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Alzahrani KJ. Repurposing of Anti-Cancer Drugs Against Moderate and Severe COVID Infection: A Network-Based Systems Biological Approach. Niger J Clin Pract 2024; 27:950-957. [PMID: 39212430 DOI: 10.4103/njcp.njcp_873_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 07/25/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND The COVID-19 pandemic caused by SARS-CoV-2 is an unparalleled health risk, needing fast antiviral medication development. One of the most effective strategies for developing therapies against novel and emerging viruses is drug repurposing. Recently, systems biology approaches toward the discovery of repurposing medications are gaining prominence. AIM This study aimed to implement a systems biology approach to identify crucial drug targets as well as potential drug candidates against COVID infection. METHODS Our approach utilizes differential gene expression in COVID conditions that enable the construction of a protein-protein interaction (PPI) network. Core clusters were extracted from this network, followed by molecular enrichment analysis. This process identified critical drug targets and potential drug candidates targeting various stages of COVID-19 infection. RESULTS The network was built using the top 200 differently expressed genes in mild, moderate, and severe COVID-19 infections. Top 3 clusters for each disease condition were identified, representing the core mechanism of the network. Molecular enrichment revealed the majority of the pathways in the mild state were associated with transcription regulation, protein folding, angiogenesis, and cytokine-signaling pathways. Whereas, the enriched pathways in moderate and severe disease states were predominately linked with the immune system and apoptotic processes, which include NF-kappaB signaling, cytokine signaling, TNF-mediated signaling, and oxidative stress-induced cell death. Further analysis identifies 28 potential drugs that can be repurposed to treat moderate and severe COVID-19, most of which are currently used in cancer treatment. CONCLUSION Interestingly, some of the proposed drugs have demonstrated inhibitory effects against SARS-CoV-2, as supported by literature evidence. Overall, the drug repurposing method described here will help develop potential antiviral medications to treat emerging COVID strains.
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Affiliation(s)
- K J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
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Chen WF, Chuang JMJ, Yang SN, Chen NF, Bhattacharya M, Liu HT, Dhama K, Chakraborty C, Wen ZH. Gene expression profiling and the isocitrate dehydrogenase mutational landscape of temozolomide‑resistant glioblastoma. Oncol Lett 2024; 28:378. [PMID: 38939621 PMCID: PMC11209862 DOI: 10.3892/ol.2024.14511] [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: 09/21/2023] [Accepted: 04/09/2024] [Indexed: 06/29/2024] Open
Abstract
Glioblastoma multiforme (GBM) is an aggressive brain cancer that occurs more frequently than other brain tumors. The present study aimed to reveal a novel mechanism of temozolomide resistance in GBM using bioinformatics and wet lab analyses, including meta-Z analysis, Kaplan-Meier survival analysis, protein-protein interaction (PPI) network establishment, cluster analysis of co-expressed gene networks, and hierarchical clustering of upregulated and downregulated genes. Next-generation sequencing and quantitative PCR analyses revealed downregulated [tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1 (TIE1), calcium voltage-gated channel auxiliary subunit α2Δ1 (CACNA2D1), calpain 6 (CAPN6) and a disintegrin and metalloproteinase with thrombospondin motifs 6 (ADAMTS6)] and upregulated [serum amyloid (SA)A1, SAA2, growth differentiation factor 15 (GDF15) and ubiquitin specific peptidase 26 (USP26)] genes. Different statistical models were developed for these genes using the Z-score for P-value conversion, and Kaplan-Meier plots were constructed using several patient cohorts with brain tumors. The highest number of nodes was observed in the PPI network was for ADAMTS6 and TIE1. The PPI network model for all genes contained 35 nodes and 241 edges. Immunohistochemical staining was performed using isocitrate dehydrogenase (IDH)-wild-type or IDH-mutant GBM samples from patients and a significant upregulation of TIE1 (P<0.001) and CAPN6 (P<0.05) protein expression was demonstrated in IDH-mutant GBM in comparison with IDH-wild-type GBM. Structural analysis revealed an IDH-mutant model demonstrating the mutant residues (R132, R140 and R172). The findings of the present study will help the future development of novel biomarkers and therapeutics for brain tumors.
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Affiliation(s)
- Wu-Fu Chen
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan, R.O.C
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, R.O.C
| | - Jimmy Ming-Jung Chuang
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan, R.O.C
| | - San-Nan Yang
- Department of Pediatrics, E-DA Hospital, School of Medicine, College of Medicine I-Shou University, Kaohsiung 82445, Taiwan, R.O.C
- School of Medicine for International Students, College of Medicine, I-Shou University, Kaohsiung 82445, Taiwan, R.O.C
| | - Nan-Fu Chen
- Division of Neurosurgery, Department of Surgery, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan, R.O.C
- Center for General Education, Cheng Shiu University, Kaohsiung 833301, Taiwan, R.O.C
| | | | - Hsin-Tzu Liu
- Department of Medical Research, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien 970374, Taiwan, R.O.C
| | - Kuldeep Dhama
- Division of Pathology, Indian Council of Agriculture Research-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India
| | - Zhi-Hong Wen
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, R.O.C
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Chakraborty C, Bhattacharya M, Alshammari A, Albekairi TH. Blueprint of differentially expressed genes reveals the dynamic gene expression landscape and the gender biases in long COVID. J Infect Public Health 2024; 17:748-766. [PMID: 38518681 DOI: 10.1016/j.jiph.2024.02.018] [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: 11/06/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/24/2024] Open
Abstract
BACKGROUND Long COVID has appeared as a significant global health issue and is an extra burden to the healthcare system. It affects a considerable number of people throughout the globe. However, substantial research gaps have been noted in understanding the mechanism and genomic landscape during the long COVID infection. A study has aimed to identify the differentially expressed genes (DEGs) in long COVID patients to fill the gap. METHODS We used the RNA-seq GEO dataset acquired through the GPL20301 Illumina HiSeq 4000 platform. The dataset contains 36 human samples derived from PBMC (Peripheral blood mononuclear cells). Thirty-six human samples contain 13 non-long COVID individuals' samples and 23 long COVID individuals' samples, considered the first direction analysis. Here, we performed two-direction analyses. In the second direction analysis, we divided the dataset gender-wise into four groups: the non-long COVID male group, the long COVID male group, the non-long COVID female group, and the long COVID female group. RESULTS In the first analysis, we found no gene expression. In the second analysis, we identified 250 DEGs. During the DEG profile analysis of the non-long COVID male group and the long COVID male group, we found three upregulated genes: IGHG2, IGHG4, and MIR8071-2. Similarly, the analysis of the non-long COVID female group and the long COVID female group reveals eight top-ranking genes. It also indicates the gender biases of differentially expressed genes among long COVID individuals. We found several DEGs involved in PPI and co-expression network formation. Similarly, cluster enrichment and gene list enrichment analysis were performed, suggesting several genes are involved in different biological pathways or processes. CONCLUSIONS This study will help better understand the gene expression landscape in long COVID. However, it might help the discovery and development of therapeutics for long COVID.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Thamer H Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
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Shahbaz MA, Kuivanen S, Lampinen R, Mussalo L, Hron T, Závodná T, Ojha R, Krejčík Z, Saveleva L, Tahir NA, Kalapudas J, Koivisto AM, Penttilä E, Löppönen H, Singh P, Topinka J, Vapalahti O, Chew S, Balistreri G, Kanninen KM. Human-derived air-liquid interface cultures decipher Alzheimer's disease-SARS-CoV-2 crosstalk in the olfactory mucosa. J Neuroinflammation 2023; 20:299. [PMID: 38098019 PMCID: PMC10722731 DOI: 10.1186/s12974-023-02979-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND The neurological effects of the coronavirus disease of 2019 (COVID-19) raise concerns about potential long-term consequences, such as an increased risk of Alzheimer's disease (AD). Neuroinflammation and other AD-associated pathologies are also suggested to increase the risk of serious SARS-CoV-2 infection. Anosmia is a common neurological symptom reported in COVID-19 and in early AD. The olfactory mucosa (OM) is important for the perception of smell and a proposed site of viral entry to the brain. However, little is known about SARS-CoV-2 infection at the OM of individuals with AD. METHODS To address this gap, we established a 3D in vitro model of the OM from primary cells derived from cognitively healthy and AD individuals. We cultured the cells at the air-liquid interface (ALI) to study SARS-CoV-2 infection under controlled experimental conditions. Primary OM cells in ALI expressed angiotensin-converting enzyme 2 (ACE-2), neuropilin-1 (NRP-1), and several other known SARS-CoV-2 receptor and were highly vulnerable to infection. Infection was determined by secreted viral RNA content and confirmed with SARS-CoV-2 nucleocapsid protein (NP) in the infected cells by immunocytochemistry. Differential responses of healthy and AD individuals-derived OM cells to SARS-CoV-2 were determined by RNA sequencing. RESULTS Results indicate that cells derived from cognitively healthy donors and individuals with AD do not differ in susceptibility to infection with the wild-type SARS-CoV-2 virus. However, transcriptomic signatures in cells from individuals with AD are highly distinct. Specifically, the cells from AD patients that were infected with the virus showed increased levels of oxidative stress, desensitized inflammation and immune responses, and alterations to genes associated with olfaction. These results imply that individuals with AD may be at a greater risk of experiencing severe outcomes from the infection, potentially driven by pre-existing neuroinflammation. CONCLUSIONS The study sheds light on the interplay between AD pathology and SARS-CoV-2 infection. Altered transcriptomic signatures in AD cells may contribute to unique symptoms and a more severe disease course, with a notable involvement of neuroinflammation. Furthermore, the research emphasizes the need for targeted interventions to enhance outcomes for AD patients with viral infection. The study is crucial to better comprehend the relationship between AD, COVID-19, and anosmia. It highlights the importance of ongoing research to develop more effective treatments for those at high risk of severe SARS-CoV-2 infection.
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Affiliation(s)
- Muhammad Ali Shahbaz
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Suvi Kuivanen
- Department of Virology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Institute of Virology, 10117, Berlin, Germany
| | - Riikka Lampinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Laura Mussalo
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Tomáš Hron
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20, Prague, Czech Republic
| | - Táňa Závodná
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine, Czech Academy of Sciences, 142 20, Prague, Czech Republic
| | - Ravi Ojha
- Department of Virology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Zdeněk Krejčík
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine, Czech Academy of Sciences, 142 20, Prague, Czech Republic
| | - Liudmila Saveleva
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Numan Ahmad Tahir
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Juho Kalapudas
- Department of Neurology, Neuro Centre, Kuopio University Hospital, 70210, Kuopio, Finland
| | - Anne M Koivisto
- Department of Neurology, Neuro Centre, Kuopio University Hospital, 70210, Kuopio, Finland
- Brain Research Unit, Department of Neurology, School of Medicine, University of Eastern Finland, 70210, Kuopio, Finland
- Department of Neurology and Geriatrics, Helsinki University Hospital and Neurosciences, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Elina Penttilä
- Department of Otorhinolaryngology, University of Eastern Finland and Kuopio University Hospital, 70210, Kuopio, Finland
| | - Heikki Löppönen
- Department of Otorhinolaryngology, University of Eastern Finland and Kuopio University Hospital, 70210, Kuopio, Finland
| | | | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine, Czech Academy of Sciences, 142 20, Prague, Czech Republic
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Sweelin Chew
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Giuseppe Balistreri
- Department of Virology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- The Queensland Brain Institute, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Katja M Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210, Kuopio, Finland.
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Sheng J, Li L, Lv X, Gao M, Chen Z, Zhou Z, Wang J, Wu A, Jiang T. Integrated interactome and transcriptome analysis reveals key host factors critical for SARS-CoV-2 infection. Virol Sin 2023; 38:508-519. [PMID: 37169126 PMCID: PMC10166720 DOI: 10.1016/j.virs.2023.05.004] [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: 01/16/2023] [Accepted: 05/05/2023] [Indexed: 05/13/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has seriously threatened global public health and caused huge economic losses. Omics studies of SARS-CoV-2 can help understand the interaction between the virus and host, thereby providing a new perspective in guiding the intervention and treatment of the SARS-CoV-2 infection. Since large amount of SARS-CoV-2 omics data have been accumulated in public databases, this study aimed to identify key host factors involved in SARS-CoV-2 infection through systematic integration of transcriptome and interactome data. By manually curating published studies, we obtained a comprehensive SARS-CoV-2-human protein-protein interactions (PPIs) network, comprising 3591 human proteins interacting with 31 SARS-CoV-2 viral proteins. Using the RobustRankAggregation method, we identified 123 multiple cell line common genes (CLCGs), of which 115 up-regulated CLCGs showed host enhanced innate immunity and chemotactic response signatures. Combined with network analysis, co-expression and functional enrichment analysis, we discovered four key host factors involved in SARS-CoV-2 infection: IFITM1, SERPINE1, DDX60, and TNFAIP2. Furthermore, SERPINE1 was found to facilitate SARS-CoV-2 replication, and can alleviate the endoplasmic reticulum (ER) stress induced by ORF8 protein through interaction with ORF8. Our findings highlight the importance of systematic integration analysis in understanding SARS-CoV-2-human interactions and provide valuable insights for future research on potential therapeutic targets against SARS-CoV-2 infection.
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Affiliation(s)
- Jie Sheng
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China; Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Lili Li
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Xueying Lv
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China; Department of Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, China
| | - Meiling Gao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Ziyi Chen
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Zhuo Zhou
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Jingfeng Wang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China.
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China.
| | - Taijiao Jiang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China; Guangzhou Laboratory, Guangzhou, 510005, China; State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, China.
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Urday P, Gayen nee’ Betal S, Sequeira Gomes R, Al-Kouatly HB, Solarin K, Chan JSY, Li D, Rahman I, Addya S, Boelig RC, Aghai ZH. SARS-CoV-2 Covid-19 Infection During Pregnancy and Differential DNA Methylation in Human Cord Blood Cells From Term Neonates. Epigenet Insights 2023; 16:25168657231184665. [PMID: 37425024 PMCID: PMC10328022 DOI: 10.1177/25168657231184665] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023] Open
Abstract
Background The global pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). About 18.4% of total Covid-19 cases were reported in children. Even though vertical transmission from mother to infant is likely to occur at a low rate, exposure to COVID-19 during fetal life may alter DNA methylation patterns with potential long-term effects. Objective To determine if COVID-19 infection during pregnancy alters the DNA methylation patterns in umbilical cord blood cells from term infants and to identify potential pathways and genes affected by exposure to COVID-19 infection. Methods Umbilical cord blood was collected from 8 infants exposed to COVID-19 during pregnancy and 8 control infants with no COVID-19 exposure. Genomic DNA was isolated from umbilical cord blood cells and genome-wide DNA methylation was performed using Illumina Methylation EPIC Array. Results 119 differentially methylated loci were identified at the FDR level of 0.20 (64 hypermethylated loci and 55 hypomethylated loci) in umbilical cord blood cells of COVID-19 exposed neonates compared to the control group. Important canonical pathways identified by Ingenuity Pathway Analysis (IPA) were related to stress response (corticotropin releasing hormone signaling, glucocorticoid receptor signaling, and oxytocin in brain signaling pathway), and cardiovascular disease and development (nitric oxide signaling in the cardiovascular system, apelin cardiomyocyte signaling pathways, factors promoting cardiogenesis, and renin-angiotensin signaling). The genes affected by the differential methylations were associated with cardiac, renal, hepatic, neurological diseases, developmental and immunological disorders. Conclusions COVID-19 induces differential DNA methylation in umbilical cord blood cells. The differentially methylated genes may contribute to hepatic, renal, cardiac, developmental and immunological disorders in offspring born to mothers with COVID-19 infection during pregnancy, and their developmental regulation.
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Affiliation(s)
- Pedro Urday
- Neonatology, Thomas Jefferson University/Nemours, Philadelphia, PA, USA
| | | | | | - Huda B Al-Kouatly
- Division of Maternal Fetal Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Kolawole Solarin
- Neonatology, Thomas Jefferson University/Nemours, Philadelphia, PA, USA
| | - Joanna SY Chan
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Dongmei Li
- Department of Clinical and Translational Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Sankar Addya
- Laboratory of Cancer Genomics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Rupsa C Boelig
- Division of Maternal Fetal Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zubair H Aghai
- Neonatology, Thomas Jefferson University/Nemours, Philadelphia, PA, USA
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Salvati A, Ferravante C, Lamberti J, Rocco T, Alexandrova E, D'Agostino Y, Sorokin M, Efimov V, Buzdin A, Strianese O, Nassa G, Tarallo R, Weisz A, Rizzo F, Giurato G. Host nasopharyngeal transcriptome dataset of a SARS-CoV-2 positive Italian cohort. Sci Data 2023; 10:379. [PMID: 37316506 PMCID: PMC10264883 DOI: 10.1038/s41597-023-02289-7] [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: 03/06/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023] Open
Abstract
The ongoing COVID-19 pandemic caused by SARS-CoV-2 has affected millions of people worldwide and has significant implications for public health. Host transcriptomics profiling provides comprehensive understanding of how the virus interacts with host cells and how the host responds to the virus. COVID-19 disease alters the host transcriptome, affecting cellular pathways and key molecular functions. To contribute to the global effort to understand the virus's effect on host cell transcriptome, we have generated a dataset from nasopharyngeal swabs of 35 individuals infected with SARS-CoV-2 from the Campania region in Italy during the three outbreaks, with different clinical conditions. This dataset will help to elucidate the complex interactions among genes and can be useful in the development of effective therapeutic pathways.
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Affiliation(s)
- Annamaria Salvati
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
| | - Carlo Ferravante
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
| | - Jessica Lamberti
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
| | - Teresa Rocco
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
| | - Elena Alexandrova
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
| | - Ylenia D'Agostino
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
| | - Maksim Sorokin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- OmicsWay Corp, Walnut, USA
- Oncobox Ltd., Moscow, Russia
| | - Victor Efimov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- Oncobox Ltd., Moscow, Russia
- World-Class Research Center 'Digital biodesign and personalized healthcare', Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anton Buzdin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- World-Class Research Center 'Digital biodesign and personalized healthcare', Sechenov First Moscow State Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Oriana Strianese
- Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi (Sa), 84081, Italy
| | - Giovanni Nassa
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
- Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi (Sa), 84081, Italy
| | - Roberta Tarallo
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
- Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi (Sa), 84081, Italy
| | - Alessandro Weisz
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
- Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi (Sa), 84081, Italy
| | - Francesca Rizzo
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy.
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy.
- Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi (Sa), 84081, Italy.
| | - Giorgio Giurato
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy.
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy.
- Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi (Sa), 84081, Italy.
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Deng X, Luo Y, Guan T, Guo X. Identification of the Genetic Influence of SARS-CoV-2 Infections on IgA Nephropathy Based on Bioinformatics Method. Kidney Blood Press Res 2023; 48:367-384. [PMID: 37040729 PMCID: PMC10308545 DOI: 10.1159/000529687] [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: 08/24/2022] [Accepted: 02/09/2023] [Indexed: 04/13/2023] Open
Abstract
INTRODUCTION Coronavirus disease-2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. It was initially detected in Wuhan, China, in December 2019. In March 2020, the World Health Organization (WHO) declared COVID-19 a global pandemic. Compared to healthy individuals, patients with IgA nephropathy (IgAN) are at a higher risk of SARS-CoV-2 infection. However, the potential mechanisms remain unclear. This study explores the underlying molecular mechanisms and therapeutic agents for the management of IgAN and COVID-19 using the bioinformatics and system biology way. METHODS We first downloaded GSE73953 and GSE164805 from the Gene Expression Omnibus (GEO) database to obtain common differentially expressed genes (DEGs). Then, we performed the functional enrichment analysis, pathway analysis, protein-protein interaction (PPI) analysis, gene regulatory networks analysis, and potential drug analysis on these common DEGs. RESULTS We acquired 312 common DEGs from the IgAN and COVID-19 datasets and used various bioinformatics tools and statistical analyses to construct the PPI network to extract hub genes. Besides, we performed gene ontology (GO) and pathway analyses to reveal the common correlation between IgAN and COVID-19. Finally, on the basis of common DEGs, we determined the interactions between DEGs-miRNAs, the transcription factor-genes (TFs-genes), protein-drug, and gene-disease networks. CONCLUSION We successfully identified hub genes that may act as biomarkers of COVID-19 and IgAN and also screened out some potential drugs to provide new ideas for COVID-19 and IgAN treatment.
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Affiliation(s)
- Xiaoqi Deng
- Department of Nephrology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yu Luo
- School of Medicine, Xiamen University, Xiamen, China
| | - Tianjun Guan
- Department of Nephrology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Xiaodan Guo
- Department of Nephrology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
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9
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Datta A, R HC, Udhaya Kumar S, Vasudevan K, Thirumal Kumar D, Zayed H, George Priya Doss C. Molecular characterization of circadian gene expression and its correlation with survival percentage in colorectal cancer patients. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 137:161-180. [PMID: 37709374 DOI: 10.1016/bs.apcsb.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Colorectal cancer (CRC) is a form of cancer characterized by many symptoms and readily metastasizes to different organs in the body. Circadian rhythm is one of the many processes that is observed to be dysregulated in CRC-affected patients. In this study, we aim to identify the dysregulated physiological processes in CRC-affected patients and correlate the expression profiles of the circadian clock genes with CRC-patients' survival rates. We performed an extensive microarray gene expression pipeline, whereby 471 differentially expressed genes (DEGs) were identified, following which, we streamlined our search to 43 circadian clock affecting DEGs. The Circadian Gene Database was accessed to retrieve the circadian rhythm-specific genes. The DEGs were then subjected to multi-level functional annotation, i.e., preliminary analysis using ClueGO/CluePedia and pathway enrichment using DAVID. The findings of our study were interesting, wherein we observed that the survival percentage of CRC-affected patients dropped significantly around the 100th-month mark. Furthermore, we identified hormonal activity, xenobiotic metabolism, and PI3K-Akt signaling pathway to be frequently dysregulated cellular functions. Additionally, we detected that the ZFYVE family of genes and the two genes, namely MYC and CDK4 were the significant DEGs that are linked to the pathogenesis and progression of CRC. This study sheds light on the importance of bioinformatics to simplify our understanding of the interactions of different genes that control different phenotypes.
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Affiliation(s)
- Ankur Datta
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Hephzibah Cathryn R
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, Karnataka, India
| | - D Thirumal Kumar
- Faculty of Allied Health Sciences, Meenakshi Academy of Higher Education and Research (MAHER), Chennai, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
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10
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Chakraborty C, Bhattacharya M, Dhama K, Lee SS. Evaluation of differentially expressed genes during replication using gene expression landscape of monkeypox-infected MK2 cells: A bioinformatics and systems biology approach to understanding the genomic pattern of viral replication. J Infect Public Health 2023; 16:399-409. [PMID: 36724696 PMCID: PMC9874307 DOI: 10.1016/j.jiph.2023.01.015] [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: 10/31/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
PURPOSE The current outbreak of monkeypox (MPX) has created colossal concerns. However, immense research gaps have been noted in our understanding of the replication process, machinery, and genomic landscape during host cell infection. To fill this gap, differentially expressed genes (DEGs) were comprehensively analyzed during viral replication in host (MK2) cells. METHODS We used a microarray GEO dataset which was divided into three groups: control, MPXV-infected MK2 cells at 3 h, and MPXV-infected MK2 cells at 7 h. Using the dataset, DEG analysis, PPI network analysis, co-expression, and pathway analysis were conducted using bioinformatics, systems biology, and statistical approaches. RESULTS We identified 250 DEGs and 24 top-ranked genes. During the DEG analysis, we identified eight up-regulated genes (LOC695323, TMEM107, LOC695427, HIST1H2AD, LOC705469, PMAIP1, HIST1H2BJ, and HIST1H3D) and 16 down-regulated genes (HOXA9, BAMBI, LMO4, PAX6, AJUBA, CREBRF, CD24, JADE1, SLC7A11, EID2, SOX4, B4GALT5, PPARGC1A, BUB3, SOS2, and CDK19). We also developed PPI networks and performed co-expression analyses using the top-ranked genes. Furthermore, five genes were listed for co-expression pattern analysis. CONCLUSIONS This study will help in better understanding the replication process, machinery, and genomic landscape of the virus. This will further aid the discovery and development of therapeutics against viruses.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon 24252, Gangwon-Do, Republic of Korea.
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11
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Phillips S, Mishra T, Khadka S, Bohan D, Espada CE, Maury W, Wu L. Epitranscriptomic N6-Methyladenosine Profile of SARS-CoV-2-Infected Human Lung Epithelial Cells. Microbiol Spectr 2023; 11:e0394322. [PMID: 36625663 PMCID: PMC9927293 DOI: 10.1128/spectrum.03943-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/18/2022] [Indexed: 01/11/2023] Open
Abstract
N6-methyladenosine (m6A) is a dynamic posttranscriptional RNA modification that plays an important role in determining transcript fate. The functional consequence of m6A deposition is dictated by a group of host proteins that specifically recognize and bind the m6A modification, leading to changes in RNA stability, transport, splicing, or translation. The cellular m6A methylome undergoes changes during certain pathogenic conditions such as viral infections. However, how m6A modification of host cell transcripts and noncoding RNAs change during severe acute respiratory syndrome coronavirus (SARS-CoV-2) infection has not been reported. Here, we define the epitranscriptomic m6A profile of SARS-CoV-2-infected human lung epithelial cells compared to uninfected controls. We identified mRNA and long and small noncoding RNA species that are differentially m6A modified in response to SARS-CoV-2 infection. The most significantly differentially methylated transcript was the precursor of microRNA-4486 (miRNA-4486), which showed significant increases in abundance and percentage of methylated transcripts in infected cells. Pathway analyses revealed that differentially methylated transcripts were significantly associated with several cancer-related pathways, protein processing in the endoplasmic reticulum, cell death, and proliferation. Upstream regulators predicted to be associated with the proteins encoded by differentially methylated mRNAs include several proteins involved in the type-I interferon response, inflammation, and cytokine signaling. IMPORTANCE Posttranscriptional modification of viral and cellular RNA by N6-methyladenosine (m6A) plays an important role in regulating the replication of many viruses and the cellular immune response to infection. We therefore sought to define the epitranscriptomic m6A profile of human lung epithelial cells infected with SARS-CoV-2. Our analyses demonstrate the differential methylation of both coding and noncoding cellular RNAs in SARS-CoV-2-infected cells compared to uninfected controls. Pathway analyses revealed that several of these RNAs may be involved in the cellular response to infection, such as type-I interferon. Our study implicates m6A modification of infected-cell RNA as a mechanism of posttranscriptional gene regulation during SARS-CoV-2 infection.
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Affiliation(s)
- Stacia Phillips
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Tarun Mishra
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Shaubhagya Khadka
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Dana Bohan
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Constanza E. Espada
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Wendy Maury
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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12
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Jeyananthan P. SARS-CoV-2 Diagnosis Using Transcriptome Data: A Machine Learning Approach. SN COMPUTER SCIENCE 2023; 4:218. [PMID: 36844504 PMCID: PMC9936926 DOI: 10.1007/s42979-023-01703-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 01/24/2023] [Indexed: 05/02/2023]
Abstract
SARS-CoV-2 pandemic is the big issue of the whole world right now. The health community is struggling to rescue the public and countries from this spread, which revives time to time with different waves. Even the vaccination seems to be not prevents this spread. Accurate identification of infected people on time is essential these days to control the spread. So far, Polymerase chain reaction (PCR) and rapid antigen tests are widely used in this identification, accepting their own drawbacks. False negative cases are the menaces in this scenario. To avoid these problems, this study uses machine learning techniques to build a classification model with higher accuracy to filter the COVID-19 cases from the non-COVID individuals. Transcriptome data of the SARS-CoV-2 patients along with the control are used in this stratification using three different feature selection algorithms and seven classification models. Differently expressed genes also studied between these two groups of people and used in this classification. Results shows that mutual information (or DEGs) along with naïve Bayes (or SVM) gives the best accuracy (0.98 ± 0.04) among these methods. Supplementary Information The online version contains supplementary material available at 10.1007/s42979-023-01703-6.
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Mailem RC, Tayo LL. Drug Repurposing Using Gene Co-Expression and Module Preservation Analysis in Acute Respiratory Distress Syndrome (ARDS), Systemic Inflammatory Response Syndrome (SIRS), Sepsis, and COVID-19. BIOLOGY 2022; 11:biology11121827. [PMID: 36552336 PMCID: PMC9775208 DOI: 10.3390/biology11121827] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 infections are highly correlated with the overexpression of pro-inflammatory cytokines in what is known as a cytokine storm, leading to high fatality rates. Such infections are accompanied by SIRS, ARDS, and sepsis, suggesting a potential link between the three phenotypes. Currently, little is known about the transcriptional similarity between these conditions. Herein, weighted gene co-expression network analysis (WGCNA) clustering was applied to RNA-seq datasets (GSE147902, GSE66890, GSE74224, GSE177477) to identify modules of highly co-expressed and correlated genes, cross referenced with dataset GSE160163, across the samples. To assess the transcriptome similarities between the conditions, module preservation analysis was performed and functional enrichment was analyzed in DAVID webserver. The hub genes of significantly preserved modules were identified, classified into upregulated or downregulated, and used to screen candidate drugs using Connectivity Map (CMap) to identify repurposed drugs. Results show that several immune pathways (chemokine signaling, NOD-like signaling, and Th1 and Th2 cell differentiation) are conserved across the four diseases. Hub genes screened using intramodular connectivity show significant relevance with the pathogenesis of cytokine storms. Transcriptomic-driven drug repurposing identified seven candidate drugs (SB-202190, eicosatetraenoic-acid, loratadine, TPCA-1, pinocembrin, mepacrine, and CAY-10470) that targeted several immune-related processes. These identified drugs warrant further study into their efficacy for treating cytokine storms, and in vitro and in vivo experiments are recommended to confirm the findings of this study.
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Affiliation(s)
- Ryan Christian Mailem
- School of Chemical, Biological, and Materials Engineering and Sciences and School of Graduate Studies, Mapúa University, Manila City 1002, Philippines
| | - Lemmuel L. Tayo
- School of Chemical, Biological, and Materials Engineering and Sciences and School of Graduate Studies, Mapúa University, Manila City 1002, Philippines
- School of Health Sciences, Mapúa University, Manila City 1002, Philippines
- Correspondence: ; Tel.: +63-02-247-5000 (ext. 3300)
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14
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Salgado Del Riego E, Saiz ML, Corte-Iglesias V, Leoz Gordillo B, Martin-Martin C, Rodríguez-Pérez M, Escudero D, Lopez-Larrea C, Suarez-Alvarez B. Divergent SARS-CoV-2-specific T cell responses in intensive care unit workers following mRNA COVID-19 vaccination. Front Immunol 2022; 13:942192. [PMID: 36275696 PMCID: PMC9582956 DOI: 10.3389/fimmu.2022.942192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
The cellular immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in response to full mRNA COVID-19 vaccination could be variable among healthy individuals. Studies based only in specific antibody levels could show an erroneous immune protection at long times. For that, we analyze the antibody levels specific to the S protein and the presence of SARS-CoV-2-specific T cells by ELISpot and AIM assays in intensive care unit (ICU) workers with no antecedents of COVID-19 and vaccinated with two doses of mRNA COVID-19 vaccines. All individuals were seronegative for the SARS-CoV-2 protein S before vaccination (Pre-v), but 34.1% (14/41) of them showed pre-existing T lymphocytes specific for some viral proteins (S, M and N). One month after receiving two doses of COVID-19 mRNA vaccine (Post-v1), all cases showed seroconversion with high levels of total and neutralizing antibodies to the spike protein, but six of them (14.6%) had no T cells reactive to the S protein. Specifically, they lack of specific CD8+ T cells, but maintain the contribution of CD4+ T cells. Analysis of the immune response against SARS-CoV-2 at 10 months after full vaccination (Post-v10), exhibited a significant reduction in the antibody levels (p<0.0001) and protein S-reactive T cells (p=0.0073) in all analyzed individuals, although none of the individuals become seronegative and 77% of them maintained a competent immune response. Thus, we can suggest that the immune response to SARS-CoV-2 elicited by the mRNA vaccines was highly variable among ICU workers. A non-negligible proportion of individuals did not develop a specific T cell response mediated by CD8+ T cells after vaccination, that may condition the susceptibility to further viral infections with SARS-CoV-2. By contrast, around 77% of individuals developed strong humoral and cellular immune responses to SARS-CoV-2 that persisted even after 10 months. Analysis of the cellular immune response is highly recommended for providing exact information about immune protection against SARS-CoV-2.
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Affiliation(s)
- Estefanía Salgado Del Riego
- Servicio de Medicina Intensiva, Hospital Universitario Central de Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - María Laura Saiz
- Translational Immunology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Viviana Corte-Iglesias
- Translational Immunology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Blanca Leoz Gordillo
- Servicio de Medicina Intensiva, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Cristina Martin-Martin
- Translational Immunology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Mercedes Rodríguez-Pérez
- Servicio de Microbiología, Hospital Universitario Central de Asturias, Oviedo, Spain
- Translational Microbiology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Dolores Escudero
- Servicio de Medicina Intensiva, Hospital Universitario Central de Asturias, Oviedo, Spain
- Translational Microbiology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Carlos Lopez-Larrea
- Translational Immunology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias, Oviedo, Spain
- Servicio de Inmunología, Hospital Universitario Central De Asturias, Oviedo, Spain
| | - Beatriz Suarez-Alvarez
- Translational Immunology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias, Oviedo, Spain
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15
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Macedo-da-Silva J, Coutinho JVP, Rosa-Fernandes L, Marie SKN, Palmisano G. Exploring COVID-19 pathogenesis on command-line: A bioinformatics pipeline for handling and integrating omics data. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 131:311-339. [PMID: 35871895 PMCID: PMC9095070 DOI: 10.1016/bs.apcsb.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in late 2019 in Wuhan, China, and has proven to be highly pathogenic, making it a global public health threat. The immediate need to understand the mechanisms and impact of the virus made omics techniques stand out, as they can offer a holistic and comprehensive view of thousands of molecules in a single experiment. Mastering bioinformatics tools to process, analyze, integrate, and interpret omics data is a powerful knowledge to enrich results. We present a robust and open access computational pipeline for extracting information from quantitative proteomics and transcriptomics public data. We present the entire pipeline from raw data to differentially expressed genes. We explore processes and pathways related to mapped transcripts and proteins. A pipeline is presented to integrate and compare proteomics and transcriptomics data using also packages available in the Bioconductor and providing the codes used. Cholesterol metabolism, immune system activity, ECM, and proteasomal degradation pathways increased in infected patients. Leukocyte activation profile was overrepresented in both proteomics and transcriptomics data. Finally, we found a panel of proteins and transcripts regulated in the same direction in the lung transcriptome and plasma proteome that distinguish healthy and infected individuals. This panel of markers was confirmed in another cohort of patients, thus validating the robustness and functionality of the tools presented.
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Affiliation(s)
- Janaina Macedo-da-Silva
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | | | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Suely Kazue Nagahashi Marie
- Cellular and Molecular Biology Laboratory (LIM 15), Neurology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil; School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
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16
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Mocci S, Littera R, Tranquilli S, Provenzano A, Mascia A, Cannas F, Lai S, Giuressi E, Chessa L, Angioni G, Campagna M, Firinu D, Del Zompo M, La Nasa G, Perra A, Giglio S. A Protective HLA Extended Haplotype Outweighs the Major COVID-19 Risk Factor Inherited From Neanderthals in the Sardinian Population. Front Immunol 2022; 13:891147. [PMID: 35514995 PMCID: PMC9063452 DOI: 10.3389/fimmu.2022.891147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Sardinia has one of the lowest incidences of hospitalization and related mortality in Europe and yet a very high frequency of the Neanderthal risk locus variant on chromosome 3 (rs35044562), considered to be a major risk factor for a severe SARS-CoV-2 disease course. We evaluated 358 SARS-CoV-2 patients and 314 healthy Sardinian controls. One hundred and twenty patients were asymptomatic, 90 were pauci-symptomatic, 108 presented a moderate disease course and 40 were severely ill. All patients were analyzed for the Neanderthal-derived genetic variants reported as being protective (rs1156361) or causative (rs35044562) for severe illness. The β°39 C>T Thalassemia variant (rs11549407), HLA haplotypes, KIR genes, KIRs and their HLA class I ligand combinations were also investigated. Our findings revealed an increased risk for severe disease in Sardinian patients carrying the rs35044562 high risk variant [OR 5.32 (95% CI 2.53 - 12.01), p = 0.000]. Conversely, the protective effect of the HLA-A*02:01, B*18:01, DRB*03:01 three-loci extended haplotype in the Sardinian population was shown to efficiently contrast the high risk of a severe and devastating outcome of the infection predicted for carriers of the Neanderthal locus [OR 15.47 (95% CI 5.8 - 41.0), p < 0.0001]. This result suggests that the balance between risk and protective immunogenetic factors plays an important role in the evolution of COVID-19. A better understanding of these mechanisms may well turn out to be the biggest advantage in the race for the development of more efficient drugs and vaccines.
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Affiliation(s)
- Stefano Mocci
- Medical Genetics Unit, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Roberto Littera
- Medical Genetics Unit, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy.,Association for the Advancement of Research on Transplantation O.d.V., Non Profit Organisation, Cagliari, Italy
| | - Stefania Tranquilli
- Medical Genetics Unit, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Aldesia Provenzano
- Medical Genetics Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Alessia Mascia
- Medical Genetics Unit, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Federica Cannas
- Medical Genetics Unit, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Sara Lai
- Medical Genetics Unit, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Erika Giuressi
- Medical Genetics Unit, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Luchino Chessa
- Association for the Advancement of Research on Transplantation O.d.V., Non Profit Organisation, Cagliari, Italy.,Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy.,Liver Unit, Department of Internal Medicine, University Hospital of Cagliari, Cagliari, Italy
| | - Goffredo Angioni
- Structure of Infectious Diseases Unit, SS Trinità Hospital, Cagliari, Italy
| | - Marcello Campagna
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Davide Firinu
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Maria Del Zompo
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Giorgio La Nasa
- Hematology Unit, Businco Hospital, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Andrea Perra
- Association for the Advancement of Research on Transplantation O.d.V., Non Profit Organisation, Cagliari, Italy.,Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Sabrina Giglio
- Medical Genetics Unit, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy.,Medical Genetics Unit, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy.,Centre for Research University Services (CeSAR, Centro Servizi di Ateneo per la Ricerca), University of Cagliari, Monserrato, Italy
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17
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Kamp JC, Neubert L, Ackermann M, Stark H, Werlein C, Fuge J, Haverich A, Tzankov A, Steinestel K, Friemann J, Boor P, Junker K, Hoeper MM, Welte T, Laenger F, Kuehnel MP, Jonigk DD. Time-Dependent Molecular Motifs of Pulmonary Fibrogenesis in COVID-19. Int J Mol Sci 2022; 23:1583. [PMID: 35163504 PMCID: PMC8835897 DOI: 10.3390/ijms23031583] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 02/01/2023] Open
Abstract
(1) Background: In COVID-19 survivors there is an increased prevalence of pulmonary fibrosis of which the underlying molecular mechanisms are poorly understood; (2) Methods: In this multicentric study, n = 12 patients who succumbed to COVID-19 due to progressive respiratory failure were assigned to an early and late group (death within ≤7 and >7 days of hospitalization, respectively) and compared to n = 11 healthy controls; mRNA and protein expression as well as biological pathway analysis were performed to gain insights into the evolution of pulmonary fibrogenesis in COVID-19; (3) Results: Median duration of hospitalization until death was 3 (IQR25-75, 3-3.75) and 14 (12.5-14) days in the early and late group, respectively. Fifty-eight out of 770 analyzed genes showed a significantly altered expression signature in COVID-19 compared to controls in a time-dependent manner. The entire study group showed an increased expression of BST2 and IL1R1, independent of hospitalization time. In the early group there was increased activity of inflammation-related genes and pathways, while fibrosis-related genes (particularly PDGFRB) and pathways dominated in the late group; (4) Conclusions: After the first week of hospitalization, there is a shift from pro-inflammatory to fibrogenic activity in severe COVID-19. IL1R1 and PDGFRB may serve as potential therapeutic targets in future studies.
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Affiliation(s)
- Jan C. Kamp
- Department of Respiratory Medicine, Hannover Medical School, 30625 Hannover, Germany; (J.F.); (M.M.H.); (T.W.)
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), 30625 Hannover, Germany; (L.N.); (H.S.); (C.W.); (A.H.); (F.L.); (M.P.K.); (D.D.J.)
| | - Lavinia Neubert
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), 30625 Hannover, Germany; (L.N.); (H.S.); (C.W.); (A.H.); (F.L.); (M.P.K.); (D.D.J.)
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
| | - Maximilian Ackermann
- Institute of Pathology and Department of Molecular Pathology, Helios University Clinic Wuppertal, University of Witten-Herdecke, 42283 Wuppertal, Germany;
- Institute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg-University Mainz, 55122 Mainz, Germany
| | - Helge Stark
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), 30625 Hannover, Germany; (L.N.); (H.S.); (C.W.); (A.H.); (F.L.); (M.P.K.); (D.D.J.)
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
| | - Christopher Werlein
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), 30625 Hannover, Germany; (L.N.); (H.S.); (C.W.); (A.H.); (F.L.); (M.P.K.); (D.D.J.)
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
| | - Jan Fuge
- Department of Respiratory Medicine, Hannover Medical School, 30625 Hannover, Germany; (J.F.); (M.M.H.); (T.W.)
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), 30625 Hannover, Germany; (L.N.); (H.S.); (C.W.); (A.H.); (F.L.); (M.P.K.); (D.D.J.)
| | - Axel Haverich
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), 30625 Hannover, Germany; (L.N.); (H.S.); (C.W.); (A.H.); (F.L.); (M.P.K.); (D.D.J.)
- Department of Cardiothoracic, Transplant and Vascular Surgery, Hannover Medical School, 30625 Hannover, Germany
| | - Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital Basel, 4031 Basel, Switzerland;
| | - Konrad Steinestel
- Institute of Pathology and Molecular Pathology, Bundeswehrkrankenhaus Ulm, 89081 Ulm, Germany;
| | - Johannes Friemann
- Institute of Pathology, Märkische Kliniken GmbH, Klinikum Lüdenscheid, 58515 Lüdenscheid, Germany;
| | - Peter Boor
- Institute of Pathology and Department of Nephrology, RWTH University of Aachen, 52062 Aachen, Germany;
| | - Klaus Junker
- Institute of Pathology, Bremen Central Hospital, 28177 Bremen, Germany;
| | - Marius M. Hoeper
- Department of Respiratory Medicine, Hannover Medical School, 30625 Hannover, Germany; (J.F.); (M.M.H.); (T.W.)
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), 30625 Hannover, Germany; (L.N.); (H.S.); (C.W.); (A.H.); (F.L.); (M.P.K.); (D.D.J.)
| | - Tobias Welte
- Department of Respiratory Medicine, Hannover Medical School, 30625 Hannover, Germany; (J.F.); (M.M.H.); (T.W.)
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), 30625 Hannover, Germany; (L.N.); (H.S.); (C.W.); (A.H.); (F.L.); (M.P.K.); (D.D.J.)
| | - Florian Laenger
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), 30625 Hannover, Germany; (L.N.); (H.S.); (C.W.); (A.H.); (F.L.); (M.P.K.); (D.D.J.)
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
| | - Mark P. Kuehnel
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), 30625 Hannover, Germany; (L.N.); (H.S.); (C.W.); (A.H.); (F.L.); (M.P.K.); (D.D.J.)
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
| | - Danny D. Jonigk
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), 30625 Hannover, Germany; (L.N.); (H.S.); (C.W.); (A.H.); (F.L.); (M.P.K.); (D.D.J.)
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
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