
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Xiaofeng Wu
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Chengxiu Pu
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Wei Guo
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Xiyan Zhu
- Department of Military Traffic Injury Prevention and Treatment, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Mengwei Yao
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Luoquan Ao
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Zhan Li
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Xiang Xu
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
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Yu F, Luo W, Xie W, Li Y, Meng S, Kan J, Ye X, Peng T, Wang H, Huang T, Hu Z. Community reassemblies of eukaryotes, prokaryotes, and viruses in the hexabromocyclododecanes-contaminated microcosms. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129159. [PMID: 35643009 DOI: 10.1016/j.jhazmat.2022.129159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/28/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The microbial community in seriously contaminated environment were not well known. This research investigated the community reassemblies in microcosms made of two distinct mangrove sediments amended with high levels of hexabromocyclododecanes (HBCDs). After eight months of contamination, the transformation of HBCDs yielded various lower brominated products and resulted in acidification (pH ~2). Therefore, the degraders and dehalogenase homologous genes involved in transformation of HBCDs only presented in low abundance to avoid further deterioration of the habitats. Moreover, in these deteriorated habitats, 1344 bacterial, 969 archaeal, 599 eukaryotic (excluded fungi), 187 fungal OTUs, and 10 viral genera, were reduced compared with controls. Specifically, in two groups of microcosms, Zetaproteobacteria, Deinococcus-Thermus, Spirochaetes, Bacteroidetes, Euryarchaeota, and Ascomycota, were positively responding taxa to HBCDs. Caloneis (Bacillariophyta) and Ascomycota turned to the dominant eukaryotic and fungal taxa. Most of predominant taxa were related to the contamination of brominated flame retardants (BFRs). Microbial communities were reassembled in divergent and sediment-dependent manner. The long-term contamination of HBCDs leaded to the change of relations between many taxa, included some of the environmental viruses and their known hosts. This research highlight the importance of monitoring the ecological effects around plants producing or processing halogenated compounds.
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Affiliation(s)
- Fei Yu
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Wenqi Luo
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Wei Xie
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Yuyang Li
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Shanshan Meng
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Jie Kan
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Xueying Ye
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Tao Peng
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Hui Wang
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Tongwang Huang
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, PR China.
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Guo SZ, Liu WJ. Constructing differential co-expression network to predict key pathways for myocardial infarction. Exp Ther Med 2019; 17:3029-3034. [PMID: 30936974 PMCID: PMC6434241 DOI: 10.3892/etm.2019.7321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 02/05/2019] [Indexed: 12/27/2022] Open
Abstract
New thoughts are warranted to develop efficient diagnosis and optimal therapeutics to combat unstable angina (UA)/myocardial infarction (MI). Therefore, the gene data of patients with UA or MI were used in this study to identify the optimal pathways which can provide comprehensive information for UA/MI development. Differentially expressed genes (DEGs) between UA and MI were detected using LIMMA package, and pathway enrichment analysis was conducted for the DEGs, based on the DAVID tool, to detect the significant pathways. Then, differential co-expression network (DCN) and sub-DCN for the DEGs were constructed. Subsequently, informative pathways were extracted using guilt-by-association (GBA) principle relying on the area under the curve (AUC), and the pathway categories with AUC >0.8 were defined as the informative pathways. Finally, we selected the optimal pathways based on the traditional pathway analysis and the sub-DCN-based-GBA pathway prediction method. A total of 203 and 266 DEGs were identified from the expression profile of blood of MI samples comparing with UAs in the time-point 1 and time-point 2 groups. Moreover, 7 and 10 informative pathway terms were identified based on AUC>0.8. Significantly, cytokine-cytokine receptor interaction, as well as MAPK signaling pathway were the common optimal pathways in the two groups. Calcium signaling pathway was unique to the whole blood of patients with acute coronary syndrome (ACS) taken at 30 days post-ACS. In conclusion, the optimal pathways (MAPK signaling pathway, cytokine-cytokine receptor interaction, and calcium signaling pathway) might play important roles in the progression of UA/MI.
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Affiliation(s)
- Su-Zhen Guo
- Department of Cardiology, Tianjin First Central Hospital, Tianjin 300192, P.R. China
| | - Wen-Jie Liu
- Department of Geriatrics, Chendong Hospital, Quanzhou First Hospital, Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
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Hu S, Zuo H, Qi J, Hu Y, Yu B. Analysis of Effect of Schisandra in the Treatment of Myocardial Infarction Based on Three-Mode Gene Ontology Network. Front Pharmacol 2019; 10:232. [PMID: 30949047 PMCID: PMC6435518 DOI: 10.3389/fphar.2019.00232] [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: 10/16/2018] [Accepted: 02/22/2019] [Indexed: 12/31/2022] Open
Abstract
Schisandra chinensis is a commonly used traditional Chinese medicine, which has been widely used in the treatment of acute myocardial infarction in China. However, it has been difficult to systematically clarify the major pharmacological effect of Schisandra, due to its multi-component complex mechanism. In order to solve this problem, a comprehensive network analysis method was established based-on “component–gene ontology–effect” interactions. Through the network analysis, reduction of cardiac preload and myocardial contractility was shown to be the major effect of Schisandra components, which was further experimentally validated. In addition, the expression of NCOR2 and NFAT in myocyte were experimentally confirmed to be associated with Schisandra in the treatment of AMI, which may be responsible for the preservation effect of myocardial contractility. In conclusion, the three-mode gene ontology network can be an effective network analysis workflow to evaluate the pharmacological effects of a multi-drug complex system.
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Affiliation(s)
- Siyao Hu
- Jiangsu Key Laboratory of Traditional Medicine and Translational Research, China Pharmaceutical University, Nanjing, China
| | - Huali Zuo
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau
| | - Jin Qi
- Jiangsu Key Laboratory of Traditional Medicine and Translational Research, China Pharmaceutical University, Nanjing, China
| | - Yuanjia Hu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau
| | - Boyang Yu
- Jiangsu Key Laboratory of Traditional Medicine and Translational Research, China Pharmaceutical University, Nanjing, China
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