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Zhang Z. The Initial COVID-19 Reliable Interactive DNA Methylation Markers and Biological Implications. BIOLOGY 2024; 13:245. [PMID: 38666857 PMCID: PMC11048280 DOI: 10.3390/biology13040245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/22/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
Earlier research has established the existence of reliable interactive genomic biomarkers. However, reliable DNA methylation biomarkers, not to mention interactivity, have yet to be identified at the epigenetic level. This study, drawing from 865,859 methylation sites, discovered two miniature sets of Infinium MethylationEPIC sites, each having eight CpG sites (genes) to interact with each other and disease subtypes. They led to the nearly perfect (96.87-100% accuracy) prediction of COVID-19 patients from patients with other diseases or healthy controls. These CpG sites can jointly explain some post-COVID-19-related conditions. These CpG sites and the optimally performing genomic biomarkers reported in the literature become potential druggable targets. Among these CpG sites, cg16785077 (gene MX1), cg25932713 (gene PARP9), and cg22930808 (gene PARP9) at DNA methylation levels indicate that the initial SARS-CoV-2 virus may be better treated as a transcribed viral DNA into RNA virus, i.e., not as an RNA virus that has concerned scientists in the field. Such a discovery can significantly change the scientific thinking and knowledge of viruses.
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Affiliation(s)
- Zhengjun Zhang
- School of Computer, Data and Information Sciences, University of Wisconsin, Madison, WI 53706, USA
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2
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Kibria MK, Ali MA, Yaseen M, Khan IA, Bhat MA, Islam MA, Mahumud RA, Mollah MNH. Discovery of Bacterial Key Genes from 16S rRNA-Seq Profiles That Are Associated with the Complications of SARS-CoV-2 Infections and Provide Therapeutic Indications. Pharmaceuticals (Basel) 2024; 17:432. [PMID: 38675393 PMCID: PMC11053588 DOI: 10.3390/ph17040432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
SARS-CoV-2 infections, commonly referred to as COVID-19, remain a critical risk to both human life and global economies. Particularly, COVID-19 patients with weak immunity may suffer from different complications due to the bacterial co-infections/super-infections/secondary infections. Therefore, different variants of alternative antibacterial therapeutic agents are required to inhibit those infection-causing drug-resistant pathogenic bacteria. This study attempted to explore these bacterial pathogens and their inhibitors by using integrated statistical and bioinformatics approaches. By analyzing bacterial 16S rRNA sequence profiles, at first, we detected five bacterial genera and taxa (Bacteroides, Parabacteroides, Prevotella Clostridium, Atopobium, and Peptostreptococcus) based on differentially abundant bacteria between SARS-CoV-2 infection and control samples that are significantly enriched in 23 metabolic pathways. A total of 183 bacterial genes were found in the enriched pathways. Then, the top-ranked 10 bacterial genes (accB, ftsB, glyQ, hldD, lpxC, lptD, mlaA, ppsA, ppc, and tamB) were selected as the pathogenic bacterial key genes (bKGs) by their protein-protein interaction (PPI) network analysis. Then, we detected bKG-guided top-ranked eight drug molecules (Bemcentinib, Ledipasvir, Velpatasvir, Tirilazad, Acetyldigitoxin, Entreatinib, Digitoxin, and Elbasvir) by molecular docking. Finally, the binding stability of the top-ranked three drug molecules (Bemcentinib, Ledipasvir, and Velpatasvir) against three receptors (hldD, mlaA, and lptD) was investigated by computing their binding free energies with molecular dynamic (MD) simulation-based MM-PBSA techniques, respectively, and was found to be stable. Therefore, the findings of this study could be useful resources for developing a proper treatment plan against bacterial co-/super-/secondary-infection in SARS-CoV-2 infections.
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Affiliation(s)
- Md. Kaderi Kibria
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Statistics, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Md. Ahad Ali
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Chemistry, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Imran Ahmad Khan
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11421, Saudi Arabia;
| | - Md. Ariful Islam
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
| | - Rashidul Alam Mahumud
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
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3
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Chujan S, Nakareangrit W, Suriyo T, Satayavivad J. Integrated Transcriptomics and Network Analysis of Potential Mechanisms and Health Effects of Convalescent COVID-19 Patients. Bioinform Biol Insights 2023; 17:11779322231206684. [PMID: 37881207 PMCID: PMC10594973 DOI: 10.1177/11779322231206684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/22/2023] [Indexed: 10/27/2023] Open
Abstract
Coronaviral disease 2019 (COVID-19) is a recent pandemic disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Currently, there are still cases of COVID-19 around the world that can develop into persistent symptoms after discharge. The constellation of symptoms, termed long COVID, persists for months and can lead to various diseases such as lung inflammation and cardiovascular disease, which may lead to considerable financial burden and possible risk to human health. Moreover, the molecular mechanisms underlying the post-pandemic syndrome of COVID-19 remain unclear. In this study, we aimed to explore the molecular mechanism, disease association, and possible health risks in convalescent COVID-19 patients. Gene expression data from a human convalescent COVID-19 data set was compared with a data set from healthy normal individuals in order to identify differentially expressed genes (DEGs). To determine biological function and potential pathway alterations, the GO and KEGG databases were used to analyze the DEGs. Disease association, tissue, and organ-specific analyses were used to identify possible health effects. A total of 250 DEGs were identified between healthy and convalescent COVID-19 subjects. The biological function alterations identified revealed cytokine interactions and increased inflammation through NF-κB1, RELA, JUN, STAT3, and SP1. Interestingly, the most significant pathways were cytokine-cytokine receptor interaction, altered lipid metabolism, and atherosclerosis that play a crucial role in convalescent COVID-19. In addition, we also found pneumonitis, dermatitis, and autoimmune diseases. Based on our study, convalescent COVID-19 is associated with inflammation in a variety of organs that could lead to autoimmune and inflammatory diseases, as well as atherosclerosis. These findings are a first step toward fully exploring the disease mechanisms in depth to understand the relationship between post-COVID-19 infection and potential health risks. This is necessary for the development of appropriate strategies for the prevention and treatment of long COVID.
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Affiliation(s)
- Suthipong Chujan
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | | | - Tawit Suriyo
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Jutamaad Satayavivad
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
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4
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Ivanov SM, Tarasova OA, Poroikov VV. Transcriptome-based analysis of human peripheral blood reveals regulators of immune response in different viral infections. Front Immunol 2023; 14:1199482. [PMID: 37795081 PMCID: PMC10546413 DOI: 10.3389/fimmu.2023.1199482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023] Open
Abstract
Introduction There are difficulties in creating direct antiviral drugs for all viruses, including new, suddenly arising infections, such as COVID-19. Therefore, pathogenesis-directed therapy is often necessary to treat severe viral infections and comorbidities associated with them. Despite significant differences in the etiopathogenesis of viral diseases, in general, they are associated with significant dysfunction of the immune system. Study of common mechanisms of immune dysfunction caused by different viral infections can help develop novel therapeutic strategies to combat infections and associated comorbidities. Methods To identify common mechanisms of immune functions disruption during infection by nine different viruses (cytomegalovirus, Ebstein-Barr virus, human T-cell leukemia virus type 1, Hepatitis B and C viruses, human immunodeficiency virus, Dengue virus, SARS-CoV, and SARS-CoV-2), we analyzed the corresponding transcription profiles from peripheral blood mononuclear cells (PBMC) using the originally developed pipeline that include transcriptome data collection, processing, normalization, analysis and search for master regulators of several viral infections. The ten datasets containing transcription data from patients infected by nine viruses and healthy people were obtained from Gene Expression Omnibus. The analysis of the data was performed by Genome Enhancer pipeline. Results We revealed common pathways, cellular processes, and master regulators for studied viral infections. We found that all nine viral infections cause immune activation, exhaustion, cell proliferation disruption, and increased susceptibility to apoptosis. Using network analysis, we identified PBMC receptors, representing proteins at the top of signaling pathways that may be responsible for the observed transcriptional changes and maintain the current functional state of cells. Discussion The identified relationships between some of them and virus-induced alteration of immune functions are new and have not been found earlier, e.g., receptors for autocrine motility factor, insulin, prolactin, angiotensin II, and immunoglobulin epsilon. Modulation of the identified receptors can be investigated as one of therapeutic strategies for the treatment of severe viral infections.
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Affiliation(s)
- Sergey M. Ivanov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
- Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Olga A. Tarasova
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
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Yang CW, Hsu HY, Lee YZ, Jan JT, Chang SY, Lin YL, Yang RB, Chao TL, Liang JJ, Lin SJ, Liao CC, Chang CS, Sytwu HK, Hung MS, Chen CT, Lee SJ. Natural fucoidans inhibit coronaviruses by targeting viral spike protein and host cell furin. Biochem Pharmacol 2023; 215:115688. [PMID: 37481137 DOI: 10.1016/j.bcp.2023.115688] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/01/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Fucoidans are a class of long chain sulfated polysaccharides and have multiple biological functions. Herein, four natural fucoidans extracted from Fucus vesiculosus, F. serratus, Laminaria japonica and Undaria pinnatifida, were tested for their HCoV-OC43 inhibition and found to demonstrate EC50 values ranging from 0.15 to 0.61 µg/mL. That from U. pinnatifida exhibited the most potent anti-HCoV-OC43 activity with an EC50 value of 0.15 ± 0.02 µg/mL, a potency largely independent of its sulfate content. Comparison of the gene expression profiles of fucoidan-treated and untreated cells infected with HCoV-OC43 revealed that fucoidan treatment effectively diminished HCoV-OC43 gene expressions associated with induced chemokines, cytokines and viral activities. Further studies using a highly fucoidan-resistant HCoV-OC43 determined that fucoidan inhibited HCoV-OC43 infection via interfering with viral entry and led to the identification of the specific site on the N-terminal region of spike protein, that located adjacent to the host cell receptor binding domain, targeted by the virus. Furthermore, in a SARS-CoV-2 pseudovirus neutralization assay, fucoidan also blocked SARS-CoV-2 entry. In vitro and in vivo, fucoidan decreased SARS-CoV-2 viral loads and inhibited viral infection in Calu-3 or Vero E6 cells and SARS-CoV-2 infected hamsters, respectively. Fucoidan was also found to inhibit furin activity, and reported furin inhibitors were found to inhibit viral infection by wild type HCoV-OC43 or SARS-CoV-2. Accordingly, we conclude that fucoidans inhibit coronaviral infection by targeting viral spike protein and host cell furin to interfere with viral entry.
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Affiliation(s)
- Cheng-Wei Yang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan, ROC
| | - Hsing-Yu Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan, ROC
| | - Yue-Zhi Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan, ROC
| | - Jia-Tsrong Jan
- Genomic Research Center, Academia Sinica, Taipei, Taiwan, ROC
| | - Sui-Yuan Chang
- Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Ruey-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Tai-Ling Chao
- Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC
| | - Jian-Jong Liang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Shu-Jing Lin
- Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC
| | - Chun-Che Liao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Chih-Shin Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Huey-Kang Sytwu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan, ROC
| | - Ming-Shiu Hung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan, ROC
| | - Chiung-Tong Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan, ROC
| | - Shiow-Ju Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan, ROC.
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Lin Y, Li Y, Chen H, Meng J, Li J, Chu J, Zheng R, Wang H, Pan P, Su J, Jiang J, Ye L, Liang H, An S. Weighted gene co-expression network analysis revealed T cell differentiation associated with the age-related phenotypes in COVID-19 patients. BMC Med Genomics 2023; 16:59. [PMID: 36966292 PMCID: PMC10039774 DOI: 10.1186/s12920-023-01490-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/15/2023] [Indexed: 03/27/2023] Open
Abstract
The risk of severe condition caused by Corona Virus Disease 2019 (COVID-19) increases with age. However, the underlying mechanisms have not been clearly understood. The dataset GSE157103 was used to perform weighted gene co-expression network analysis on 100 COVID-19 patients in our analysis. Through weighted gene co-expression network analysis, we identified a key module which was significantly related with age. This age-related module could predict Intensive Care Unit status and mechanical-ventilation usage, and enriched with positive regulation of T cell receptor signaling pathway biological progress. Moreover, 10 hub genes were identified as crucial gene of the age-related module. Protein-protein interaction network and transcription factors-gene interactions were established. Lastly, independent data sets and RT-qPCR were used to validate the key module and hub genes. Our conclusion revealed that key genes were associated with the age-related phenotypes in COVID-19 patients, and it would be beneficial for clinical doctors to develop reasonable therapeutic strategies in elderly COVID-19 patients.
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Affiliation(s)
- Yao Lin
- Medical Laboratory Centre, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Yueqi Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Hubin Chen
- Medical Laboratory Centre, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jun Meng
- Medical Laboratory Centre, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jingyi Li
- Biosafety Level 3 Laboratory and Guangxi Collaborative Innovation Centre for Biomedicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jiemei Chu
- Medical Laboratory Centre, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Ruili Zheng
- Biosafety Level 3 Laboratory and Guangxi Collaborative Innovation Centre for Biomedicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Hailong Wang
- Biosafety Level 3 Laboratory and Guangxi Collaborative Innovation Centre for Biomedicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Peijiang Pan
- Biosafety Level 3 Laboratory and Guangxi Collaborative Innovation Centre for Biomedicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jinming Su
- Biosafety Level 3 Laboratory and Guangxi Collaborative Innovation Centre for Biomedicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Junjun Jiang
- Medical Laboratory Centre, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Li Ye
- Biosafety Level 3 Laboratory and Guangxi Collaborative Innovation Centre for Biomedicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Hao Liang
- Medical Laboratory Centre, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China
- Biosafety Level 3 Laboratory and Guangxi Collaborative Innovation Centre for Biomedicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Sanqi An
- Medical Laboratory Centre, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China.
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7
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Wismans LV, Lopuhaä B, de Koning W, Moeniralam H, van Oosterhout M, Ambarus C, Hofman FN, Kuiken T, Endeman H, Mustafa DAM, von der Thüsen JH. Increase of mast cells in COVID-19 pneumonia may contribute to pulmonary fibrosis and thrombosis. Histopathology 2023; 82:407-419. [PMID: 36366933 PMCID: PMC9877713 DOI: 10.1111/his.14838] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/10/2022] [Accepted: 11/05/2022] [Indexed: 11/13/2022]
Abstract
AIMS Lung tissue from COVID-19 patients shares similar histomorphological features with chronic lung allograft disease, also suggesting activation of autoimmune-related pathways in COVID-19. To more clearly understand the underlying spectrum of pathophysiology in COVID-19 pneumonia, we analysed mRNA expression of autoimmune-related genes in post-mortem lung tissue from COVID-19 patients. METHODS AND RESULTS Formalin-fixed, paraffin-embedded lung tissue samples of 18 COVID-19 patients and eight influenza patients were used for targeted gene expression profiling using NanoString technology. Multiplex immunofluorescence for tryptase and chymase was applied for validation. Genes related to mast cells were significantly increased in COVID-19. This finding was strengthened by multiplex immunofluorescence also showing a significant increase of tryptase- and chymase-positive cells in COVID-19. Furthermore, receptors for advanced glycation end-products (RAGE) and pro-platelet basic protein (PPBP) were up-regulated in COVID-19 compared to influenza. Genes associated with Type I interferon signalling showed a significant correlation to detected SARS-CoV2 pathway-related genes. The comparison of lung tissue samples from both groups based on the presence of histomorphological features indicative of acute respiratory distress syndrome did not result in finding any specific gene or pathways. CONCLUSION Two separate means of measuring show a significant increase of mast cells in SARS-CoV-2-infected lung tissue compared to influenza. Additionally, several genes involved in fibrosis and thrombosis, among which are RAGE and PPBP, are up-regulated in COVID-19. As mast cells are able to induce thrombosis and fibrosis, they may play an important role in the pathogenesis of COVID-19.
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Affiliation(s)
- Leonoor V Wismans
- Present address:
Department of SurgeryErasmus Medical CenterRotterdamthe Netherlands,The Tumor Immuno‐Pathology Laboratory, Department of PathologyJosephine Nefkens Institute, Erasmus Medical CenterRotterdamthe Netherlands
| | - Boaz Lopuhaä
- Present address:
Department of SurgeryErasmus Medical CenterRotterdamthe Netherlands,Department of PathologyJosephine Nefkens Institute, Erasmus Medical CenterRotterdamthe Netherlands
| | - Willem de Koning
- The Tumor Immuno‐Pathology Laboratory, Department of PathologyJosephine Nefkens Institute, Erasmus Medical CenterRotterdamthe Netherlands,Clinical Bioinformatics Unit, Department of PathologyErasmus Medical CenterRotterdamthe Netherlands
| | - Hazra Moeniralam
- Department of Internal Medicine and Intensive CareSt. Antonius HospitalNieuwegeinthe Netherlands
| | | | - Carmen Ambarus
- Department of Pathology DNASt. Antonius HospitalNieuwegeinthe Netherlands
| | - Frederik N Hofman
- Department of Cardiothoracic SurgerySt. Antonius HospitalNieuwegeinthe Netherlands
| | - Thijs Kuiken
- Department of ViroscienceErasmus Medical CenterRotterdamthe Netherlands
| | - Henrik Endeman
- Department of Adult Intensive CareErasmus Medical CenterRotterdamthe Netherlands
| | - Dana A M Mustafa
- The Tumor Immuno‐Pathology Laboratory, Department of PathologyJosephine Nefkens Institute, Erasmus Medical CenterRotterdamthe Netherlands,Department of PathologyJosephine Nefkens Institute, Erasmus Medical CenterRotterdamthe Netherlands
| | - Jan H von der Thüsen
- Department of PathologyJosephine Nefkens Institute, Erasmus Medical CenterRotterdamthe Netherlands
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Non-coding RNA in SARS-CoV-2: Progress toward therapeutic significance. Int J Biol Macromol 2022; 222:1538-1550. [PMID: 36152703 PMCID: PMC9492401 DOI: 10.1016/j.ijbiomac.2022.09.105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 12/18/2022]
Abstract
The recently developed pathogenic virus, SARS-CoV-2, was found in the Hubei Province, China. Giving rise to a broad spectrum of symptoms, SARS-CoV-2 rapidly spread across the globe, causing multi-systemic and dangerous complications, with death in extreme cases. Thereby, the number of research cases increases every day on preventing infection and treating its resulting damage. Accumulating evidence suggests noncoding RNAs (ncRNAs) are necessary for modifying virus infection and antiviral immune reaction, along with biological processes regulating SARS-CoV-2 and subsequent disease states. Therefore, understanding these mechanisms might provide a further understanding of the pathogenesis and feasible therapy alternatives against SARS-CoV2. Consequently, the molecular biology of SARS-CoV-2, ncRNA's role in its infection, and various RNA therapy tactics against the virus have been presented in this review section.
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Mosharaf MP, Kibria MK, Hossen MB, Islam MA, Reza MS, Mahumud RA, Alam K, Gow J, Mollah MNH. Meta-Data Analysis to Explore the Hub of the Hub-Genes That Influence SARS-CoV-2 Infections Highlighting Their Pathogenetic Processes and Drugs Repurposing. Vaccines (Basel) 2022; 10:vaccines10081248. [PMID: 36016137 PMCID: PMC9415433 DOI: 10.3390/vaccines10081248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 01/09/2023] Open
Abstract
The pandemic of SARS-CoV-2 infections is a severe threat to human life and the world economic condition. Although vaccination has reduced the outspread, but still the situation is not under control because of the instability of RNA sequence patterns of SARS-CoV-2, which requires effective drugs. Several studies have suggested that the SARS-CoV-2 infection causing hub differentially expressed genes (Hub-DEGs). However, we observed that there was not any common hub gene (Hub-DEGs) in our analyses. Therefore, it may be difficult to take a common treatment plan against SARS-CoV-2 infections globally. The goal of this study was to examine if more representative Hub-DEGs from published studies by means of hub of Hub-DEGs (hHub-DEGs) and associated potential candidate drugs. In this study, we reviewed 41 articles on transcriptomic data analysis of SARS-CoV-2 and found 370 unique hub genes or studied genes in total. Then, we selected 14 more representative Hub-DEGs (AKT1, APP, CXCL8, EGFR, IL6, INS, JUN, MAPK1, STAT3, TNF, TP53, UBA52, UBC, VEGFA) as hHub-DEGs by their protein-protein interaction analysis. Their associated biological functional processes, transcriptional, and post-transcriptional regulatory factors. Then we detected hHub-DEGs guided top-ranked nine candidate drug agents (Digoxin, Avermectin, Simeprevir, Nelfinavir Mesylate, Proscillaridin, Linifanib, Withaferin, Amuvatinib, Atazanavir) by molecular docking and cross-validation for treatment of SARS-CoV-2 infections. Therefore, the findings of this study could be useful in formulating a common treatment plan against SARS-CoV-2 infections globally.
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Affiliation(s)
- Md. Parvez Mosharaf
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
- School of Business, Faculty of Business, Education, Law and Arts, University of Southern Queensland, Toowoomba, QLD 4350, Australia; (K.A.); (J.G.)
| | - Md. Kaderi Kibria
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
| | - Md. Bayazid Hossen
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
| | - Md. Ariful Islam
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
| | - Md. Selim Reza
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
| | - Rashidul Alam Mahumud
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia;
| | - Khorshed Alam
- School of Business, Faculty of Business, Education, Law and Arts, University of Southern Queensland, Toowoomba, QLD 4350, Australia; (K.A.); (J.G.)
| | - Jeff Gow
- School of Business, Faculty of Business, Education, Law and Arts, University of Southern Queensland, Toowoomba, QLD 4350, Australia; (K.A.); (J.G.)
- School of Accounting, Economics and Finance, University of KwaZulu Natal, Durban 4001, South Africa
| | - Md. Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
- Correspondence:
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10
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Ahmed FF, Reza MS, Sarker MS, Islam MS, Mosharaf MP, Hasan S, Mollah MNH. Identification of host transcriptome-guided repurposable drugs for SARS-CoV-1 infections and their validation with SARS-CoV-2 infections by using the integrated bioinformatics approaches. PLoS One 2022; 17:e0266124. [PMID: 35390032 PMCID: PMC8989220 DOI: 10.1371/journal.pone.0266124] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 03/15/2022] [Indexed: 12/18/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is one of the most severe global pandemic due to its high pathogenicity and death rate starting from the end of 2019. Though there are some vaccines available against SAER-CoV-2 infections, we are worried about their effectiveness, due to its unstable sequence patterns. Therefore, beside vaccines, globally effective supporting drugs are also required for the treatment against SARS-CoV-2 infection. To explore commonly effective repurposable drugs for the treatment against different variants of coronavirus infections, in this article, an attempt was made to explore host genomic biomarkers guided repurposable drugs for SARS-CoV-1 infections and their validation with SARS-CoV-2 infections by using the integrated bioinformatics approaches. At first, we identified 138 differentially expressed genes (DEGs) between SARS-CoV-1 infected and control samples by analyzing high throughput gene-expression profiles to select drug target key receptors. Then we identified top-ranked 11 key DEGs (SMAD4, GSK3B, SIRT1, ATM, RIPK1, PRKACB, MED17, CCT2, BIRC3, ETS1 and TXN) as hub genes (HubGs) by protein-protein interaction (PPI) network analysis of DEGs highlighting their functions, pathways, regulators and linkage with other disease risks that may influence SARS-CoV-1 infections. The DEGs-set enrichment analysis significantly detected some crucial biological processes (immune response, regulation of angiogenesis, apoptotic process, cytokine production and programmed cell death, response to hypoxia and oxidative stress), molecular functions (transcription factor binding and oxidoreductase activity) and pathways (transcriptional mis-regulation in cancer, pathways in cancer, chemokine signaling pathway) that are associated with SARS-CoV-1 infections as well as SARS-CoV-2 infections by involving HubGs. The gene regulatory network (GRN) analysis detected some transcription factors (FOXC1, GATA2, YY1, FOXL1, TP53 and SRF) and micro-RNAs (hsa-mir-92a-3p, hsa-mir-155-5p, hsa-mir-106b-5p, hsa-mir-34a-5p and hsa-mir-19b-3p) as the key transcriptional and post- transcriptional regulators of HubGs, respectively. We also detected some chemicals (Valproic Acid, Cyclosporine, Copper Sulfate and arsenic trioxide) that may regulates HubGs. The disease-HubGs interaction analysis showed that our predicted HubGs are also associated with several other diseases including different types of lung diseases. Then we considered 11 HubGs mediated proteins and their regulatory 6 key TFs proteins as the drug target proteins (receptors) and performed their docking analysis with the SARS-CoV-2 3CL protease-guided top listed 90 anti-viral drugs out of 3410. We found Rapamycin, Tacrolimus, Torin-2, Radotinib, Danoprevir, Ivermectin and Daclatasvir as the top-ranked 7 candidate-drugs with respect to our proposed target proteins for the treatment against SARS-CoV-1 infections. Then, we validated these 7 candidate-drugs against the already published top-ranked 11 target proteins associated with SARS-CoV-2 infections by molecular docking simulation and found their significant binding affinity scores with our proposed candidate-drugs. Finally, we validated all of our findings by the literature review. Therefore, the proposed candidate-drugs might play a vital role for the treatment against different variants of SARS-CoV-2 infections with comorbidities, since the proposed HubGs are also associated with several comorbidities.
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Affiliation(s)
- Fee Faysal Ahmed
- Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
- Bioinformatics Lab., Department of Statistics, Rajshahi University, Rajshahi, Bangladesh
| | - Md. Selim Reza
- Bioinformatics Lab., Department of Statistics, Rajshahi University, Rajshahi, Bangladesh
| | - Md. Shahin Sarker
- Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Samiul Islam
- Department of Plant Pathology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Md. Parvez Mosharaf
- Bioinformatics Lab., Department of Statistics, Rajshahi University, Rajshahi, Bangladesh
| | - Sohel Hasan
- Department of Biochemistry and Molecular Biology, Rajshahi University, Rajshhi, Bangladesh
| | - Md. Nurul Haque Mollah
- Bioinformatics Lab., Department of Statistics, Rajshahi University, Rajshahi, Bangladesh
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11
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Kuchi A, Wu J, Fuloria J, Hicks C. Landscape of Molecular Crosstalk Perturbation between Lung Cancer and COVID-19. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:3454. [PMID: 35329141 PMCID: PMC8953719 DOI: 10.3390/ijerph19063454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Lung cancer patients have the worst outcomes when affected by coronavirus disease 2019 (COVID-19). The molecular mechanisms underlying the association between lung cancer and COVID-19 remain unknown. The objective of this investigation was to determine whether there is crosstalk in molecular perturbation between COVID-19 and lung cancer, and to identify a molecular signature, molecular networks and signaling pathways shared by the two diseases. METHODS We analyzed publicly available gene expression data from 52 severely affected COVID-19 human lung samples, 594 lung tumor samples and 54 normal disease-free lung samples. We performed network and pathways analysis to identify molecular networks and signaling pathways shared by the two diseases. RESULTS The investigation revealed a signature of genes associated with both diseases and signatures of genes uniquely associated with each disease, confirming crosstalk in molecular perturbation between COVID-19 and lung cancer. In addition, the analysis revealed molecular networks and signaling pathways associated with both diseases. CONCLUSIONS The investigation revealed crosstalk in molecular perturbation between COVID-19 and lung cancer, and molecular networks and signaling pathways associated with the two diseases. Further research on a population impacted by both diseases is recommended to elucidate molecular drivers of the association between the two diseases.
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Affiliation(s)
- Aditi Kuchi
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA
| | - Jiande Wu
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA
| | - Jyotsna Fuloria
- University Medical Center New Orleans, 2000 Canal Street, New Orleans, LA 70112, USA
| | - Chindo Hicks
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA
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12
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Computational identification of host genomic biomarkers highlighting their functions, pathways and regulators that influence SARS-CoV-2 infections and drug repurposing. Sci Rep 2022; 12:4279. [PMID: 35277538 PMCID: PMC8915158 DOI: 10.1038/s41598-022-08073-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 02/15/2022] [Indexed: 12/13/2022] Open
Abstract
The pandemic threat of COVID-19 has severely destroyed human life as well as the economy around the world. Although, the vaccination has reduced the outspread, but people are still suffering due to the unstable RNA sequence patterns of SARS-CoV-2 which demands supplementary drugs. To explore novel drug target proteins, in this study, a transcriptomics RNA-Seq data generated from SARS-CoV-2 infection and control samples were analyzed. We identified 109 differentially expressed genes (DEGs) that were utilized to identify 10 hub-genes/proteins (TLR2, USP53, GUCY1A2, SNRPD2, NEDD9, IGF2, CXCL2, KLF6, PAG1 and ZFP36) by the protein–protein interaction (PPI) network analysis. The GO functional and KEGG pathway enrichment analyses of hub-DEGs revealed some important functions and signaling pathways that are significantly associated with SARS-CoV-2 infections. The interaction network analysis identified 5 TFs proteins and 6 miRNAs as the key regulators of hub-DEGs. Considering 10 hub-proteins and 5 key TFs-proteins as drug target receptors, we performed their docking analysis with the SARS-CoV-2 3CL protease-guided top listed 90 FDA approved drugs. We found Torin-2, Rapamycin, Radotinib, Ivermectin, Thiostrepton, Tacrolimus and Daclatasvir as the top ranked seven candidate drugs. We investigated their resistance performance against the already published COVID-19 causing top-ranked 11 independent and 8 protonated receptor proteins by molecular docking analysis and found their strong binding affinities, which indicates that the proposed drugs are effective against the state-of-the-arts alternatives independent receptor proteins also. Finally, we investigated the stability of top three drugs (Torin-2, Rapamycin and Radotinib) by using 100 ns MD-based MM-PBSA simulations with the two top-ranked proposed receptors (TLR2, USP53) and independent receptors (IRF7, STAT1), and observed their stable performance. Therefore, the proposed drugs might play a vital role for the treatment against different variants of SARS-CoV-2 infections.
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13
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Bernasconi A, Cascianelli S. Scenarios for the Integration of Microarray Gene Expression Profiles in COVID-19-Related Studies. Methods Mol Biol 2022; 2401:195-215. [PMID: 34902130 DOI: 10.1007/978-1-0716-1839-4_13] [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] [Indexed: 06/14/2023]
Abstract
The COVID-19 pandemic has hit heavily many aspects of our lives. At this time, genomic research is concerned with exploiting available datasets and knowledge to fuel discovery on this novel disease. Studies that can precisely characterize the gene expression profiles of human hosts infected by SARS-CoV-2 are of significant relevance. However, not many such experiments have yet been produced to date, nor made publicly available online. Thus, it is of paramount importance that data analysts explore all possibilities to integrate information coming from similar viruses and related diseases; interestingly, microarray gene profile experiments become extremely valuable for this purpose. This chapter reviews the aspects that should be considered when integrating transcriptomics data, considering mainly samples infected by different viruses and combining together various data types and also the extracted knowledge. It describes a series of scenarios from studies performed in literature and it suggests possible other directions of noteworthy integration.
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Affiliation(s)
- Anna Bernasconi
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy.
| | - Silvia Cascianelli
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
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14
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Adil MS, Khulood D, Narayanan SP, Somanath PR. Bioinformatics analyses reveal cell-barrier junction modulations in lung epithelial cells on SARS-CoV-2 infection. Tissue Barriers 2021; 10:2000300. [PMID: 34740309 DOI: 10.1080/21688370.2021.2000300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cell junctions maintain the blood-tissue barriers to preserve vascular and tissue integrity. Viral infections reportedly modulate cell-cell junctions to facilitate their invasion. However, information on the effect of COVID-19 infection on the gene expression of cell junction and cytoskeletal proteins is limited. Using the Gene Expression Omnibus and Reactome databases, we analyzed the data on human lung A549, NHBE, and Calu-3 cells for the expression changes in cell junction and cytoskeletal proteins by SARS-CoV-2 (CoV-2) infection. The analysis revealed changes in 3,660 genes in A549, 100 genes in NHBE, and 592 genes in Calu-3 cells with CoV-2 infection. Interestingly, EGOT (9.8-, 3- and 8.3-fold; p < .05) and CSF3 (4.3-, 33- and 56.3-fold; p < .05) were the only two genes significantly elevated in all three cell lines (A549, NHBE and Calu-3, respectively). On the other hand, 39 genes related to cell junctions and cytoskeleton were modulated in lung cells, with DLL1 demonstrating alterations in all cells. Alterations were also seen in several miRNAs associated with the cell junction and cytoskeleton genes modulated in the analysis. Further, matrix metalloproteinases involved in disease pathologies, including MMP-3, -9, and -12 demonstrated elevated expression on CoV-2 infection (p < .05). The study findings emphasize the integral role of cell junction and cytoskeletal genes in COVID-19, suggesting their therapeutic potential. Our analysis also identified a distinct EGOT gene that has not been previously implicated in COVID-19. Further studies on these newly identified genes and miRNAs could lead to advances in the pathogenesis and therapeutics of COVID-19.
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Affiliation(s)
- Mir S Adil
- Clinical and Experimental Therapeutics, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA, USA
| | - Daulat Khulood
- Clinical and Experimental Therapeutics, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA, USA
| | - S Priya Narayanan
- Clinical and Experimental Therapeutics, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA, USA
| | - Payaningal R Somanath
- Clinical and Experimental Therapeutics, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA, USA
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15
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Nashiry MA, Sumi SS, Sharif Shohan MU, Alyami SA, Azad AKM, Moni MA. Bioinformatics and system biology approaches to identify the diseasome and comorbidities complexities of SARS-CoV-2 infection with the digestive tract disorders. Brief Bioinform 2021; 22:bbab126. [PMID: 33993223 PMCID: PMC8194728 DOI: 10.1093/bib/bbab126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19), although most commonly demonstrates respiratory symptoms, but there is a growing set of evidence reporting its correlation with the digestive tract and faeces. Interestingly, recent studies have shown the association of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection with gastrointestinal symptoms in infected patients but any sign of respiratory issues. Moreover, some studies have also shown that the presence of live SARS-CoV-2 virus in the faeces of patients with COVID-19. Therefore, the pathophysiology of digestive symptoms associated with COVID-19 has raised a critical need for comprehensive investigative efforts. To address this issue we have developed a bioinformatics pipeline involving a system biological framework to identify the effects of SARS-CoV-2 messenger RNA expression on deciphering its association with digestive symptoms in COVID-19 positive patients. Using two RNA-seq datasets derived from COVID-19 positive patients with celiac (CEL), Crohn's (CRO) and ulcerative colitis (ULC) as digestive disorders, we have found a significant overlap between the sets of differentially expressed genes from SARS-CoV-2 exposed tissue and digestive tract disordered tissues, reporting 7, 22 and 13 such overlapping genes, respectively. Moreover, gene set enrichment analysis, comprehensive analyses of protein-protein interaction network, gene regulatory network, protein-chemical agent interaction network revealed some critical association between SARS-CoV-2 infection and the presence of digestive disorders. The infectome, diseasome and comorbidity analyses also discover the influences of the identified signature genes in other risk factors of SARS-CoV-2 infection to human health. We hope the findings from this pathogenetic analysis may reveal important insights in deciphering the complex interplay between COVID-19 and digestive disorders and underpins its significance in therapeutic development strategy to combat against COVID-19 pandemic.
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Affiliation(s)
- Md Asif Nashiry
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Shauli Sarmin Sumi
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | | | - Salem A Alyami
- Department of Mathematics and Statistics, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13318, Saudi Arabia
| | - A K M Azad
- iThree Institute, Faculty of Science, University Technology of Sydney, Australia
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Australia
- Healthy Ageing Theme, The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
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16
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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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17
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Sun J, Fahmi NA, Nassereddeen H, Cheng S, Martinez I, Fan D, Yong J, Zhang W. Computational Methods to Study Human Transcript Variants in COVID-19 Infected Lung Cancer Cells. Int J Mol Sci 2021; 22:9684. [PMID: 34575842 PMCID: PMC8464664 DOI: 10.3390/ijms22189684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 12/23/2022] Open
Abstract
Microbes and viruses are known to alter host transcriptomes by means of infection. In light of recent challenges posed by the COVID-19 pandemic, a deeper understanding of the disease at the transcriptome level is needed. However, research about transcriptome reprogramming by post-transcriptional regulation is very limited. In this study, computational methods developed by our lab were applied to RNA-seq data to detect transcript variants (i.e., alternative splicing (AS) and alternative polyadenylation (APA) events). The RNA-seq data were obtained from a publicly available source, and they consist of mock-treated and SARS-CoV-2 infected (COVID-19) lung alveolar (A549) cells. Data analysis results show that more AS events are found in SARS-CoV-2 infected cells than in mock-treated cells, whereas fewer APA events are detected in SARS-CoV-2 infected cells. A combination of conventional differential gene expression analysis and transcript variants analysis revealed that most of the genes with transcript variants are not differentially expressed. This indicates that no strong correlation exists between differential gene expression and the AS/APA events in the mock-treated or SARS-CoV-2 infected samples. These genes with transcript variants can be applied as another layer of molecular signatures for COVID-19 studies. In addition, the transcript variants are enriched in important biological pathways that were not detected in the studies that only focused on differential gene expression analysis. Therefore, the pathways may lead to new molecular mechanisms of SARS-CoV-2 pathogenesis.
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Affiliation(s)
- Jiao Sun
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA; (J.S.); (N.A.F.)
- Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA;
| | - Naima Ahmed Fahmi
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA; (J.S.); (N.A.F.)
- Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA;
| | - Heba Nassereddeen
- Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA;
- Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL 32816, USA
| | - Sze Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA;
| | - Irene Martinez
- Department of Molecular Biotechnology, Universität Heidelberg, 69120 Heidelberg, Germany;
| | - Deliang Fan
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ 85287, USA;
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA;
| | - Wei Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA; (J.S.); (N.A.F.)
- Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA;
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18
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Meng Z, Guo S, Zhou Y, Li M, Wang M, Ying B. Applications of laboratory findings in the prevention, diagnosis, treatment, and monitoring of COVID-19. Signal Transduct Target Ther 2021; 6:316. [PMID: 34433805 PMCID: PMC8386162 DOI: 10.1038/s41392-021-00731-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 07/21/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
The worldwide pandemic of coronavirus disease 2019 (COVID-19) presents us with a serious public health crisis. To combat the virus and slow its spread, wider testing is essential. There is a need for more sensitive, specific, and convenient detection methods of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Advanced detection can greatly improve the ability and accuracy of the clinical diagnosis of COVID-19, which is conducive to the early suitable treatment and supports precise prophylaxis. In this article, we combine and present the latest laboratory diagnostic technologies and methods for SARS-CoV-2 to identify the technical characteristics, considerations, biosafety requirements, common problems with testing and interpretation of results, and coping strategies of commonly used testing methods. We highlight the gaps in current diagnostic capacity and propose potential solutions to provide cutting-edge technical support to achieve a more precise diagnosis, treatment, and prevention of COVID-19 and to overcome the difficulties with the normalization of epidemic prevention and control.
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Affiliation(s)
- Zirui Meng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Shuo Guo
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Mengjiao Li
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
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19
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Karami H, Derakhshani A, Ghasemigol M, Fereidouni M, Miri-Moghaddam E, Baradaran B, Tabrizi NJ, Najafi S, Solimando AG, Marsh LM, Silvestris N, De Summa S, Paradiso AV, Racanelli V, Safarpour H. Weighted Gene Co-Expression Network Analysis Combined with Machine Learning Validation to Identify Key Modules and Hub Genes Associated with SARS-CoV-2 Infection. J Clin Med 2021; 10:3567. [PMID: 34441862 PMCID: PMC8397209 DOI: 10.3390/jcm10163567] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/25/2021] [Accepted: 08/03/2021] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease-2019 (COVID-19) pandemic has caused an enormous loss of lives. Various clinical trials of vaccines and drugs are being conducted worldwide; nevertheless, as of today, no effective drug exists for COVID-19. The identification of key genes and pathways in this disease may lead to finding potential drug targets and biomarkers. Here, we applied weighted gene co-expression network analysis and LIME as an explainable artificial intelligence algorithm to comprehensively characterize transcriptional changes in bronchial epithelium cells (primary human lung epithelium (NHBE) and transformed lung alveolar (A549) cells) during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Our study detected a network that significantly correlated to the pathogenicity of COVID-19 infection based on identified hub genes in each cell line separately. The novel hub gene signature that was detected in our study, including PGLYRP4 and HEPHL1, may shed light on the pathogenesis of COVID-19, holding promise for future prognostic and therapeutic approaches. The enrichment analysis of hub genes showed that the most relevant biological process and KEGG pathways were the type I interferon signaling pathway, IL-17 signaling pathway, cytokine-mediated signaling pathway, and defense response to virus categories, all of which play significant roles in restricting viral infection. Moreover, according to the drug-target network, we identified 17 novel FDA-approved candidate drugs, which could potentially be used to treat COVID-19 patients through the regulation of four hub genes of the co-expression network. In conclusion, the aforementioned hub genes might play potential roles in translational medicine and might become promising therapeutic targets. Further in vitro and in vivo experimental studies are needed to evaluate the role of these hub genes in COVID-19.
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Affiliation(s)
- Hassan Karami
- Student Research Committee, Birjand University of Medical Sciences, Birjand 9717853577, Iran;
| | - Afshin Derakhshani
- Laboratory of Experimental Pharmacology, IRCCS-Istituto Tumori Giovanni Paolo II, 70124 Bari, Italy;
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 516615731, Iran; (B.B.); (N.J.T.); (S.N.)
| | - Mohammad Ghasemigol
- Department of Computer Engineering, University of Birjand, Birjand 9717434765, Iran;
| | - Mohammad Fereidouni
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand 9717853577, Iran;
| | - Ebrahim Miri-Moghaddam
- Cardiovascular Diseases Research Center & Department of Molecular Medicine, School of Medicine, Birjand University of Medical Sciences, Birjand 9717853577, Iran;
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 516615731, Iran; (B.B.); (N.J.T.); (S.N.)
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz 516615731, Iran
| | - Neda Jalili Tabrizi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 516615731, Iran; (B.B.); (N.J.T.); (S.N.)
| | - Souzan Najafi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 516615731, Iran; (B.B.); (N.J.T.); (S.N.)
| | - Antonio Giovanni Solimando
- Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70121 Bari, Italy; (A.G.S.); (N.S.)
| | - Leigh M. Marsh
- Ludwig Boltzmann Institute for Lung Vascular Research, Neue Stiftingtalstraße 6/VI, 8010 Graz, Austria;
| | - Nicola Silvestris
- Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70121 Bari, Italy; (A.G.S.); (N.S.)
- Medical Oncology Unit, IRCCS-Istituto Tumori “Giovanni Paolo II” of Bari, 70124 Bari, Italy
| | - Simona De Summa
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS-Istituto Tumori ‘Giovanni Paolo II’, 70124 Bari, Italy;
| | | | - Vito Racanelli
- Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70121 Bari, Italy; (A.G.S.); (N.S.)
| | - Hossein Safarpour
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand 9717853577, Iran;
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20
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Auwul MR, Rahman MR, Gov E, Shahjaman M, Moni MA. Bioinformatics and machine learning approach identifies potential drug targets and pathways in COVID-19. Brief Bioinform 2021; 22:6220170. [PMID: 33839760 PMCID: PMC8083354 DOI: 10.1093/bib/bbab120] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/15/2021] [Accepted: 03/13/2021] [Indexed: 12/12/2022] Open
Abstract
Current coronavirus disease-2019 (COVID-19) pandemic has caused massive loss of lives. Clinical trials of vaccines and drugs are currently being conducted around the world; however, till now no effective drug is available for COVID-19. Identification of key genes and perturbed pathways in COVID-19 may uncover potential drug targets and biomarkers. We aimed to identify key gene modules and hub targets involved in COVID-19. We have analyzed SARS-CoV-2 infected peripheral blood mononuclear cell (PBMC) transcriptomic data through gene coexpression analysis. We identified 1520 and 1733 differentially expressed genes (DEGs) from the GSE152418 and CRA002390 PBMC datasets, respectively (FDR < 0.05). We found four key gene modules and hub gene signature based on module membership (MMhub) statistics and protein-protein interaction (PPI) networks (PPIhub). Functional annotation by enrichment analysis of the genes of these modules demonstrated immune and inflammatory response biological processes enriched by the DEGs. The pathway analysis revealed the hub genes were enriched with the IL-17 signaling pathway, cytokine-cytokine receptor interaction pathways. Then, we demonstrated the classification performance of hub genes (PLK1, AURKB, AURKA, CDK1, CDC20, KIF11, CCNB1, KIF2C, DTL and CDC6) with accuracy >0.90 suggesting the biomarker potential of the hub genes. The regulatory network analysis showed transcription factors and microRNAs that target these hub genes. Finally, drug-gene interactions analysis suggests amsacrine, BRD-K68548958, naproxol, palbociclib and teniposide as the top-scored repurposed drugs. The identified biomarkers and pathways might be therapeutic targets to the COVID-19.
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Affiliation(s)
- Md Rabiul Auwul
- School of Economics and Statistics, Guangzhou University, Guangzhou 510006, China
| | - Md Rezanur Rahman
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Sirajgonj-6751, Bangladesh
| | - Esra Gov
- Department of Bioengineering, Adana Alparslan Turkes Science and Technology University, Adana-01250, Turkey
| | - Md Shahjaman
- Department of Statistics, Begum Rokeya University, Rangpur-5400, Bangladesh
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Australia
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21
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Taz TA, Ahmed K, Paul BK, Al-Zahrani FA, Mahmud SMH, Moni MA. Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients. Brief Bioinform 2021; 22:1451-1465. [PMID: 33611340 PMCID: PMC7929374 DOI: 10.1093/bib/bbab026] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
This study aimed to identify significant gene expression profiles of the human lung epithelial cells caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. We performed a comparative genomic analysis to show genomic observations between SARS-CoV and SARS-CoV-2. A phylogenetic tree has been carried for genomic analysis that confirmed the genomic variance between SARS-CoV and SARS-CoV-2. Transcriptomic analyses have been performed for SARS-CoV-2 infection responses and pulmonary arterial hypertension (PAH) patients' lungs as a number of patients have been identified who faced PAH after being diagnosed with coronavirus disease 2019 (COVID-19). Gene expression profiling showed significant expression levels for SARS-CoV-2 infection responses to human lung epithelial cells and PAH lungs as well. Differentially expressed genes identification and integration showed concordant genes (SAA2, S100A9, S100A8, SAA1, S100A12 and EDN1) for both SARS-CoV-2 and PAH samples, including S100A9 and S100A8 genes that showed significant interaction in the protein-protein interactions network. Extensive analyses of gene ontology and signaling pathways identification provided evidence of inflammatory responses regarding SARS-CoV-2 infections. The altered signaling and ontology pathways that have emerged from this research may influence the development of effective drugs, especially for the people with preexisting conditions. Identification of regulatory biomolecules revealed the presence of active promoter gene of SARS-CoV-2 in Transferrin-micro Ribonucleic acid (TF-miRNA) co-regulatory network. Predictive drug analyses provided concordant drug compounds that are associated with SARS-CoV-2 infection responses and PAH lung samples, and these compounds showed significant immune response against the RNA viruses like SARS-CoV-2, which is beneficial in therapeutic development in the COVID-19 pandemic.
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Affiliation(s)
- Tasnimul Alam Taz
- Department of Software Engineering, Daffodil International University, Bangladesh
| | - Kawsar Ahmed
- Department of Information and Communication Technology (ICT) at Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Bikash Kumar Paul
- Department of ICT at Mawlana Bhashani Science and Technology University, Bangladesh
| | | | - S M Hasan Mahmud
- Department of Software Engineering, Daffodil International University, Bangladesh
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22
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Moni MA, Lin PI, Quinn JMW, Eapen V. COVID-19 patient transcriptomic and genomic profiling reveals comorbidity interactions with psychiatric disorders. Transl Psychiatry 2021; 11:160. [PMID: 33723208 PMCID: PMC7957287 DOI: 10.1038/s41398-020-01151-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/28/2020] [Accepted: 12/07/2020] [Indexed: 12/16/2022] Open
Abstract
Psychiatric symptoms are seen in some COVID-19 patients, as direct or indirect sequelae, but it is unclear whether SARS-CoV-2 infection interacts with underlying neuronal or psychiatric susceptibilities. Such interactions might arise from COVID-19 immune responses, from infection of neurons themselves or may reflect social-psychological causes. To clarify this we sought the key gene expression pathways altered in COVID-19 also affected in bipolar disorder, post-traumatic stress disorder (PTSD) and schizophrenia, since this may identify pathways of interaction that could be treatment targets. We performed large scale comparisons of whole transcriptome data and immune factor transcript data in peripheral blood mononuclear cells (PBMC) from COVID-19 patients and patients with psychiatric disorders. We also analysed genome-wide association study (GWAS) data for symptomatic COVID-19 patients, comparing GWAS and whole-genome sequence data from patients with bipolar disorder, PTSD and schizophrenia patients. These studies revealed altered signalling and ontology pathways shared by COVID-19 patients and the three psychiatric disorders. Finally, co-expression and network analyses identified gene clusters common to the conditions. COVID-19 patients had peripheral blood immune system profiles that overlapped with those of patients with psychiatric conditions. From the pathways identified, PTSD profiles were the most highly correlated with COVID-19, perhaps consistent with stress-immune system interactions seen in PTSD. We also revealed common inflammatory pathways that may exacerbate psychiatric disorders, which may support the usage of anti-inflammatory medications in these patients. It also highlights the potential clinical application of multi-level dataset studies in difficult-to-treat psychiatric disorders in this COVID-19 pandemic.
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Affiliation(s)
- Mohammad Ali Moni
- Faculty of Medicine, School of Psychiatry, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Ping-I Lin
- Faculty of Medicine, School of Psychiatry, University of New South Wales, Sydney, NSW, 2052, Australia
- South Western Sydney Area Health Service, Sydney, NSW, 2170, Australia
| | - Julian M W Quinn
- The Garvan Institute of Medical Research, Healthy Ageing Theme, Darlinghurst, NSW, 2010, Australia
- Division of Surgery and Anesthesia, Royal North Shore Hospital SERT Institute, St Leonards, NSW, 2065, Australia
| | - Valsamma Eapen
- Faculty of Medicine, School of Psychiatry, University of New South Wales, Sydney, NSW, 2052, Australia.
- South Western Sydney Area Health Service, Sydney, NSW, 2170, Australia.
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