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Dong W, Jin Y, Shi H, Zhang X, Chen J, Jia H, Zhang Y. Using bioinformatics and systems biology methods to identify the mechanism of interaction between COVID-19 and nonalcoholic fatty liver disease. Medicine (Baltimore) 2023; 102:e33912. [PMID: 37335656 DOI: 10.1097/md.0000000000033912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is considered a risk factor for severe COVID-19, but the mechanism remains unknown. This study used bioinformatics to help define the relationship between these diseases. The GSE147507 (COVID-19), GSE126848 (NAFLD), and GSE63067 (NAFLD-2) datasets were screened using the Gene Expression Omnibus. Common differentially expressed genes were then identified using a Venn diagram. Gene ontology analysis and KEGG pathway enrichment were performed on the differentially expressed genes. A protein-protein interaction network was also constructed using the STRING platform, and key genes were identified using the Cytoscape plugin. GES63067 was selected for validation of the results. Analysis of ferroptosis gene expression during the development of the 2 diseases and prediction of their upstream miRNAs and lncRNAs. In addition, transcription factors (TFs) and miRNAs related to key genes were identified. Effective drugs that act on target genes were found in the DSigDB. The GSE147507 and GSE126848 datasets were crossed to obtain 28 co-regulated genes, 22 gene ontology terms, 3 KEGG pathways, and 10 key genes. NAFLD may affect COVID-19 progression through immune function and inflammatory signaling pathways. CYBB was predicted to be a differential ferroptosis gene associated with 2 diseases, and the CYBB-hsa-miR-196a/b-5p-TUG1 regulatory axis was identified. TF-gene interactions and TF-miRNA coregulatory network were constructed successfully. A total of 10 drugs, (such as Eckol, sulfinpyrazone, and phenylbutazone) were considered as target drugs for Patients with COVID-19 and NAFLD. This study identified key gene and defined molecular mechanisms associated with the progression of COVID-19 and NAFLD. COVID-19 and NAFLD progression may regulate ferroptosis through the CYBB-hsa-miR-196a/b-5p-TUG1 axis. This study provides additional drug options for the treatment of COVID-19 combined with NAFLD disease.
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Affiliation(s)
- Wenbo Dong
- Shandong Traditional Chinese Medicine University, Jinan, China
| | - Yan Jin
- Shandong Traditional Chinese Medicine University, Jinan, China
| | - Hongshuo Shi
- Shandong Traditional Chinese Medicine University, Jinan, China
| | | | - Jinshu Chen
- Shandong Traditional Chinese Medicine University, Jinan, China
| | - Hongling Jia
- The Second Affiliated Hospital of Shandong University of Chinese Medicine, Jinan, China
| | - Yongchen Zhang
- Shandong Traditional Chinese Medicine University, Jinan, China
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
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Zou M, Su X, Wang L, Yi X, Qiu Y, Yin X, Zhou X, Niu X, Wang L, Su M. The Molecular Mechanism of Multiple Organ Dysfunction and Targeted Intervention of COVID-19 Based on Time-Order Transcriptomic Analysis. Front Immunol 2021; 12:729776. [PMID: 34504502 PMCID: PMC8421734 DOI: 10.3389/fimmu.2021.729776] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/04/2021] [Indexed: 12/22/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic is caused by the novel coronavirus that has spread rapidly around the world, leading to high mortality because of multiple organ dysfunction; however, its underlying molecular mechanism is unknown. To determine the molecular mechanism of multiple organ dysfunction, a bioinformatics analysis method based on a time-order gene co-expression network (TO-GCN) was performed. First, gene expression profiles were downloaded from the gene expression omnibus database (GSE161200), and a TO-GCN was constructed using the breadth-first search (BFS) algorithm to infer the pattern of changes in the different organs over time. Second, Gene Ontology enrichment analysis was used to analyze the main biological processes related to COVID-19. The initial gene modules for the immune response of different organs were defined as the research object. The STRING database was used to construct a protein-protein interaction network of immune genes in different organs. The PageRank algorithm was used to identify five hub genes in each organ. Finally, the Comparative Toxicogenomics Database played an important role in exploring the potential compounds that target the hub genes. The results showed that there were two types of biological processes: the body's stress response and cell-mediated immune response involving the lung, trachea, and olfactory bulb (olf) after being infected by COVID-19. However, a unique biological process related to the stress response is the regulation of neuronal signals in the brain. The stress response was heterogeneous among different organs. In the lung, the regulation of DNA morphology, angiogenesis, and mitochondrial-related energy metabolism are specific biological processes related to the stress response. In particular, an effect on tracheal stress response was made by the regulation of protein metabolism and rRNA metabolism-related biological processes, as biological processes. In the olf, the distinctive stress responses consist of neural signal transmission and brain behavior. In addition, myeloid leukocyte activation and myeloid leukocyte-mediated immunity in response to COVID-19 can lead to a cytokine storm. Immune genes such as SRC, RHOA, CD40LG, CSF1, TNFRSF1A, FCER1G, ICAM1, LAT, LCN2, PLAU, CXCL10, ICAM1, CD40, IRF7, and B2M were predicted to be the hub genes in the cytokine storm. Furthermore, we inferred that resveratrol, acetaminophen, dexamethasone, estradiol, statins, curcumin, and other compounds are potential target drugs in the treatment of COVID-19.
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Affiliation(s)
- Miao Zou
- Department of Regenerative Medicine, School of Pharmaceutical Sciences, Jilin University, ChangChun, China
| | - Xiaoyun Su
- Department of Regenerative Medicine, School of Pharmaceutical Sciences, Jilin University, ChangChun, China
| | - Luoying Wang
- Department of Regenerative Medicine, School of Pharmaceutical Sciences, Jilin University, ChangChun, China
| | - Xingcheng Yi
- Department of Regenerative Medicine, School of Pharmaceutical Sciences, Jilin University, ChangChun, China
| | - Yue Qiu
- Department of Regenerative Medicine, School of Pharmaceutical Sciences, Jilin University, ChangChun, China
| | - Xirui Yin
- Department of Regenerative Medicine, School of Pharmaceutical Sciences, Jilin University, ChangChun, China
| | - Xuan Zhou
- Department of Regenerative Medicine, School of Pharmaceutical Sciences, Jilin University, ChangChun, China
| | - Xinhui Niu
- Department of Regenerative Medicine, School of Pharmaceutical Sciences, Jilin University, ChangChun, China
| | - Liuli Wang
- Department of Regenerative Medicine, School of Pharmaceutical Sciences, Jilin University, ChangChun, China
| | - Manman Su
- Department of Regenerative Medicine, School of Pharmaceutical Sciences, Jilin University, ChangChun, China
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Yuan W, Yan J, Liu H, Li L, Wu B, Guo C, Zhang M. Identification of Prognostic Related Genes of Tumor Microenvironment Derived From Esophageal Cancer Patients. Pathol Oncol Res 2021; 27:589662. [PMID: 34257539 PMCID: PMC8262216 DOI: 10.3389/pore.2021.589662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 03/05/2021] [Indexed: 12/29/2022]
Abstract
Background and Objective: Esophageal cancer (ESCA) is a commonly occurring cancer worldwide with poor survival and limited therapeutic options. Due to the lack of biomarkers that facilitate early detection, its treatment remains a great challenge. This study aims at identifying the tumor microenvironment (TME)-related genes, which might affect prognosis and accelerate clinical treatment for ESCA patients. Methods: We integrated the expression profiles from ESCA patients in The Cancer Genome Atlas. Then, we determined the stromal and immune scores of each sample using the R package. The Gene Expression Omnibus database was used to validate the expression profile of the key genes. Results: Tumor mutational burden showed a significant difference between the groups of ESCA patients with high and low ESTIMATE scores. We identified 859 intersection genes among patients with different immune and stromal scores. Moreover, gene ontology analysis demonstrated that these 859 intersection genes were closely related to adaptive immune response and regulation of lymphocyte activation. Kyoto Encyclopedia of Genes and Genomes showed the enrichment of cytokine-cytokine receptor interaction and chemokine signaling pathway in the TME. Furthermore, the protein–protein interaction network consisted of 175 nodes. We selected 35 hub genes, including ITGAM, CXCL10, CCR2, CCR5, and CCR1. Of these, 23 intersection genes predicted the overall survival rate. C1QA and FCER1G correlated with overall survival of the ESCA patients in the two databases. Conclusion: We identified a set of stromal and immune score-related prognostic differentially expressed genes that could influence the complexity of the TME. C1QA and FCER1G were identified and validated with respect to their role in the progression of ESCA.
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Affiliation(s)
- Wei Yuan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jiaqin Yan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongtao Liu
- College of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Ling Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - BoWen Wu
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Can Guo
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Mingzhi Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Dang D, Taheri S, Das S, Ghosh P, Prince LS, Sahoo D. Computational Approach to Identifying Universal Macrophage Biomarkers. Front Physiol 2020; 11:275. [PMID: 32322218 PMCID: PMC7156600 DOI: 10.3389/fphys.2020.00275] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 03/10/2020] [Indexed: 12/11/2022] Open
Abstract
Macrophages engulf and digest microbes, cellular debris, and various disease-associated cells throughout the body. Understanding the dynamics of macrophage gene expression is crucial for studying human diseases. As both bulk RNAseq and single cell RNAseq datasets become more numerous and complex, identifying a universal and reliable marker of macrophage cell becomes paramount. Traditional approaches have relied upon tissue specific expression patterns. To identify universal biomarkers of macrophage, we used a previously published computational approach called BECC (Boolean Equivalent Correlated Clusters) that was originally used to identify conserved cell cycle genes. We performed BECC analysis using the known macrophage marker CD14 as a seed gene. The main idea behind BECC is that it uses massive database of public gene expression dataset to establish robust co-expression patterns identified using a combination of correlation, linear regression and Boolean equivalences. Our analysis identified and validated FCER1G and TYROBP as novel universal biomarkers for macrophages in human and mouse tissues.
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Affiliation(s)
- Dharanidhar Dang
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, United States.,Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
| | - Sahar Taheri
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, United States
| | - Soumita Das
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Pradipta Ghosh
- Departments of Medicine and Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States.,Moores Cancer Center, San Diego, CA, United States
| | - Lawrence S Prince
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States.,Rady Children's Hospital, San Diego, CA, United States
| | - Debashis Sahoo
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, United States.,Department of Pediatrics, University of California, San Diego, San Diego, CA, United States.,Moores Cancer Center, San Diego, CA, United States
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Eggel A, Baumann MJ, Amstutz P, Stadler BM, Vogel M. DARPins as bispecific receptor antagonists analyzed for immunoglobulin E receptor blockage. J Mol Biol 2009; 393:598-607. [PMID: 19683003 DOI: 10.1016/j.jmb.2009.08.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 08/06/2009] [Accepted: 08/07/2009] [Indexed: 10/20/2022]
Abstract
The concept of multispecific antibodies is of high therapeutic interest but has failed to produce pharmaceutical products due to the poor biophysical properties of such molecules. Here, we propose an alternative and simple way to generate bispecific binding molecules using designed ankyrin repeat proteins (DARPins). For this purpose, monovalent DARPins with different epitope specificities were selected against the alpha chain of the high-affinity receptor for human immunoglobulin E (IgE) (FcepsilonRIalpha). Two of the isolated binders interfering with IgE binding to the receptor were joined to each other or to themselves via a flexible protein linker. The resulting bivalent and bispecific DARPins were tested for their ability to prevent allergen-induced cell degranulation using rat basophilic leukemia cells stably transfected with human FcepsilonRIalpha. The bispecific DARPin construct was the most potent one, efficiently blocking the IgE-FcepsilonRI interaction and preventing the release of proinflammatory mediators. Noteworthy, the multivalent and multispecific DARPin construct did not show any alteration of the beneficial biophysical properties of the monovalent parental DARPins. Hence, bispecific DARPins may be used to generate receptor antagonists simultaneously targeting different epitopes on the same molecule. Moreover, they easily overcome the limiting immunoglobulin binding paradigm (one binding molecule=one epitope) and thereby represent an alternative to monoclonal antibodies in cases where the immunoglobulin scaffold is unsuitable.
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Affiliation(s)
- Alexander Eggel
- Institute of Immunology, University of Bern, Inselspital, Sahlihaus 2, Bern, Switzerland
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Hopkin J, Cookson W. Genetic variation in the beta subunit of the high affinity IgE receptor and atopy and asthma. Clin Exp Allergy 2007; 36:855-7. [PMID: 16839398 DOI: 10.1111/j.1365-2222.2006.02535.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Chu KH, Tang CY, Wu A, Leung PSC. Seafood allergy: lessons from clinical symptoms, immunological mechanisms and molecular biology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2005; 97:205-35. [PMID: 16261809 DOI: 10.1007/b135827] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Food allergy consists of a wide range of disorders that result from adverse immune responses to dietary antigens. Manifestations of allergic response includes acute, potentially fatal anaphylactic reactions and a variety of chronic diseases that mainly affect the gastrointestinal tract, skin, and respiratory tract. Tools for clinical diagnosis and management, which have not changed much in the past two decades, include the clinical history, tests for specific IgE antibody to suspected foods, elimination diets, oral food challenges, and provision of medications such as epinephrine for emergency treatment. On the other hand, recent immunological and molecular biological research have enhanced our understanding of the mechanisms of these disorders and revealed the identities of many food allergens. Here, we will discuss seafood allergies with respect to the clinical manifestations, diagnosis, immunological mechanisms, and molecular biology of seafood allergens. Furthermore, potential applications and future directions in the clinical management of seafood allergies are discussed.
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Affiliation(s)
- Ka Hou Chu
- Department of Biology, The Chinese University of Hong Kong, Hong Kong, China
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