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Mao Y, Hou X, Fu S, Luan J. Transcriptomic and machine learning analyses identify hub genes of metabolism and host immune response that are associated with the progression of breast capsular contracture. Genes Dis 2024; 11:101087. [PMID: 38292203 PMCID: PMC10825289 DOI: 10.1016/j.gendis.2023.101087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/03/2023] [Accepted: 08/16/2023] [Indexed: 02/01/2024] Open
Abstract
Capsular contracture is a prevalent and severe complication that affects the postoperative outcomes of patients who receive silicone breast implants. At present, prosthesis replacement is the major treatment for capsular contracture after both breast augmentation procedures and breast reconstruction following breast cancer surgery. However, the mechanism(s) underlying breast capsular contracture remains unclear. This study aimed to identify the biological features of breast capsular contracture and reveal the potential underlying mechanism using RNA sequencing. Sample tissues from 12 female patients (15 breast capsules) were divided into low capsular contracture (LCC) and high capsular contracture (HCC) groups based on the Baker grades. Subsequently, 41 lipid metabolism-related genes were identified through enrichment analysis, and three of these genes were identified as candidate genes by SVM-RFE and LASSO algorithms. We then compared the proportions of the 22 types of immune cells between the LCC and HCC groups using a CIBERSORT analysis and explored the correlation between the candidate hub features and immune cells. Notably, PRKAR2B was positively correlated with the differentially clustered immune cells, which were M1 macrophages and follicular helper T cells (area under the ROC = 0.786). In addition, the expression of PRKAR2B at the mRNA or protein level was lower in the HCC group than in the LCC group. Potential molecular mechanisms were identified based on the expression levels in the high and low PRKAR2B groups. Our findings indicate that PRKAR2B is a novel diagnostic biomarker for breast capsular contracture and might also influence the grade and progression of capsular contracture.
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Affiliation(s)
- Yukun Mao
- Breast Plastic and Reconstructive Surgery Center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100144, China
| | - Xueying Hou
- Breast Plastic and Reconstructive Surgery Center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100144, China
| | - Su Fu
- Breast Plastic and Reconstructive Surgery Center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100144, China
| | - Jie Luan
- Breast Plastic and Reconstructive Surgery Center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100144, China
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Noor F, Ashfaq UA, Bakar A, ul Haq W, Allemailem KS, Alharbi BF, Al-Megrin WAI, Tahir ul Qamar M. Discovering common pathogenic processes between COVID-19 and HFRS by integrating RNA-seq differential expression analysis with machine learning. Front Microbiol 2023; 14:1175844. [PMID: 37234545 PMCID: PMC10208410 DOI: 10.3389/fmicb.2023.1175844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/29/2023] [Indexed: 05/28/2023] Open
Abstract
Zoonotic virus spillover in human hosts including outbreaks of Hantavirus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) imposes a serious impact on the quality of life of patients. Recent studies provide a shred of evidence that patients with Hantavirus-caused hemorrhagic fever with renal syndrome (HFRS) are at risk of contracting SARS-CoV-2. Both RNA viruses shared a higher degree of clinical features similarity including dry cough, high fever, shortness of breath, and certain reported cases with multiple organ failure. However, there is currently no validated treatment option to tackle this global concern. This study is attributed to the identification of common genes and perturbed pathways by combining differential expression analysis with bioinformatics and machine learning approaches. Initially, the transcriptomic data of hantavirus-infected peripheral blood mononuclear cells (PBMCs) and SARS-CoV-2 infected PBMCs were analyzed through differential gene expression analysis for identification of common differentially expressed genes (DEGs). The functional annotation by enrichment analysis of common genes demonstrated immune and inflammatory response biological processes enriched by DEGs. The protein-protein interaction (PPI) network of DEGs was then constructed and six genes named RAD51, ALDH1A1, UBA52, CUL3, GADD45B, and CDKN1A were identified as the commonly dysregulated hub genes among HFRS and COVID-19. Later, the classification performance of these hub genes were evaluated using Random Forest (RF), Poisson Linear Discriminant Analysis (PLDA), Voom-based Nearest Shrunken Centroids (voomNSC), and Support Vector Machine (SVM) classifiers which demonstrated accuracy >70%, suggesting the biomarker potential of the hub genes. To our knowledge, this is the first study that unveiled biological processes and pathways commonly dysregulated in HFRS and COVID-19, which could be in the next future used for the design of personalized treatment to prevent the linked attacks of COVID-19 and HFRS.
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Affiliation(s)
- Fatima Noor
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Abu Bakar
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Waqar ul Haq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Basmah F. Alharbi
- Department of Basic Health Science, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Wafa Abdullah I. Al-Megrin
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Muhammad Tahir ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
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Jahanimoghadam A, Abdolahzadeh H, Rad NK, Zahiri J. Discovering Common Pathogenic Mechanisms of COVID-19 and Parkinson Disease: An Integrated Bioinformatics Analysis. J Mol Neurosci 2022; 72:2326-2337. [PMID: 36301487 PMCID: PMC9607846 DOI: 10.1007/s12031-022-02068-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 09/13/2022] [Indexed: 12/14/2022]
Abstract
Coronavirus disease 2019 (COVID-19) has emerged since December 2019 and was later characterized as a pandemic by WHO, imposing a major public health threat globally. Our study aimed to identify common signatures from different biological levels to enlighten the current unclear association between COVID-19 and Parkinson's disease (PD) as a number of possible links, and hypotheses were reported in the literature. We have analyzed transcriptome data from peripheral blood mononuclear cells (PBMCs) of both COVID-19 and PD patients, resulting in a total of 81 common differentially expressed genes (DEGs). The functional enrichment analysis of common DEGs are mostly involved in the complement system, type II interferon gamma (IFNG) signaling pathway, oxidative damage, microglia pathogen phagocytosis pathway, and GABAergic synapse. The protein-protein interaction network (PPIN) construction was carried out followed by hub detection, revealing 10 hub genes (MX1, IFI27, C1QC, C1QA, IFI6, NFIX, C1S, XAF1, IFI35, and ELANE). Some of the hub genes were associated with molecular mechanisms such as Lewy bodies-induced inflammation, microglia activation, and cytokine storm. We investigated regulatory elements of hub genes at transcription factor and miRNA levels. The major transcription factors regulating hub genes are SOX2, XAF1, RUNX1, MITF, and SPI1. We propose that these events may have important roles in the onset or progression of PD. To sum up, our analysis describes possible mechanisms linking COVID-19 and PD, elucidating some unknown clues in between.
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Affiliation(s)
- Aria Jahanimoghadam
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, Würzburg, Germany
| | - Hadis Abdolahzadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Niloofar Khoshdel Rad
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Javad Zahiri
- Department of Neuroscience, University of California San Diego, La Jolla, San Diego, CA, USA.
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Network-Based Data Analysis Reveals Ion Channel-Related Gene Features in COVID-19: A Bioinformatic Approach. Biochem Genet 2022; 61:471-505. [PMID: 36104591 PMCID: PMC9473477 DOI: 10.1007/s10528-022-10280-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 09/01/2022] [Indexed: 11/02/2022]
Abstract
Coronavirus disease 2019 (COVID-19) seriously threatens human health and has been disseminated worldwide. Although there are several treatments for COVID-19, its control is currently suboptimal. Therefore, the development of novel strategies to treat COVID-19 is necessary. Ion channels are located on the membranes of all excitable cells and many intracellular organelles and are key components involved in various biological processes. They are a target of interest when searching for drug targets. This study aimed to reveal the relevant molecular features of ion channel genes in COVID-19 based on bioinformatic analyses. The RNA-sequencing data of patients with COVID-19 and healthy subjects (GSE152418 and GSE171110 datasets) were obtained from the Gene Expression Omnibus (GEO) database. Ion channel genes were selected from the Hugo Gene Nomenclature Committee (HGNC) database. The RStudio software was used to process the data based on the corresponding R language package to identify ion channel-associated differentially expressed genes (DEGs). Based on the DEGs, Gene Ontology (GO) functional and pathway enrichment analyses were performed using the Enrichr web tool. The STRING database was used to generate a protein-protein interaction (PPI) network, and the Cytoscape software was used to screen for hub genes in the PPI network based on the cytoHubba plug-in. Transcription factors (TF)-DEG, DEG-microRNA (miRNA) and DEG-disease association networks were constructed using the NetworkAnalyst web tool. Finally, the screened hub genes as drug targets were subjected to enrichment analysis based on the DSigDB using the Enrichr web tool to identify potential therapeutic agents for COVID-19. A total of 29 ion channel-associated DEGs were identified. GO functional analysis showed that the DEGs were integral components of the plasma membrane and were mainly involved in inorganic cation transmembrane transport and ion channel activity functions. Pathway analysis showed that the DEGs were mainly involved in nicotine addiction, calcium regulation in the cardiac cell and neuronal system pathways. The top 10 hub genes screened based on the PPI network included KCNA2, KCNJ4, CACNA1A, CACNA1E, NALCN, KCNA5, CACNA2D1, TRPC1, TRPM3 and KCNN3. The TF-DEG and DEG-miRNA networks revealed significant TFs (FOXC1, GATA2, HINFP, USF2, JUN and NFKB1) and miRNAs (hsa-mir-146a-5p, hsa-mir-27a-3p, hsa-mir-335-5p, hsa-let-7b-5p and hsa-mir-129-2-3p). Gene-disease association network analysis revealed that the DEGs were closely associated with intellectual disability and cerebellar ataxia. Drug-target enrichment analysis showed that the relevant drugs targeting the hub genes CACNA2D1, CACNA1A, CACNA1E, KCNA2 and KCNA5 were gabapentin, gabapentin enacarbil, pregabalin, guanidine hydrochloride and 4-aminopyridine. The results of this study provide a valuable basis for exploring the mechanisms of ion channel genes in COVID-19 and clues for developing therapeutic strategies for COVID-19.
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Li XY, Wang JB, An HB, Wen MZ, You JX, Yang XT. Effect of SARS-CoV-2 infection on asthma patients. Front Med (Lausanne) 2022; 9:928637. [PMID: 35983093 PMCID: PMC9378965 DOI: 10.3389/fmed.2022.928637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundSARS-CoV-2 causes coronavirus disease 2019 (COVID-19), a new coronavirus pneumonia, and containing such an international pandemic catastrophe remains exceedingly difficult. Asthma is a severe chronic inflammatory airway disease that is becoming more common around the world. However, the link between asthma and COVID-19 remains unknown. Through bioinformatics analysis, this study attempted to understand the molecular pathways and discover potential medicines for treating COVID-19 and asthma.MethodsTo investigate the relationship between SARS-CoV-2 and asthma patients, a transcriptome analysis was used to discover shared pathways and molecular signatures in asthma and COVID-19. Here, two RNA-seq data (GSE147507 and GSE74986) from the Gene Expression Omnibus were used to detect differentially expressed genes (DEGs) in asthma and COVID-19 patients to find the shared pathways and the potential drug candidates.ResultsThere were 66 DEGs in all that were classified as common DEGs. Using a protein-protein interaction (PPI) network created using various bioinformatics techniques, five hub genes were found. We found that asthma has some shared links with the progression of COVID-19. Additionally, protein-drug interactions with common DEGs were also identified in the datasets.ConclusionWe investigated possible links between COVID-19 and asthma using bioinformatics databases, which might be useful in treating COVID-19 patients. More studies on populations affected by these diseases are needed to elucidate the molecular mechanism behind their association.
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Affiliation(s)
- Xin-yu Li
- Department of Interventional Therapy, Multidisciplinary Team of Vascular Anomalies, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- Department of Neurosurgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jing-bing Wang
- Department of Interventional Therapy, Multidisciplinary Team of Vascular Anomalies, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Hong-bang An
- Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Ming-zhe Wen
- Department of Interventional Therapy, Multidisciplinary Team of Vascular Anomalies, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jian-xiong You
- Department of Interventional Therapy, Multidisciplinary Team of Vascular Anomalies, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xi-tao Yang
- Department of Interventional Therapy, Multidisciplinary Team of Vascular Anomalies, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Xi-tao Yang,
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Huang J, Wang Y, Zha Y, Zeng X, Li W, Zhou M. Transcriptome Analysis Reveals Hub Genes Regulating Autophagy in Patients With Severe COVID-19. Front Genet 2022; 13:908826. [PMID: 35923698 PMCID: PMC9340158 DOI: 10.3389/fgene.2022.908826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 11/21/2022] Open
Abstract
Background: The COVID-19 pandemic has currently developed into a worldwide threat to humankind. Importantly, patients with severe COVID-19 are believed to have a higher mortality risk than those with mild conditions. However, despite the urgent need to develop novel therapeutic strategies, the biological features and pathogenic mechanisms of severe COVID-19 are poorly understood. Methods: Here, peripheral blood mononuclear cells (PBMCs) from four patients with severe COVID-19, four patients with mild COVID-19, and four healthy controls were examined by RNA sequencing (RNA-Seq). We conducted gene expression analysis and Venn diagrams to detect specific differentially expressed genes (DEGs) in patients with severe disease compared with those with mild conditions. Gene Ontology (GO) enrichment analysis was performed to identify the significant biological processes, and protein–protein interaction networks were constructed to extract hub genes. These hub genes were then subjected to regulatory signatures and protein–chemical interaction analysis for certain regulatory checkpoints and identification of potent chemical agents. Finally, to demonstrate the cell type-specific expression of these genes, we performed single-cell RNA-Seq analyses using an online platform. Results: A total of 144 DEGs were specifically expressed in severe COVID-19, and GO enrichment analysis revealed a significant association of these specific DEGs with autophagy. Hub genes such as MVB12A, CHMP6, STAM, and VPS37B were then found to be most significantly involved in the biological processes of autophagy at the transcriptome level. In addition, six transcription factors, including SRF, YY1, CREB1, PPARG, NFIC, and GATA2, as well as miRNAs, namely, hsa-mir-1-3p, and potent chemical agents such as copper sulfate and cobalt chloride, may cooperate in regulating the autophagy hub genes. Furthermore, classical monocytes may play a central role in severe COVID-19. Conclusion: We suggest that autophagy plays a crucial role in severe COVID-19. This study might facilitate a more profound knowledge of the biological characteristics and progression of COVID-19 and the development of novel therapeutic approaches to achieve a breakthrough in the current COVID-19 pandemic.
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Affiliation(s)
- Jinfeng Huang
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, China
| | - Yimeng Wang
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yawen Zha
- Department of Radiation Oncology Ⅱ, Zhongshan People’s Hospital, Zhongshan, China
| | - Xin Zeng
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wenxing Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Southern Medical University, Guangzhou, China
| | - Meijuan Zhou
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, China
- *Correspondence: Meijuan Zhou,
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Li XY, Wang SL, Chen DH, Liu H, You JX, Su LX, Yang XT. Construction and Validation of a m7G-Related Gene-Based Prognostic Model for Gastric Cancer. Front Oncol 2022; 12:861412. [PMID: 35847903 PMCID: PMC9281447 DOI: 10.3389/fonc.2022.861412] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/26/2022] [Indexed: 12/14/2022] Open
Abstract
Background Gastric cancer (GC) is one of the most common malignant tumors of the digestive system. Chinese cases of GC account for about 40% of the global rate, with approximately 1.66 million people succumbing to the disease each year. Despite the progress made in the treatment of GC, most patients are diagnosed at an advanced stage due to the lack of obvious clinical symptoms in the early stages of GC, and their prognosis is still very poor. The m7G modification is one of the most common forms of base modification in post-transcriptional regulation, and it is widely distributed in the 5′ cap region of tRNA, rRNA, and eukaryotic mRNA. Methods RNA sequencing data of GC were downloaded from The Cancer Genome Atlas. The differentially expressed m7G-related genes in normal and tumour tissues were determined, and the expression and prognostic value of m7G-related genes were systematically analysed. We then built models using the selected m7G-related genes with the help of machine learning methods.The model was then validated for prognostic value by combining the receiver operating characteristic curve (ROC) and forest plots. The model was then validated on an external dataset. Finally, quantitative real-time PCR (qPCR) was performed to detect gene expression levels in clinical gastric cancer and paraneoplastic tissue. Results The model is able to determine the prognosis of GC samples quantitatively and accurately. The ROC analysis of model has an AUC of 0.761 and 0.714 for the 3-year overall survival (OS) in the training and validation sets, respectively. We determined a correlation between risk scores and immune cell infiltration and concluded that immune cell infiltration affects the prognosis of GC patients. NUDT10, METTL1, NUDT4, GEMIN5, EIF4E1B, and DCPS were identified as prognostic hub genes and potential therapeutic agents were identified based on these genes. Conclusion The m7G-related gene-based prognostic model showed good prognostic discrimination. Understanding how m7G modification affect the infiltration of the tumor microenvironment (TME) cells will enable us to better understand the TME’s anti-tumor immune response, and hopefully guide more effective immunotherapy methods.
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Affiliation(s)
- Xin-yu Li
- Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Neurosurgery, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Shou-lian Wang
- Department of General Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - De-hu Chen
- Department of Gastrointestinal Surgery, Hospital Affiliated 5 to Nantong University (Taizhou People's Hospital), Taizhou, China
| | - Hui Liu
- Department of Clinical Medicine, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Jian-Xiong You
- Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-xin Su
- Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi-tao Yang
- Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xi-tao Yang,
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Zhang G, Cui X, Zhang L, Liu G, Zhu X, Shangguan J, Zhang W, Zheng Y, Zhang H, Tang J, Zhang J. Uncovering the genetic links of SARS-CoV-2 infections on heart failure co-morbidity by a systems biology approach. ESC Heart Fail 2022; 9:2937-2954. [PMID: 35727093 PMCID: PMC9349450 DOI: 10.1002/ehf2.14003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/24/2022] [Accepted: 05/19/2022] [Indexed: 01/08/2023] Open
Abstract
Aims The co‐morbidities contribute to the inferior prognosis of COVID‐19 patients. Recent reports suggested that the higher co‐morbidity rate between COVID‐19 and heart failure (HF) leads to increased mortality. However, the common pathogenic mechanism between them remained elusive. Here, we aimed to reveal underlying molecule mechanisms and genetic correlation between COVID‐19 and HF, providing a new perspective on current clinical management for patients with co‐morbidity. Methods The gene expression profiles of HF (GSE26887) and COVID‐19 (GSE147507) were retrieved from the GEO database. After identifying the common differentially expressed genes (|log2FC| > 1 and adjusted P < 0.05), integrated analyses were performed, namely, enrichment analyses, protein–protein interaction network, module construction, critical gene identification, and functional co‐expression analysis. The performance of critical genes was validation combining hierarchical clustering, correlation, and principal component analysis in external datasets (GSE164805 and GSE9128). Potential transcription factors and miRNAs were obtained from the JASPER and RegNetwork repository used to construct co‐regulatory networks. The candidate drug compounds in potential genetic link targets were further identified using the DSigDB database. Results The alteration of 12 genes was identified as a shared transcriptional signature, with the role of immune inflammatory pathway, especially Toll‐like receptor, NF‐kappa B, chemokine, and interleukin‐related pathways that primarily emphasized in response to SARS‐CoV‐2 complicated with HF. Top 10 critical genes (TLR4, TLR2, CXCL8, IL10, STAT3, IL1B, TLR1, TP53, CCL20, and CXCL10) were identified from protein–protein interaction with topological algorithms. The unhealthy microbiota status and gut–heart axis in co‐morbidity were identified as potential disease roads in bridging pathogenic mechanism, and lipopolysaccharide acts as a potential marker for monitoring HF during COVID‐19. For transcriptional and post‐transcriptional levels, regulation networks tightly coupling with both disorders were constructed, and significant regulator signatures with high interaction degree, especially FOXC1, STAT3, NF‐κB1, miR‐181, and miR‐520, were detected to regulate common differentially expressed genes. According to genetic links targets, glutathione‐based antioxidant strategy combined with muramyl dipeptide‐based microbe‐derived immunostimulatory therapies was identified as promising anti‐COVID‐19 and anti‐HF therapeutics. Conclusions This study identified shared transcriptomic and corresponding regulatory signatures as emerging therapeutic targets and detected a set of pharmacologic agents targeting genetic links. Our findings provided new insights for underlying pathogenic mechanisms between COVID‐19 and HF.
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Affiliation(s)
- Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Cardiac Injury and Repair of Henan Province, Zhengzhou, China.,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, China
| | - Xiaolin Cui
- Christchurch Regenerative Medicine and Tissue Engineering (CReaTE) Group, Department of Orthopaedic Surgery and Musculoskeletal Medicine, University of Otago, Christchurch, Canterbury, New Zealand
| | - Li Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Cardiac Injury and Repair of Henan Province, Zhengzhou, China.,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, China
| | - Gangqiong Liu
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Cardiac Injury and Repair of Henan Province, Zhengzhou, China.,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, China
| | - Xiaodan Zhu
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Cardiac Injury and Repair of Henan Province, Zhengzhou, China.,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, China
| | - Jiahong Shangguan
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Cardiac Injury and Repair of Henan Province, Zhengzhou, China.,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, China
| | - Wenjing Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Cardiac Injury and Repair of Henan Province, Zhengzhou, China.,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, China
| | - Yingying Zheng
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Cardiac Injury and Repair of Henan Province, Zhengzhou, China.,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, China
| | - Hui Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Cardiac Injury and Repair of Henan Province, Zhengzhou, China.,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, China
| | - Junnan Tang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Cardiac Injury and Repair of Henan Province, Zhengzhou, China.,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, China
| | - Jinying Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Cardiac Injury and Repair of Henan Province, Zhengzhou, China.,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, China
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Chen J, Lu Z, Yang X, Zhou Y, Gao J, Zhang S, Huang S, Cai J, Yu J, Zhao W, Zhang B. Severe Acute Respiratory Syndrome Coronavirus 2 ORF8 Protein Inhibits Type I Interferon Production by Targeting HSP90B1 Signaling. Front Cell Infect Microbiol 2022; 12:899546. [PMID: 35677655 PMCID: PMC9168264 DOI: 10.3389/fcimb.2022.899546] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/08/2022] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global pandemic that has currently infected over 430 million individuals worldwide. With the variant strains of SARS-CoV-2 emerging, a region of high mutation rates in ORF8 was identified during the early pandemic, which resulted in a mutation from leucine (L) to serine (S) at amino acid 84. A typical feature of ORF8 is the immune evasion by suppressing interferon response; however, the mechanisms by which the two variants of ORF8 antagonize the type I interferon (IFN-I) pathway have not yet been clearly investigated. Here, we reported that SARS-CoV-2 ORF8L and ORF8S with no difference inhibit the production of IFN-β, MDA5, RIG-I, ISG15, ISG56, IRF3, and other IFN-related genes induced by poly(I:C). In addition, both ORF8L and ORF8S proteins were found to suppress the nuclear translocation of IRF3. Mechanistically, the SARS-CoV-2 ORF8 protein interacts with HSP90B1, which was later investigated to induce the production of IFN-β and IRF3. Taken together, these results indicate that SARS-CoV-2 ORF8 antagonizes the RIG-I/MDA-5 signaling pathway by targeting HSP90B1, which subsequently exhibits an inhibitory effect on the production of IFN-I. These functions appeared not to be influenced by the genotypes of ORF8L and ORF8S. Our study provides an explanation for the antiviral immune suppression of SARS-CoV-2 and suggests implications for the pathogenic mechanism and treatment of COVID-19.
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Affiliation(s)
- Jiayi Chen
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Zixin Lu
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xiuwen Yang
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yezhen Zhou
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jing Gao
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Shihao Zhang
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Shan Huang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jintai Cai
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jianhai Yu
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wei Zhao
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- *Correspondence: Bao Zhang, ; Wei Zhao,
| | - Bao Zhang
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- *Correspondence: Bao Zhang, ; Wei Zhao,
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Sagulkoo P, Suratanee A, Plaimas K. Immune-Related Protein Interaction Network in Severe COVID-19 Patients toward the Identification of Key Proteins and Drug Repurposing. Biomolecules 2022; 12:biom12050690. [PMID: 35625619 PMCID: PMC9138873 DOI: 10.3390/biom12050690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is still an active global public health issue. Although vaccines and therapeutic options are available, some patients experience severe conditions and need critical care support. Hence, identifying key genes or proteins involved in immune-related severe COVID-19 is necessary to find or develop the targeted therapies. This study proposed a novel construction of an immune-related protein interaction network (IPIN) in severe cases with the use of a network diffusion technique on a human interactome network and transcriptomic data. Enrichment analysis revealed that the IPIN was mainly associated with antiviral, innate immune, apoptosis, cell division, and cell cycle regulation signaling pathways. Twenty-three proteins were identified as key proteins to find associated drugs. Finally, poly (I:C), mitomycin C, decitabine, gemcitabine, hydroxyurea, tamoxifen, and curcumin were the potential drugs interacting with the key proteins to heal severe COVID-19. In conclusion, IPIN can be a good representative network for the immune system that integrates the protein interaction network and transcriptomic data. Thus, the key proteins and target drugs in IPIN help to find a new treatment with the use of existing drugs to treat the disease apart from vaccination and conventional antiviral therapy.
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Affiliation(s)
- Pakorn Sagulkoo
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand;
- Center of Biomedical Informatics, Department of Family Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Apichat Suratanee
- Department of Mathematics, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok, Bangkok 10800, Thailand;
- Intelligent and Nonlinear Dynamics Innovations Research Center, Science and Technology Research Institute, King Mongkut’s University of Technology North Bangkok, Bangkok 10800, Thailand
| | - Kitiporn Plaimas
- Advance Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence:
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11
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Chowdhury UN, Faruqe MO, Mehedy M, Ahmad S, Islam MB, Shoombuatong W, Azad A, Moni MA. Effects of Bacille Calmette Guerin (BCG) vaccination during COVID-19 infection. Comput Biol Med 2021; 138:104891. [PMID: 34624759 PMCID: PMC8479467 DOI: 10.1016/j.compbiomed.2021.104891] [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] [Received: 06/15/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022]
Abstract
The coronavirus disease 2019 (COVID-19) is caused by the infection of highly contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as the novel coronavirus. In most countries, the containment of this virus spread is not controlled, which is driving the pandemic towards a more difficult phase. In this study, we investigated the impact of the Bacille Calmette Guerin (BCG) vaccination on the severity and mortality of COVID-19 by performing transcriptomic analyses of SARS-CoV-2 infected and BCG vaccinated samples in peripheral blood mononuclear cells (PBMC). A set of common differentially expressed genes (DEGs) were identified and seeded into their functional enrichment analyses via Gene Ontology (GO)-based functional terms and pre-annotated molecular pathways databases, and their Protein-Protein Interaction (PPI) network analysis. We further analysed the regulatory elements, possible comorbidities and putative drug candidates for COVID-19 patients who have not been BCG-vaccinated. Differential expression analyses of both BCG-vaccinated and COVID-19 infected samples identified 62 shared DEGs indicating their discordant expression pattern in their respected conditions compared to control. Next, PPI analysis of those DEGs revealed 10 hub genes, namely ITGB2, CXCL8, CXCL1, CCR2, IFNG, CCL4, PTGS2, ADORA3, TLR5 and CD33. Functional enrichment analyses found significantly enriched pathways/GO terms including cytokine activities, lysosome, IL-17 signalling pathway, TNF-signalling pathways. Moreover, a set of identified TFs, miRNAs and potential drug molecules were further investigated to assess their biological involvements in COVID-19 and their therapeutic possibilities. Findings showed significant genetic interactions between BCG vaccination and SARS-CoV-2 infection, suggesting an interesting prospect of the BCG vaccine in relation to the COVID-19 pandemic. We hope it may potentially trigger further research on this critical phenomenon to combat COVID-19 spread.
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Affiliation(s)
- Utpala Nanda Chowdhury
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Omar Faruqe
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Mehedy
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Shamim Ahmad
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - M. Babul Islam
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - A.K.M. Azad
- Faculty of Science, Engineering & Technology, Swinburne University of Technology Sydney, Australia
| | - Mohammad Ali Moni
- School of Health and Rehabilitation Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, QLD 4072, Australia,Corresponding author
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