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Jahan E, Mazumder T, Hasan T, Ahmed KS, Amanat M, Hossain H, Supty SJ, Liya IJ, Shuvo MSR, Daula AFMSU. Metabolomic Approach to Identify the Potential Metabolites from Alpinia malaccensis for Treating SARS-CoV-2 Infection. Biochem Genet 2024:10.1007/s10528-024-10869-4. [PMID: 38955878 DOI: 10.1007/s10528-024-10869-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/10/2024] [Indexed: 07/04/2024]
Abstract
The advent of the new coronavirus, leading to the SARS-CoV-2 pandemic, has presented a substantial worldwide health hazard since its inception in the latter part of 2019. The severity of the current pandemic is exacerbated by the occurrence of re-infection or co-infection with SARS-CoV-2. Hence, comprehending the molecular process underlying the pathophysiology of sepsis and discerning possible molecular targets for therapeutic intervention holds significant importance. For the first time, 31 metabolites were tentatively identified by GC-MS analysis from Alpinia malaccensis. On the other hand, five phenolic compounds were identified and quantified from the plant in HPLC-DAD analysis, including (-) epicatechin, rutin hydrate, rosmarinic acid, quercetin, and kaempferol. Nine GC-MS and five HPLC-identified metabolites had shown interactions with 45 and 30 COVID-19-associated human proteins, respectively. Among the proteins, PARP1, FN1, PRKCA, EGFR, ALDH2, AKR1C3, AHR, and IKBKB have been found as potential therapeutic targets to mitigate SARS-CoV-2 infection. KEGG pathway analysis also showed a strong association of FN1, EGFR, and IKBKB genes with SARS-CoV-2 viral replication and cytokine overexpression due to viral infection. Protein-protein interaction (PPI) analysis also showed that TP53, MMP9, FN1, EGFR, and NOS2 proteins are highly related to the genes involved in COVID-19 comorbidity. These proteins showed interaction with the plant phytoconstituents as well. As the study offers a robust network-based procedure for identifying biomolecules relevant to COVID-19 disease, A. malaccensis could be a good source of effective therapeutic agents against COVID-19 and related viral diseases.
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Affiliation(s)
- Esrat Jahan
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Tanoy Mazumder
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Tarek Hasan
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Khondoker Shahin Ahmed
- Chemical Research Division, Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
| | - Muhammed Amanat
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Hemayet Hossain
- Chemical Research Division, Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
| | - Sumaiya Jannat Supty
- Department of Soil, Water and Environment, University of Dhaka, Dhaka, Bangladesh
| | - Israt Jahan Liya
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Md Sadikur Rahman Shuvo
- Department of Microbiology, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh.
| | - A F M Shahid Ud Daula
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh.
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Chatterjee S, Sanjeev BS. Over-representation analysis of angiogenic factors in immunosuppressive mechanisms in neoplasms and neurological conditions during COVID-19. Microb Pathog 2023; 185:106386. [PMID: 37865274 DOI: 10.1016/j.micpath.2023.106386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/27/2023] [Accepted: 10/09/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Recent studies emphasized the necessity to identify key (human) biological processes and pathways targeted by the Coronaviridae family of viruses, especially Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronavirus Disease (COVID-19) caused up to 33-55 % death rates in COVID-19 patients with malignant neoplasms and Alzheimer's disease. Given this scenario, we identified biological processes and pathways involved in various diseases which are most likely affected by COVID-19. METHODS The COVID-19 DisGeNET data set (v4.0) contains the associations between various diseases and human genes known to interact with viruses from Coronaviridae family and were obtained from the IntAct Coronavirus data set annotated with DisGeNET data. We constructed the disease-gene network to identify genes that are involved in various comorbid diseased states. Communities from the disease-gene network were identified using Louvain method and functional enrichment through over-representation analysis methodology was used to discover significant biological processes and pathways shared between COVID-19 and other diseases. RESULT The COVID-19 DisGeNET data set (v4.0) comprised of 828 human genes and 10,473 diseases (including various phenotypes) that together constituted nodes in the disease-gene network. Each of the 70,210 edges connects a human gene with an associated disease. The top 10 genes linked to most number of diseases were VEGFA, BCL2, CTNNB1, ALB, COX2, AGT, HLA-A, HMOX1, FGF2 and COMT. The most vulnerable group of patients thus discovered had comorbid conditions such as carcinomas, malignant neoplasms and Alzheimer's disease. Finally, we identified 15 potentially useful biological processes and pathways for improved therapies. Vascular endothelial growth factor (VEGF) is the key mediator of angiogenesis in cancer. It is widely distributed in the brain and plays a crucial role in brain inflammation regulating the level of angiopoietins. With a degree of 1899, VEGFA was associated with maximum number of diseases in the disease-gene network. Previous studies have indicated that increased levels of VEGFA in the blood results in dyspnea, Pulmonary Edema (PE), Acute Lung Injury (ALI) and Acute Respiratory Distress Syndrome (ARDS). In case of COVID-19 patients with neoplasms and other neurological symptoms, our results indicate VEGFA as a therapeutic target for inflammation suppression. As VEGFs are known to disproportionately affect cancer patients, improving endothelial permeability and vasodilation with anti-VEGF therapy could lead to suppression of inflammation and also improve oxygenation. As an outcome of our study, we make case for clinical investigations towards anti-VEGF therapies for such comorbid conditions affected by COVID-19 for better therapeutic outcomes.
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Affiliation(s)
- S Chatterjee
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, India.
| | - B S Sanjeev
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, India.
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Moretti AIS, Schreiber R, Wanschel ABA. Editorial: COVID-19 mechanisms on cardio-vascular dysfunction: from membrane receptors to immune response, volume II. Front Cardiovasc Med 2023; 10:1278067. [PMID: 37900568 PMCID: PMC10613079 DOI: 10.3389/fcvm.2023.1278067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/11/2023] [Indexed: 10/31/2023] Open
Affiliation(s)
- Ana Iochabel Soares Moretti
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
| | - Roberto Schreiber
- Department of Internal Medicine, School of Medical Sciences, State University of Campinas (UNICAMP), São Paulo, Brazil
| | - Amarylis B. A. Wanschel
- Department of Basic Pharmaceutical Sciences, Fred Wilson School of Pharmacy, High Point University, High Point, NC, United States
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Omit SBS, Akhter S, Rana HK, Rana ARMMH, Podder NK, Rakib MI, Nobi A. Identification of Comorbidities, Genomic Associations, and Molecular Mechanisms for COVID-19 Using Bioinformatics Approaches. BIOMED RESEARCH INTERNATIONAL 2023; 2023:6996307. [PMID: 36685671 PMCID: PMC9848821 DOI: 10.1155/2023/6996307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/09/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023]
Abstract
Several studies have been done to identify comorbidities of COVID-19. In this work, we developed an analytical bioinformatics framework to reveal COVID-19 comorbidities, their genomic associations, and molecular mechanisms accomplishing transcriptomic analyses of the RNA-seq datasets provided by the Gene Expression Omnibus (GEO) database, where normal and infected tissues were evaluated. Using the framework, we identified 27 COVID-19 correlated diseases out of 7,092 collected diseases. Analyzing clinical and epidemiological research, we noticed that our identified 27 diseases are associated with COVID-19, where hypertension, diabetes, obesity, and lung cancer are observed several times in COVID-19 patients. Therefore, we selected the above four diseases and performed assorted analyses to demonstrate the association between COVID-19 and hypertension, diabetes, obesity, and lung cancer as comorbidities. We investigated genomic associations with the cross-comparative analysis and Jaccard's similarity index, identifying shared differentially expressed genes (DEGs) and linking DEGs of COVID-19 and the comorbidities, in which we identified hypertension as the most associated illness. We also revealed molecular mechanisms by identifying statistically significant ten pathways and ten ontologies. Moreover, to understand cellular physiology, we did protein-protein interaction (PPI) analyses among the comorbidities and COVID-19. We also used the degree centrality method and identified ten biomarker hub proteins (IL1B, CXCL8, FN1, MMP9, CXCL10, IL1A, IRF7, VWF, CXCL9, and ISG15) that associate COVID-19 with the comorbidities. Finally, we validated our findings by searching the published literature. Thus, our analytical approach elicited interconnections between COVID-19 and the aforementioned comorbidities in terms of remarkable DEGs, pathways, ontologies, PPI, and biomarker hub proteins.
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Affiliation(s)
- Shudeb Babu Sen Omit
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Salma Akhter
- Department of Environmental Science and Disaster Management, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Humayan Kabir Rana
- Department of Computer Science and Engineering, Green University of Bangladesh, Dhaka 1207, Bangladesh
| | - A. R. M. Mahamudul Hasan Rana
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Nitun Kumar Podder
- Department of Computer Science and Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh
| | - Mahmudul Islam Rakib
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Ashadun Nobi
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
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Li C, Yue L, Ju Y, Wang J, Chen M, Lu H, Liu S, Liu T, Wang J, Hu X, Tuohetaerbaike B, Wen H, Zhang W, Xu S, Jiang C, Chen F. Serum Proteomic Analysis for New Types of Long-Term Persistent COVID-19 Patients in Wuhan. Microbiol Spectr 2022; 10:e0127022. [PMID: 36314975 PMCID: PMC9784772 DOI: 10.1128/spectrum.01270-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/07/2022] [Indexed: 12/24/2022] Open
Abstract
The emergence of a new type of COVID-19 patients, who were retested positive after hospital discharge with long-term persistent SARS-CoV-2 infection but without COVID-19 clinical symptoms (hereinafter, LTPPs), poses novel challenges to COVID-19 treatment and prevention. Why was there such a contradictory phenomenon in LTPPs? To explore the mechanism underlying this phenomenon, we performed quantitative proteomic analyses using the sera of 12 LTPPs (Wuhan Pulmonary Hospital), with the longest carrying history of 132 days, and mainly focused on 7 LTPPs without hypertension (LTPPs-NH). The results showed differential serum protein profiles between LTPPs/LTPPs-NH and health controls. Further analysis identified 174 differentially-expressed-proteins (DEPs) for LTPPs, and 165 DEPs for LTPPs-NH, most of which were shared. GO and KEGG analyses for these DEPs revealed significant enrichment of "coagulation" and "immune response" in both LTPPs and LTPPs-NH. A unity of contradictory genotypes in the 2 aspects were then observed: some DEPs showed the same dysregulated expressed trend as that previously reported for patients in the acute phase of COVID-19, which might be caused by long-term stimulation of persistent SARS-CoV-2 infection in LTPPs, further preventing them from complete elimination; in contrast, some DEPs showed the opposite expression trend in expression, so as to retain control of COVID-19 clinical symptoms in LTPPs. Overall, the contrary effects of these DEPs worked together to maintain the balance of LTPPs, further endowing their contradictory steady-state with long-term persistent SARS-CoV-2 infection but without symptoms. Additionally, our study revealed some potential therapeutic targets of COVID-19. Further studies on these are warranted. IMPORTANCE This study reported a new type of COVID-19 patients and explored the underlying molecular mechanism by quantitative proteomic analyses. DEPs were significantly enriched in "coagulation" and "immune response". Importantly, we identified 7 "coagulation system"- and 9 "immune response"-related DEPs, the expression levels of which were consistent with those previously reported for patients in the acute phase of COVID-19, which appeared to play a role in avoiding the complete elimination of SARS-CoV-2 in LTPPs. On the contrary, 6 "coagulation system"- and 5 "immune response"-related DEPs showed the opposite trend in expression. The 11 inconsistent serum proteins seem to play a key role in the fight against long-term persistent SARS-CoV-2 infection, further retaining control of COVID-19 clinical symptom of LTPPs. The 26 proteins can serve as potential therapeutic targets and are thus valuable for the treatment of LTPPs; further studies on them are warranted.
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Affiliation(s)
- Cuidan Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
| | - Liya Yue
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
| | - Yingjiao Ju
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengfan Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Lu
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sitong Liu
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Liu
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
| | - Xin Hu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
| | - Bahetibieke Tuohetaerbaike
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
| | - Hao Wen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
| | - Wenbao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
| | - Sihong Xu
- Division II of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Chunlai Jiang
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China
| | - Fei Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, China
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Abavisani M, Rahimian K, Mahdavi B, Tokhanbigli S, Mollapour Siasakht M, Farhadi A, Kodori M, Mahmanzar M, Meshkat Z. Mutations in SARS-CoV-2 structural proteins: a global analysis. Virol J 2022; 19:220. [PMID: 36528612 PMCID: PMC9759450 DOI: 10.1186/s12985-022-01951-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Emergence of new variants mainly variants of concerns (VOC) is caused by mutations in main structural proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, we aimed to investigate the mutations among structural proteins of SARS-CoV-2 globally. METHODS We analyzed samples of amino-acid sequences (AASs) for envelope (E), membrane (M), nucleocapsid (N), and spike (S) proteins from the declaration of the coronavirus 2019 (COVID-19) as pandemic to January 2022. The presence and location of mutations were then investigated by aligning the sequences to the reference sequence and categorizing them based on frequency and continent. Finally, the related human genes with the viral structural genes were discovered, and their interactions were reported. RESULTS The results indicated that the most relative mutations among the E, M, N, and S AASs occurred in the regions of 7 to 14, 66 to 88, 164 to 205, and 508 to 635 AAs, respectively. The most frequent mutations in E, M, N, and S proteins were T9I, I82T, R203M/R203K, and D614G. D614G was the most frequent mutation in all six geographical areas. Following D614G, L18F, A222V, E484K, and N501Y, respectively, were ranked as the most frequent mutations in S protein globally. Besides, A-kinase Anchoring Protein 8 Like (AKAP8L) was shown as the linkage unit between M, E, and E cluster genes. CONCLUSION Screening the structural protein mutations can help scientists introduce better drug and vaccine development strategies.
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Affiliation(s)
- Mohammad Abavisani
- grid.411583.a0000 0001 2198 6209Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran ,grid.411583.a0000 0001 2198 6209Department of Microbiology and Virology, School of Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Karim Rahimian
- grid.46072.370000 0004 0612 7950Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Bahar Mahdavi
- grid.417689.5Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Samaneh Tokhanbigli
- grid.411463.50000 0001 0706 2472Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Mahsa Mollapour Siasakht
- grid.5645.2000000040459992XDepartment of Biochemistry, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Amin Farhadi
- grid.412462.70000 0000 8810 3346Department of Biology, Payame Noor University, Tehran, Iran
| | - Mansoor Kodori
- grid.510756.00000 0004 4649 5379Non Communicable Diseases Research Center, Bam University of Medical Sciences, Bam, Iran
| | - Mohammadamin Mahmanzar
- grid.46072.370000 0004 0612 7950Department of Bioinformatics, Kish International Campus University of Tehran, Kish, Iran
| | - Zahra Meshkat
- grid.411583.a0000 0001 2198 6209Department of Microbiology and Virology, School of Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Mujalli A, Alghamdi KS, Nasser KK, Al-Rayes N, Banaganapalli B, Shaik NA, Elango R. Bioinformatics insights into the genes and pathways on severe COVID-19 pathology in patients with comorbidities. Front Physiol 2022; 13:1045469. [PMID: 36589459 PMCID: PMC9795193 DOI: 10.3389/fphys.2022.1045469] [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: 09/15/2022] [Accepted: 11/15/2022] [Indexed: 12/23/2022] Open
Abstract
Background: Coronavirus disease (COVID-19) infection is known for its severe clinical pathogenesis among individuals with pre-existing comorbidities. However, the molecular basis of this observation remains elusive. Thus, this study aimed to map key genes and pathway alterations in patients with COVID-19 and comorbidities using robust systems biology approaches. Methods: The publicly available genome-wide transcriptomic datasets from 120 COVID-19 patients, 281 patients suffering from different comorbidities (like cardiovascular diseases, atherosclerosis, diabetes, and obesity), and 252 patients with different infectious diseases of the lung (respiratory syncytial virus, influenza, and MERS) were studied using a range of systems biology approaches like differential gene expression, gene ontology (GO), pathway enrichment, functional similarity, mouse phenotypic analysis and drug target identification. Results: By cross-mapping the differentially expressed genes (DEGs) across different datasets, we mapped 274 shared genes to severe symptoms of COVID-19 patients or with comorbidities alone. GO terms and functional pathway analysis highlighted genes in dysregulated pathways of immune response, interleukin signaling, FCGR activation, regulation of cytokines, chemokines secretion, and leukocyte migration. Using network topology parameters, phenotype associations, and functional similarity analysis with ACE2 and TMPRSS2-two key receptors for this virus-we identified 17 genes with high connectivity (CXCL10, IDO1, LEPR, MME, PTAFR, PTGS2, MAOB, PDE4B, PLA2G2A, COL5A1, ICAM1, SERPINE1, ABCB1, IL1R1, ITGAL, NCAM1 and PRKD1) potentially contributing to the clinical severity of COVID-19 infection in patients with comorbidities. These genes are predicted to be tractable and/or with many existing approved inhibitors, modulators, and enzymes as drugs. Conclusion: By systemic implementation of computational methods, this study identified potential candidate genes and pathways likely to confer disease severity in COVID-19 patients with pre-existing comorbidities. Our findings pave the way to develop targeted repurposed therapies in COVID-19 patients.
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Affiliation(s)
- Abdulrahman Mujalli
- Department of Genetic Medicine, King Abdulaziz University, Jeddah, Saudi Arabia,Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia,Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia,*Correspondence: Abdulrahman Mujalli, ; Ramu Elango,
| | - Kawthar Saad Alghamdi
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia,Department of Biology, Faculty of Science, University of Hafr Al Batin, Hafar Al-Batin, Saudi Arabia
| | - Khalidah Khalid Nasser
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia,Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nuha Al-Rayes
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia,Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banaganapalli
- Department of Genetic Medicine, King Abdulaziz University, Jeddah, Saudi Arabia,Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor Ahmad Shaik
- Department of Genetic Medicine, King Abdulaziz University, Jeddah, Saudi Arabia,Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ramu Elango
- Department of Genetic Medicine, King Abdulaziz University, Jeddah, Saudi Arabia,Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia,*Correspondence: Abdulrahman Mujalli, ; Ramu Elango,
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Taheri G, Habibi M. Comprehensive analysis of pathways in Coronavirus 2019 (COVID-19) using an unsupervised machine learning method. Appl Soft Comput 2022; 128:109510. [PMID: 35992221 PMCID: PMC9384336 DOI: 10.1016/j.asoc.2022.109510] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/07/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022]
Abstract
The World Health Organization (WHO) introduced “Coronavirus disease 19” or “COVID-19” as a novel coronavirus in March 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the fast discovery of effective treatments to fight this worldwide crisis. Artificial intelligence and bioinformatics analysis pipelines can assist with finding biomarkers, explanations, and cures. Artificial intelligence and machine learning methods provide powerful infrastructures for interpreting and understanding the available data. On the other hand, pathway enrichment analysis, as a dominant tool, could help researchers discover potential key targets present in biological pathways of host cells that are targeted by SARS-CoV-2. In this work, we propose a two-stage machine learning approach for pathway analysis. During the first stage, four informative gene sets that can represent important COVID-19 related pathways are selected. These “representative genes” are associated with the COVID-19 pathology. Then, two distinctive networks were constructed for COVID-19 related signaling and disease pathways. In the second stage, the pathways of each network are ranked with respect to some unsupervised scorning method based on our defined informative features. Finally, we present a comprehensive analysis of the top important pathways in both networks. Materials and implementations are available at: https://github.com/MahnazHabibi/Pathway.
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Affiliation(s)
- Golnaz Taheri
- Department of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Mahnaz Habibi
- Department of Mathematics, Qazvin Branch, Islamic Azad University, Qazvin, Iran
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9
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Méndez-Frausto G, Godina-González S, Rivas-Santiago CE, Nungaray-Anguiano E, Mendoza-Almanza G, Rivas-Santiago B, Galván-Tejada CE, Gonzalez-Curiel IE. Downregulation of sCD40 and sCTLA4 in Recovered COVID-19 Patients with Comorbidities. Pathogens 2022; 11:pathogens11101128. [PMID: 36297185 PMCID: PMC9608172 DOI: 10.3390/pathogens11101128] [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: 08/03/2022] [Revised: 09/15/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022] Open
Abstract
The aim of this study was to analyze molecules associated with regulatory immune response in unvaccinated, recovered COVID-19 patients with and without diabetes mellitus (DM) and hypertension (HTN). We determined anti-SARS-CoV-2 nucleocapsid IgG in plasma by electrochemiluminescence immunoassay. The levels of sCD40, TGF-ß, IL-10, and sCTLA-4 were assessed by ELISA in the serum of the subjects, as well as in healthy donors. We observed that only half of the subjects in the non-comorbid group produced antibodies, whereas all subjects in comorbid groups were IgG-positive for the anti-SARS-CoV-2 nucleocapsid. High levels of sCTL-4 were observed in the non-comorbid group, and the level of IL-10 was observed to increase in seropositive subjects without comorbidities. TGF-ß concentration was similar in all groups studied. Finally, sCD40 decreased in the comorbid group. In conclusion, our results suggest that comorbidities such as DM and HTN alter the production of co-stimulatory inhibitory molecules sCTLA-4 and sCD40 in subjects recovering from mild COVID-19. The alterations observed here were independent of seropositivity, suggesting an effective humoral immune response against COVID-19 separate from the levels of co-stimulatory inhibitory molecules.
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Affiliation(s)
- Gwendolyne Méndez-Frausto
- Laboratorio de Inmunotoxicología y Terapéutica Experimental, Unidad Académica de Ciencias Químicas, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico
| | - Susana Godina-González
- Laboratorio de Biomarcadores, Unidad Académica de Ciencias Químicas, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico
| | - César E. Rivas-Santiago
- CONACYT-Academic Unit of Chemical Sciences, Autonomous University of Zacatecas, Zacatecas 98160, Mexico
| | - Edna Nungaray-Anguiano
- Laboratorio de Inmunotoxicología y Terapéutica Experimental, Unidad Académica de Ciencias Químicas, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico
| | - Gretel Mendoza-Almanza
- CONACYT-Academic Unit of Chemical Sciences, Autonomous University of Zacatecas, Zacatecas 98160, Mexico
| | | | - Carlos E. Galván-Tejada
- Unidad Académica de Ingeniería Eléctrica, Universidad Autónoma de Zacatecas, Zacatecas 98000, Mexico
| | - Irma E. Gonzalez-Curiel
- Laboratorio de Inmunotoxicología y Terapéutica Experimental, Unidad Académica de Ciencias Químicas, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico
- Correspondence: ; Tel.: +52-492-1324310
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10
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Das D, Podder S. Deregulation of ceRNA Networks in Frontal Cortex and Choroid Plexus of Brain during SARS-CoV-2 Infection Aggravates Neurological Manifestations: An Insight from Bulk and Single-Cell Transcriptomic Analyses. Adv Biol (Weinh) 2022; 6:e2101310. [PMID: 35661455 PMCID: PMC9348399 DOI: 10.1002/adbi.202101310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/20/2022] [Indexed: 01/28/2023]
Abstract
Although transcriptomic studies of SARS-CoV-2-infected brains have depicted variability in gene expression, the landscape of deregulated cell-specific regulatory circuits has not been elucidated yet. Hence, bulk and single-cell RNA-seq data are analyzed to gain detailed insights. Initially, two ceRNA networks with 19 and 3 differentially expressed (DE) hub lncRNAs are reconstructed in SARS-CoV-2 infected Frontal Cortex (FC) and Choroid Plexus (CP), respectively. Functional and pathway enrichment analyses of downstream mRNAs of deregulated ceRNA axes demonstrate impairment of neurological processes. Mapping of hub lncRNA-mRNA pairs from bulk RNA-seq with snRNA-seq data has indicated that NORAD, NEAT1, and STXBP5-AS1 are downregulated across 4, 4, and 2 FC cell types, respectively. At the same time, MIRLET7BHG and MALAT1 are upregulated in excitatory neurons of FC and neurons of CP, respectively. Here, it is hypothesized that downregulation of NORAD, NEAT1, and STXBP5-AS1, and upregulation of MIRLET7BHG and MALAT1 might deregulate respectively 51, 6, and 37, and 31 and 19 mRNAs in cell types of FC and CP. Afterward, 13 therapeutic miRNAs are traced that might safeguard against deregulated lncRNA-mRNA pairs of NORAD, NEAT1, and MIRLET7BHG in FC. This study helps to explain the plausible mechanism of post-COVID neurological manifestation and also to devise therapeutics against it.
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Affiliation(s)
- Deepyaman Das
- Department of MicrobiologyRaiganj UniversityRaiganjUttar DinajpurWest Bengal733134India
| | - Soumita Podder
- Department of MicrobiologyRaiganj UniversityRaiganjUttar DinajpurWest Bengal733134India
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11
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Al-Mustanjid M, Mahmud SMH, Akter F, Rahman MS, Hossen MS, Rahman MH, Moni MA. Systems biology models to identify the influence of SARS-CoV-2 infections to the progression of human autoimmune diseases. INFORMATICS IN MEDICINE UNLOCKED 2022; 32:101003. [PMID: 35818398 PMCID: PMC9259025 DOI: 10.1016/j.imu.2022.101003] [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: 02/17/2022] [Revised: 06/25/2022] [Accepted: 06/25/2022] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been circulating since 2019, and its global dominance is rising. Evidences suggest the respiratory illness SARS-CoV-2 has a sensitive affect on causing organ damage and other complications to the patients with autoimmune diseases (AD), posing a significant risk factor. The genetic interrelationships and molecular appearances between SARS-CoV-2 and AD are yet unknown. We carried out the transcriptomic analytical framework to delve into the SARS-CoV-2 impacts on AD progression. We analyzed both gene expression microarray and RNA-Seq datasets from SARS-CoV-2 and AD affected tissues. With neighborhood-based benchmarks and multilevel network topology, we obtained dysfunctional signaling and ontological pathways, gene disease (diseasesome) association network and protein-protein interaction network (PPIN), uncovered essential shared infection recurrence connectivities with biological insights underlying between SARS-CoV-2 and AD. We found a total of 77, 21, 9, 54 common DEGs for SARS-CoV-2 and inflammatory bowel disorder (IBD), SARS-CoV-2 and rheumatoid arthritis (RA), SARS-CoV-2 and systemic lupus erythematosus (SLE) and SARS-CoV-2 and type 1 diabetes (T1D). The enclosure of these common DEGs with bimolecular networks revealed 10 hub proteins (FYN, VEGFA, CTNNB1, KDR, STAT1, B2M, CD3G, ITGAV, TGFB3). Drugs such as amlodipine besylate, vorinostat, methylprednisolone, and disulfiram have been identified as a common ground between SARS-CoV-2 and AD from drug repurposing investigation which will stimulate the optimal selection of medications in the battle against this ongoing pandemic triggered by COVID-19.
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Affiliation(s)
- Md Al-Mustanjid
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - S M Hasan Mahmud
- Department of Computer Science, American International University-Bangladesh, Dhaka, 1229, Bangladesh
| | - Farzana Akter
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Shazzadur Rahman
- Department of Computer Science & Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Sajid Hossen
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia-7003, Bangladesh
| | - Mohammad Ali Moni
- Department of Computer Science and Engineering, Pabna Science & Technology University, Pabna, 6600, Bangladesh
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12
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Sefik E, Qu R, Junqueira C, Kaffe E, Mirza H, Zhao J, Brewer JR, Han A, Steach HR, Israelow B, Blackburn HN, Velazquez SE, Chen YG, Halene S, Iwasaki A, Meffre E, Nussenzweig M, Lieberman J, Wilen CB, Kluger Y, Flavell RA. Inflammasome activation in infected macrophages drives COVID-19 pathology. Nature 2022; 606:585-593. [PMID: 35483404 PMCID: PMC9288243 DOI: 10.1038/s41586-022-04802-1] [Citation(s) in RCA: 239] [Impact Index Per Article: 119.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 04/25/2022] [Indexed: 01/18/2023]
Abstract
Severe COVID-19 is characterized by persistent lung inflammation, inflammatory cytokine production, viral RNA and a sustained interferon (IFN) response, all of which are recapitulated and required for pathology in the SARS-CoV-2-infected MISTRG6-hACE2 humanized mouse model of COVID-19, which has a human immune system1-20. Blocking either viral replication with remdesivir21-23 or the downstream IFN-stimulated cascade with anti-IFNAR2 antibodies in vivo in the chronic stages of disease attenuates the overactive immune inflammatory response, especially inflammatory macrophages. Here we show that SARS-CoV-2 infection and replication in lung-resident human macrophages is a critical driver of disease. In response to infection mediated by CD16 and ACE2 receptors, human macrophages activate inflammasomes, release interleukin 1 (IL-1) and IL-18, and undergo pyroptosis, thereby contributing to the hyperinflammatory state of the lungs. Inflammasome activation and the accompanying inflammatory response are necessary for lung inflammation, as inhibition of the NLRP3 inflammasome pathway reverses chronic lung pathology. Notably, this blockade of inflammasome activation leads to the release of infectious virus by the infected macrophages. Thus, inflammasomes oppose host infection by SARS-CoV-2 through the production of inflammatory cytokines and suicide by pyroptosis to prevent a productive viral cycle.
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Affiliation(s)
- Esen Sefik
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Rihao Qu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Caroline Junqueira
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Eleanna Kaffe
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Haris Mirza
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Jun Zhao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - J Richard Brewer
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Ailin Han
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Holly R Steach
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Benjamin Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Holly N Blackburn
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Sofia E Velazquez
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Michel Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Yuval Kluger
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Program of Applied Mathematics, Yale University, New Haven, CT, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.
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13
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Sefik E, Israelow B, Mirza H, Zhao J, Qu R, Kaffe E, Song E, Halene S, Meffre E, Kluger Y, Nussenzweig M, Wilen CB, Iwasaki A, Flavell RA. A humanized mouse model of chronic COVID-19. Nat Biotechnol 2022; 40:906-920. [PMID: 34921308 PMCID: PMC9203605 DOI: 10.1038/s41587-021-01155-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 11/05/2021] [Indexed: 12/15/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease that can present as an uncontrolled, hyperactive immune response, causing severe immunological injury. Existing rodent models do not recapitulate the sustained immunopathology of patients with severe disease. Here we describe a humanized mouse model of COVID-19 that uses adeno-associated virus to deliver human ACE2 to the lungs of humanized MISTRG6 mice. This model recapitulates innate and adaptive human immune responses to severe acute respiratory syndrome coronavirus 2 infection up to 28 days after infection, with key features of chronic COVID-19, including weight loss, persistent viral RNA, lung pathology with fibrosis, a human inflammatory macrophage response, a persistent interferon-stimulated gene signature and T cell lymphopenia. We used this model to study two therapeutics on immunopathology, patient-derived antibodies and steroids and found that the same inflammatory macrophages crucial to containing early infection later drove immunopathology. This model will enable evaluation of COVID-19 disease mechanisms and treatments.
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Affiliation(s)
- Esen Sefik
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Benjamin Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Haris Mirza
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Jun Zhao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Rihao Qu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Eleanna Kaffe
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Yuval Kluger
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Michel Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.
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14
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Fricke-Galindo I, Buendia-Roldan I, Chavez-Galan L, Pérez-Rubio G, Hernández-Zenteno RDJ, Ramos-Martinez E, Zazueta-Márquez A, Reyes-Melendres F, Alarcón-Dionet A, Guzmán-Vargas J, Bravo-Gutiérrez OA, Quintero-Puerta T, Gutiérrez-Pérez IA, Ortega-Martínez A, Ambrocio-Ortiz E, Nava-Quiroz KJ, Bañuelos-Flores JL, Jaime-Capetillo ME, Mejía M, Rojas-Serrano J, Falfán-Valencia R. SERPINE1 rs6092 Variant Is Related to Plasma Coagulation Proteins in Patients with Severe COVID-19 from a Tertiary Care Hospital. BIOLOGY 2022; 11:biology11040595. [PMID: 35453794 PMCID: PMC9029072 DOI: 10.3390/biology11040595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/17/2022] [Accepted: 04/12/2022] [Indexed: 12/24/2022]
Abstract
An impaired coagulation process has been described in patients with severe or critical coronavirus disease (COVID-19). Nevertheless, the implication of coagulation-related genes has not been explored. We aimed to evaluate the impact of F5 rs6025 and SERPINE1 rs6092 on invasive mechanical ventilation (IMV) requirement and the levels of coagulation proteins among patients with severe COVID-19. Four-hundred fifty-five patients with severe COVID-19 were genotyped using TaqMan assays. Coagulation-related proteins (P-Selectin, D-dimer, P-selectin glycoprotein ligand-1, tissue plasminogen activator [tPA], plasminogen activator inhibitor-1, and Factor IX) were assessed by cytometric bead arrays in one- and two-time determinations. Accordingly, SERPINE1 rs6092, P-Selectin (GG 385 pg/mL vs. AG+AA 632 pg/mL, p = 0.0037), and tPA (GG 1858 pg/mL vs. AG+AA 2546 pg/mL, p = 0.0284) levels were different. Patients carrying the CT F5-rs6025 genotype exhibited lower levels of factor IX (CC 17,136 pg/mL vs. CT 10,247 pg/mL, p = 0.0355). Coagulation proteins were also different among IMV patients than non-IMV. PSGL-1 levels were significantly increased in the late stage of COVID-19 (>10 days). The frequencies of F5 rs6025 and SERPINE1 rs6092 variants were not different among IMV and non-IMV. The SERPINE1 rs6092 variant is related to the impaired coagulation process in patients with COVID-19 severe.
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Affiliation(s)
- Ingrid Fricke-Galindo
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Ivette Buendia-Roldan
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico; (I.B.-R.); (A.A.-D.)
| | - Leslie Chavez-Galan
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico;
| | - Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | | | - Espiridión Ramos-Martinez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 06720, Mexico;
| | - Armando Zazueta-Márquez
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Felipe Reyes-Melendres
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Aimé Alarcón-Dionet
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico; (I.B.-R.); (A.A.-D.)
| | - Javier Guzmán-Vargas
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Omar Andrés Bravo-Gutiérrez
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Teresa Quintero-Puerta
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Ilse Adriana Gutiérrez-Pérez
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Alejandro Ortega-Martínez
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Enrique Ambrocio-Ortiz
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Karol J. Nava-Quiroz
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - José Luis Bañuelos-Flores
- Clinical Laboratory Service, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.L.B.-F.); (M.E.J.-C.)
| | - María Esther Jaime-Capetillo
- Clinical Laboratory Service, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.L.B.-F.); (M.E.J.-C.)
| | - Mayra Mejía
- Interstitial Pulmonary Diseases and Rheumatology Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 06720, Mexico; (M.M.); (J.R.-S.)
| | - Jorge Rojas-Serrano
- Interstitial Pulmonary Diseases and Rheumatology Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 06720, Mexico; (M.M.); (J.R.-S.)
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
- Correspondence: ; Tel.: +52-55-5487-1700 (ext. 5152)
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15
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A Journey into the Clinical Relevance of Heme Oxygenase 1 for Human Inflammatory Disease and Viral Clearance: Why Does It Matter on the COVID-19 Scene? Antioxidants (Basel) 2022; 11:antiox11020276. [PMID: 35204159 PMCID: PMC8868141 DOI: 10.3390/antiox11020276] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/27/2023] Open
Abstract
Heme oxygenase 1 (HO-1), the rate-limiting enzyme in heme degradation, is involved in the maintenance of cellular homeostasis, exerting a cytoprotective role by its antioxidative and anti-inflammatory functions. HO-1 and its end products, biliverdin, carbon monoxide and free iron (Fe2+), confer cytoprotection against inflammatory and oxidative injury. Additionally, HO-1 exerts antiviral properties against a diverse range of viral infections by interfering with replication or activating the interferon (IFN) pathway. Severe cases of coronavirus disease 2019 (COVID-19), an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are characterized by systemic hyperinflammation, which, in some cases, leads to severe or fatal symptoms as a consequence of respiratory failure, lung and heart damage, kidney failure, and nervous system complications. This review summarizes the current research on the protective role of HO-1 in inflammatory diseases and against a wide range of viral infections, positioning HO-1 as an attractive target to ameliorate clinical manifestations during COVID-19.
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16
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Hasankhani A, Bahrami A, Sheybani N, Aria B, Hemati B, Fatehi F, Ghaem Maghami Farahani H, Javanmard G, Rezaee M, Kastelic JP, Barkema HW. Differential Co-Expression Network Analysis Reveals Key Hub-High Traffic Genes as Potential Therapeutic Targets for COVID-19 Pandemic. Front Immunol 2022; 12:789317. [PMID: 34975885 PMCID: PMC8714803 DOI: 10.3389/fimmu.2021.789317] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/26/2021] [Indexed: 01/08/2023] Open
Abstract
Background The recent emergence of COVID-19, rapid worldwide spread, and incomplete knowledge of molecular mechanisms underlying SARS-CoV-2 infection have limited development of therapeutic strategies. Our objective was to systematically investigate molecular regulatory mechanisms of COVID-19, using a combination of high throughput RNA-sequencing-based transcriptomics and systems biology approaches. Methods RNA-Seq data from peripheral blood mononuclear cells (PBMCs) of healthy persons, mild and severe 17 COVID-19 patients were analyzed to generate a gene expression matrix. Weighted gene co-expression network analysis (WGCNA) was used to identify co-expression modules in healthy samples as a reference set. For differential co-expression network analysis, module preservation and module-trait relationships approaches were used to identify key modules. Then, protein-protein interaction (PPI) networks, based on co-expressed hub genes, were constructed to identify hub genes/TFs with the highest information transfer (hub-high traffic genes) within candidate modules. Results Based on differential co-expression network analysis, connectivity patterns and network density, 72% (15 of 21) of modules identified in healthy samples were altered by SARS-CoV-2 infection. Therefore, SARS-CoV-2 caused systemic perturbations in host biological gene networks. In functional enrichment analysis, among 15 non-preserved modules and two significant highly-correlated modules (identified by MTRs), 9 modules were directly related to the host immune response and COVID-19 immunopathogenesis. Intriguingly, systemic investigation of SARS-CoV-2 infection identified signaling pathways and key genes/proteins associated with COVID-19's main hallmarks, e.g., cytokine storm, respiratory distress syndrome (ARDS), acute lung injury (ALI), lymphopenia, coagulation disorders, thrombosis, and pregnancy complications, as well as comorbidities associated with COVID-19, e.g., asthma, diabetic complications, cardiovascular diseases (CVDs), liver disorders and acute kidney injury (AKI). Topological analysis with betweenness centrality (BC) identified 290 hub-high traffic genes, central in both co-expression and PPI networks. We also identified several transcriptional regulatory factors, including NFKB1, HIF1A, AHR, and TP53, with important immunoregulatory roles in SARS-CoV-2 infection. Moreover, several hub-high traffic genes, including IL6, IL1B, IL10, TNF, SOCS1, SOCS3, ICAM1, PTEN, RHOA, GDI2, SUMO1, CASP1, IRAK3, HSPA5, ADRB2, PRF1, GZMB, OASL, CCL5, HSP90AA1, HSPD1, IFNG, MAPK1, RAB5A, and TNFRSF1A had the highest rates of information transfer in 9 candidate modules and central roles in COVID-19 immunopathogenesis. Conclusion This study provides comprehensive information on molecular mechanisms of SARS-CoV-2-host interactions and identifies several hub-high traffic genes as promising therapeutic targets for the COVID-19 pandemic.
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Affiliation(s)
- Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.,Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Negin Sheybani
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Behzad Aria
- Department of Physical Education and Sports Science, School of Psychology and Educational Sciences, Yazd University, Yazd, Iran
| | - Behzad Hemati
- Biotechnology Research Center, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Farhang Fatehi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | | | - Ghazaleh Javanmard
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Mahsa Rezaee
- Department of Medical Mycology, School of Medical Science, Tarbiat Modares University, Tehran, Iran
| | - John P Kastelic
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Herman W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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17
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The roles of cellular protease interactions in viral infections and programmed cell death: a lesson learned from the SARS-CoV-2 outbreak and COVID-19 pandemic. Pharmacol Rep 2022; 74:1149-1165. [PMID: 35997950 PMCID: PMC9395814 DOI: 10.1007/s43440-022-00394-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/03/2022] [Accepted: 07/18/2022] [Indexed: 12/13/2022]
Abstract
The unprecedented pandemic of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), which leads to COVID-19, is threatening global health. Over the last 2 years, we have witnessed rapid progress in research focusing on developing new antiviral vaccines and drugs, as well as in academic and clinical efforts to understand the biology and pathology of COVID-19. The roles of proteases among master regulators of SARS-CoV-2 invasion and replication and their pivotal roles in host defence against this pathogen, including programmed cell death, have not been well established. Our understanding of protease function in health and disease has increased considerably over the last two decades, with caspases, matrix metalloproteases, and transmembrane serine proteases representing the most prominent examples. Therefore, during the COVID-19 pandemic, these enzymes have been investigated as potential molecular targets for therapeutic interventions. Proteases that are responsible for SARS-CoV-2 cell entry and replication, such as TMPRSS2, ACE2 or cathepsins, are screened with inhibitor libraries to discover lead structures for further drug design that would prevent virus multiplication. On the other hand, proteases that orchestrate programmed cell death can also be harnessed to enhance the desired demise of infected cells through apoptosis or to attenuate highly inflammatory lytic cell death that leads to undesired cytokine storms, a major hallmark of severe COVID-19. Given the prominent role of proteases in SARS-CoV-2-induced cell death, we discuss the individual roles of these enzymes and their catalytic interactions in the pathology of COVID-19 in this article. We provide a rationale for targeting proteases participating in cell death as potential COVID-19 treatments and identify knowledge gaps that might be investigated to better understand the mechanism underlying SARS-CoV-2-induced cell death.
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18
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Aguirre-García GM, Ramonfaur D, Torre-Amione G, Ramírez-Elizondo MT, Lara-Medrano R, Moreno-Hoyos JF, Velázquez-Ávila ES, Diaz-Garza CA, Sanchez-Nava VM, Castilleja-Leal F, Rhoades GM, Martínez-Reséndez MF. Stratifying risk outcomes among adult COVID-19 inpatients with high flow oxygen: The R4 score. Pulmonology 2021; 29:200-206. [PMID: 34728168 PMCID: PMC8506226 DOI: 10.1016/j.pulmoe.2021.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/03/2021] [Accepted: 10/03/2021] [Indexed: 11/22/2022] Open
Abstract
Background High flow oxygen therapy (HFO) is a widely used intervention for pulmonary complications. Amid the coronavirus infectious disease 2019 (COVID-19) pandemic, HFO became a popular alternative to conventional oxygen supplementation therapies. Risk stratification tools have been repurposed –and new ones developed– to estimate outcome risks among COVID-19 patients. This study aims to provide a simple risk stratification system to predict invasive mechanical ventilation (IMV) or death among COVID-19 inpatients on HFO. Methods Among 529 adult inpatients with COVID-19 pneumonia, we selected unadjusted clinical risk factors for developing the composite endpoint of IMV or death. The risk for the primary outcome by each category was estimated using a Cox proportional hazards model. Bootstrapping was used to validate the results. Results Age above 62, eGFR under 60 ml/min, room air SpO2 ≤89 % upon admission, history of hypertension, history of diabetes, and any comorbidity (cancer, cardiovascular disease, COPD/ asthma, hypothyroidism, or autoimmune disease) were considered for the score. Each of the six criteria scored 1 point. The score was further simplified into 4 categories: 1) 0 criteria, 2) 1 criterion, 3) 2-3 criteria, and 4) ≥4 criteria. Taking the first category as the reference, risk estimates for the primary endpoint were HR; 2.94 [1.67 – 5.26], 4.08 [2.63 – 7.05], and 6.63 [3.74 – 11.77], respectively. In ROC analysis, the AUC for the model was 0.72. Conclusions Our score uses simple criteria to estimate the risk for IMV or death among COVID-19 inpatients with HFO. Higher category reflects consistent increases in risk for the endpoint.
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Affiliation(s)
- G M Aguirre-García
- Instituto Tecnologico y de Estudios Superiores de Monterrey, School of Medicine and Health Sciences, Monterrey, Nuevo Leon, Mexico
| | - D Ramonfaur
- Harvard Medical School, Division of Postgraduate Medical Education, 25 Shattuck St, Boston, MA 02115, United States
| | - G Torre-Amione
- Instituto Tecnologico y de Estudios Superiores de Monterrey, School of Medicine and Health Sciences, Monterrey, Nuevo Leon, Mexico
| | - M T Ramírez-Elizondo
- Instituto Tecnologico y de Estudios Superiores de Monterrey, School of Medicine and Health Sciences, Monterrey, Nuevo Leon, Mexico
| | - R Lara-Medrano
- Instituto Tecnologico y de Estudios Superiores de Monterrey, School of Medicine and Health Sciences, Monterrey, Nuevo Leon, Mexico
| | - J F Moreno-Hoyos
- Instituto Tecnologico y de Estudios Superiores de Monterrey, School of Medicine and Health Sciences, Monterrey, Nuevo Leon, Mexico
| | - E S Velázquez-Ávila
- Hospital San Jose-Tec Salud, Epidemiological Surveillance Unit, Monterrey, Nuevo Leon, Mexico
| | - C A Diaz-Garza
- Instituto Tecnologico y de Estudios Superiores de Monterrey, School of Medicine and Health Sciences, Monterrey, Nuevo Leon, Mexico
| | - V M Sanchez-Nava
- Instituto Tecnologico y de Estudios Superiores de Monterrey, School of Medicine and Health Sciences, Monterrey, Nuevo Leon, Mexico
| | - F Castilleja-Leal
- Instituto Tecnologico y de Estudios Superiores de Monterrey, School of Medicine and Health Sciences, Monterrey, Nuevo Leon, Mexico
| | - G M Rhoades
- Instituto Tecnologico y de Estudios Superiores de Monterrey, School of Medicine and Health Sciences, Monterrey, Nuevo Leon, Mexico
| | - M F Martínez-Reséndez
- Instituto Tecnologico y de Estudios Superiores de Monterrey, School of Medicine and Health Sciences, Monterrey, Nuevo Leon, Mexico; Hospital San Jose-Tec Salud, Epidemiological Surveillance Unit, Monterrey, Nuevo Leon, Mexico.
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19
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Viera-Segura O, Vega-Magaña N, García-Chagollán M, Peña-Rodríguez M, Muñoz-Sánchez G, Carranza-Aranda AS, Llamas-Covarrubias IM, Ramos-Solano M, Mora-Mora J, Díaz-Palomera CD, León GED, Zepeda-Nuño JS, Santillán-López E, García-Arellano S, Hernández-Silva CD, Zerpa-Hernandez DA, Muñoz-Rios G, Rodríguez-Sanabria JS, Muñoz-Valle JF. A Comprehensive Descriptive Epidemiological and Clinical Analysis of SARS-CoV-2 in West-Mexico during COVID-19 Pandemic 2020. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:10644. [PMID: 34682388 PMCID: PMC8535709 DOI: 10.3390/ijerph182010644] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 11/17/2022]
Abstract
This study aimed to summarize the epidemiological and clinical characteristics of COVID-19 from Western Mexico people during 2020. A retrospective analysis from an electronic database of people visiting a sentinel center for molecular SARS-CoV-2 confirmatory diagnosis by RT-PCR from April to December 2020 was carried out for epidemiological and clinical description of COVID-19. Out of 23,211 patients evaluated, 6918 (29.8%) were confirmed for SARS-CoV-2 infection (mean age 38.5 ± 13.99), mostly females (53.8%). Comorbidities, such as diabetes (34.7%), obesity (31.15%), and hypertension (31.8%), presented an increased odds OR = 1.27, CI = 1.14-1.41; OR = 1.08, CI = 1.01-1.16; and OR = 1.09, CI = 0.99-1.19, respectively, for viral-infection. Moreover, fever, headache, and dry cough were the most frequent symptoms. No infection difference among sex was found. Those patients >60 years old were prone to COVID-19 severity (OR = 3.59, CI = 2.10-6.14), evaluated by the number of manifested symptoms, increasing with age. In conclusion, a high SARS-CoV-2 prevalence was found in Western Mexico. Comorbidities were frequent in infected people; nevertheless, no association with disease outcomes was observed, in contrast with the highest disease severity risk found in older patients; however, continuous monitoring should be carried since comorbidities have been reported as aggravating factors. This study can help the health officials for the elaboration of planning efforts of the disease management and others in the future.
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Affiliation(s)
- Oliver Viera-Segura
- Laboratorio de Diagnóstico de Enfermedades Emergentes y Reemergentes, Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (O.V.-S.); (N.V.-M.); (M.P.-R.); (J.M.-M.); (C.D.D.-P.); (G.E.-D.L.); (G.M.-R.)
| | - Natali Vega-Magaña
- Laboratorio de Diagnóstico de Enfermedades Emergentes y Reemergentes, Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (O.V.-S.); (N.V.-M.); (M.P.-R.); (J.M.-M.); (C.D.D.-P.); (G.E.-D.L.); (G.M.-R.)
- Instituto de Investigación de Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (M.G.-C.); (S.G.-A.); (D.A.Z.-H.)
| | - Mariel García-Chagollán
- Instituto de Investigación de Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (M.G.-C.); (S.G.-A.); (D.A.Z.-H.)
| | - Marcela Peña-Rodríguez
- Laboratorio de Diagnóstico de Enfermedades Emergentes y Reemergentes, Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (O.V.-S.); (N.V.-M.); (M.P.-R.); (J.M.-M.); (C.D.D.-P.); (G.E.-D.L.); (G.M.-R.)
- Centro de Investigación y Diagnóstico de Patologia, Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico;
| | - Germán Muñoz-Sánchez
- Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (G.M.-S.); (A.S.C.-A.); (E.S.-L.); (C.D.H.-S.)
| | - Ahtziri Socorro Carranza-Aranda
- Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (G.M.-S.); (A.S.C.-A.); (E.S.-L.); (C.D.H.-S.)
| | - Iris Monserrat Llamas-Covarrubias
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, CP, Mexico;
| | | | - Jesús Mora-Mora
- Laboratorio de Diagnóstico de Enfermedades Emergentes y Reemergentes, Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (O.V.-S.); (N.V.-M.); (M.P.-R.); (J.M.-M.); (C.D.D.-P.); (G.E.-D.L.); (G.M.-R.)
- Maestría en Ciencias Médicas, Universidad de Colima, Colima 28040, Mexico
| | - Carlos Daniel Díaz-Palomera
- Laboratorio de Diagnóstico de Enfermedades Emergentes y Reemergentes, Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (O.V.-S.); (N.V.-M.); (M.P.-R.); (J.M.-M.); (C.D.D.-P.); (G.E.-D.L.); (G.M.-R.)
- Doctorado en Ciencias en Biología Molecular en Medicina, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico;
| | - Gabriela Espinoza-De León
- Laboratorio de Diagnóstico de Enfermedades Emergentes y Reemergentes, Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (O.V.-S.); (N.V.-M.); (M.P.-R.); (J.M.-M.); (C.D.D.-P.); (G.E.-D.L.); (G.M.-R.)
| | - José Sergio Zepeda-Nuño
- Centro de Investigación y Diagnóstico de Patologia, Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico;
| | - Enrique Santillán-López
- Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (G.M.-S.); (A.S.C.-A.); (E.S.-L.); (C.D.H.-S.)
| | - Samuel García-Arellano
- Instituto de Investigación de Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (M.G.-C.); (S.G.-A.); (D.A.Z.-H.)
| | - Christian David Hernández-Silva
- Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (G.M.-S.); (A.S.C.-A.); (E.S.-L.); (C.D.H.-S.)
| | - Darbi Alfredo Zerpa-Hernandez
- Instituto de Investigación de Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (M.G.-C.); (S.G.-A.); (D.A.Z.-H.)
- Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (G.M.-S.); (A.S.C.-A.); (E.S.-L.); (C.D.H.-S.)
| | - Guillermina Muñoz-Rios
- Laboratorio de Diagnóstico de Enfermedades Emergentes y Reemergentes, Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (O.V.-S.); (N.V.-M.); (M.P.-R.); (J.M.-M.); (C.D.D.-P.); (G.E.-D.L.); (G.M.-R.)
- Doctorado en Ciencias Médicas, Universidad de Colima, Colima 280440, Mexico
| | - J. Samael Rodríguez-Sanabria
- Doctorado en Ciencias en Biología Molecular en Medicina, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico;
| | - José Francisco Muñoz-Valle
- Instituto de Investigación de Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (M.G.-C.); (S.G.-A.); (D.A.Z.-H.)
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Varela AA, Cheng S, Werren JH. Novel ACE2 protein interactions relevant to COVID-19 predicted by evolutionary rate correlations. PeerJ 2021; 9:e12159. [PMID: 34616619 PMCID: PMC8449537 DOI: 10.7717/peerj.12159] [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: 06/09/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2) is the cell receptor that the coronavirus SARS-CoV-2 binds to and uses to enter and infect human cells. COVID-19, the pandemic disease caused by the coronavirus, involves diverse pathologies beyond those of a respiratory disease, including micro-thrombosis (micro-clotting), cytokine storms, and inflammatory responses affecting many organ systems. Longer-term chronic illness can persist for many months, often well after the pathogen is no longer detected. A better understanding of the proteins that ACE2 interacts with can reveal information relevant to these disease manifestations and possible avenues for treatment. We have undertaken an approach to predict candidate ACE2 interacting proteins which uses evolutionary inference to identify a set of mammalian proteins that “coevolve” with ACE2. The approach, called evolutionary rate correlation (ERC), detects proteins that show highly correlated evolutionary rates during mammalian evolution. Such proteins are candidates for biological interactions with the ACE2 receptor. The approach has uncovered a number of key ACE2 protein interactions of potential relevance to COVID-19 pathologies. Some proteins have previously been reported to be associated with severe COVID-19, but are not currently known to interact with ACE2, while additional predicted novel ACE2 interactors are of potential relevance to the disease. Using reciprocal rankings of protein ERCs, we have identified strongly interconnected ACE2 associated protein networks relevant to COVID-19 pathologies. ACE2 has clear connections to coagulation pathway proteins, such as Coagulation Factor V and fibrinogen components FGA, FGB, and FGG, the latter possibly mediated through ACE2 connections to Clusterin (which clears misfolded extracellular proteins) and GPR141 (whose functions are relatively unknown). ACE2 also connects to proteins involved in cytokine signaling and immune response (e.g. XCR1, IFNAR2 and TLR8), and to Androgen Receptor (AR). The ERC prescreening approach has elucidated possible functions for relatively uncharacterized proteins and possible new functions for well-characterized ones. Suggestions are made for the validation of ERC-predicted ACE2 protein interactions. We propose that ACE2 has novel protein interactions that are disrupted during SARS-CoV-2 infection, contributing to the spectrum of COVID-19 pathologies.
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Affiliation(s)
- Austin A Varela
- Department of Biology, University of Rochester, Rochester, New York, United States
| | - Sammy Cheng
- Department of Biology, University of Rochester, Rochester, New York, United States
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, New York, United States
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21
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Towards AI-Enabled Multimodal Diagnostics and Management of COVID-19 and Comorbidities in Resource-Limited Settings. INFORMATICS 2021. [DOI: 10.3390/informatics8040063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A conceptual artificial intelligence (AI)-enabled framework is presented in this study involving triangulation of various diagnostic methods for management of coronavirus disease 2019 (COVID-19) and its associated comorbidities in resource-limited settings (RLS). The proposed AI-enabled framework will afford capabilities to harness low-cost polymerase chain reaction (PCR)-based molecular diagnostics, radiological image-based assessments, and end-user provided information for the detection of COVID-19 cases and management of symptomatic patients. It will support self-data capture, clinical risk stratification, explanation-based intelligent recommendations for patient triage, disease diagnosis, patient treatment, contact tracing, and case management. This will enable communication with end-users in local languages through cheap and accessible means, such as WhatsApp/Telegram, social media, and SMS, with careful consideration of the need for personal data protection. The objective of the AI-enabled framework is to leverage multimodal diagnostics of COVID-19 and associated comorbidities in RLS for the diagnosis and management of COVID-19 cases and general support for pandemic recovery. We intend to test the feasibility of implementing the proposed framework through community engagement in sub-Saharan African (SSA) countries where many people are living with pre-existing comorbidities. A multimodal approach to disease diagnostics enabling access to point-of-care testing is required to reduce fragmentation of essential services across the continuum of COVID-19 care.
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22
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Unraveling the molecular crosstalk between Atherosclerosis and COVID-19 comorbidity. Comput Biol Med 2021; 134:104459. [PMID: 34020127 PMCID: PMC8088080 DOI: 10.1016/j.compbiomed.2021.104459] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
Background Corona virus disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus −2 (SARS-CoV-2) has created ruckus throughout the world. Growing epidemiological studies have depicted atherosclerosis as a comorbid factor of COVID-19. Though both these diseases are triggered via inflammatory rage that leads to injury of healthy tissues, the molecular linkage between them and their co-influence in causing fatality is not yet understood. Methods We have retrieved the data of differentially expressed genes (DEGs) for both atherosclerosis and COVID-19 from publicly available microarray and RNA-Seq datasets. We then reconstructed the protein-protein interaction networks (PPIN) for these diseases from protein-protein interaction data of corresponding DEGs. Using RegNetwork and TRRUST, we mapped the transcription factors (TFs) in atherosclerosis and their targets (TGs) in COVID-19 PPIN. Results From the atherosclerotic PPIN, we have identified 6 hubs (TLR2, TLR4, EGFR, SPI1, MYD88 and IRF8) as differentially expressed TFs that might control the expression of their 17 targets in COVID-19 PPIN. The important target proteins include IL1B, CCL5, ITGAM, IFIT3, CXCL1, CXCL2, CXCL3 and CXCL8. Consequent functional enrichment analysis of these TGs have depicted inflammatory responses to be overrepresented among the gene sets. Conclusion Finally, analyzing the DEGs in cardiomyocytes infected with SARS-CoV-2, we have concluded that MYD88 is a crucial linker of atherosclerosis and COVID-19, the co-existence of which lead to fatal outcomes. Anti-inflammatory therapy targeting MYD88 could be a potent strategy for combating this comorbidity.
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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: 52] [Impact Index Per Article: 17.3] [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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Sefik E, Israelow B, Zhao J, Qu R, Song E, Mirza H, Kaffe E, Halene S, Meffre E, Kluger Y, Nussenzweig M, Wilen CB, Iwasaki A, Flavell RA. A humanized mouse model of chronic COVID-19 to evaluate disease mechanisms and treatment options. RESEARCH SQUARE 2021:rs.3.rs-279341. [PMID: 33758831 PMCID: PMC7987100 DOI: 10.21203/rs.3.rs-279341/v1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Coronavirus-associated acute respiratory disease, called coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). More than 90 million people have been infected with SARS-CoV-2 and more than 2 million people have died of complications due to COVID-19 worldwide. COVID-19, in its severe form, presents with an uncontrolled, hyperactive immune response and severe immunological injury or organ damage that accounts for morbidity and mortality. Even in the absence of complications, COVID-19 can last for several months with lingering effects of an overactive immune system. Dysregulated myeloid and lymphocyte compartments have been implicated in lung immunopathology. Currently, there are limited clinically-tested treatments of COVID-19 with disparities in the apparent efficacy in patients. Accurate model systems are essential to rapidly evaluate promising discoveries but most currently available in mice, ferrets and hamsters do not recapitulate sustained immunopathology described in COVID19 patients. Here, we present a comprehensively humanized mouse COVID-19 model that faithfully recapitulates the innate and adaptive human immune responses during infection with SARS-CoV-2 by adapting recombinant adeno-associated virus (AAV)-driven gene therapy to deliver human ACE2 to the lungs 1 of MISTRG6 mice. Our unique model allows for the first time the study of chronic disease due to infection with SARS-CoV-2 in the context of patient-derived antibodies to characterize in real time the potential culprits of the observed human driving immunopathology; most importantly this model provides a live view into the aberrant macrophage response that is thought to be the effector of disease morbidity and ARDS in patients. Application of therapeutics such as patient-derived antibodies and steroids to our model allowed separation of the two aspects of the immune response, infectious viral clearance and immunopathology. Inflammatory cells seeded early in infection drove immune-patholgy later, but this very same early anti-viral response was also crucial to contain infection.
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Affiliation(s)
- Esen Sefik
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Ben Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Jun Zhao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Rihao Qu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Haris Mirza
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Eleanna Kaffe
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Stephanie Halene
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
| | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Yuval Kluger
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Michel Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT,USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
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25
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Singh MK, Mobeen A, Chandra A, Joshi S, Ramachandran S. A meta-analysis of comorbidities in COVID-19: Which diseases increase the susceptibility of SARS-CoV-2 infection? Comput Biol Med 2021; 130:104219. [PMID: 33486379 PMCID: PMC7836641 DOI: 10.1016/j.compbiomed.2021.104219] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 02/06/2023]
Abstract
Comorbidities in COVID-19 patients often lead to more severe outcomes. The disease-specific molecular events, which may induce susceptibility to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, are being investigated. To assess this, we retrieved array-based gene expression datasets from patients of 30 frequently occurring acute, chronic, or infectious diseases. Comparative analyses of the datasets were performed after quantile normalization and log2 transformation. Among the 78 host genes prominently implicated in COVID-19 infection, ACE2 (receptor for SARS-CoV-2) was positively regulated in several cases, namely, leukemia, psoriasis, lung cancer, non-alcoholic fatty liver disease (NAFLD), breast cancer, and pulmonary arterial hypertension (PAH). FURIN was positively regulated in some cases, such as leukemia, psoriasis, NAFLD, lung cancer, and type II diabetes (T2D), while TMPRSS2 was positively regulated in only 3 cases, namely, leukemia, lung cancer, and T2D. Genes encoding various interferons, cytokines, chemokines, and mediators of JAK-STAT pathway were positively regulated in leukemia, NAFLD, and T2D cases. Among the 161 genes that are positively regulated in the lungs of COVID-19 patients, 99–111 genes in leukemia (including various studied subtypes), 77 genes in NAFLD, and 48 genes in psoriasis were also positively regulated. Because of the high similarity in gene expression patterns, the patients of leukemia, NAFLD, T2D, psoriasis, and PAH may need additional preventive care against acquiring SARS-CoV-2 infections. Further, two genes CARBONIC ANHYDRASE 11 (CA11) and CLUSTERIN (CLU) were positively regulated in the lungs of patients infected with either SARS-CoV-2, or SARS-CoV or Middle East Respiratory Syndrome Coronavirus (MERS-CoV).
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Affiliation(s)
- Manoj Kumar Singh
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ahmed Mobeen
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Amit Chandra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sweta Joshi
- Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Srinivasan Ramachandran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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