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Cury S, Oliveira J, Biagi-Júnior C, Silva Jr W, Reis P, Cabral-Marques O, Hasimoto E, Freire P, Carvalho R. Transcriptional profiles and common genes link lung cancer with the development and severity of COVID-19. Gene 2023; 852:147047. [PMID: 36379381 PMCID: PMC9659360 DOI: 10.1016/j.gene.2022.147047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/14/2022]
Abstract
Lung cancer patients with COVID-19 present an increased risk of developing severe disease and, consequently, have poor outcomes. Determining SARS-CoV-2-host interactome in lung cancer cells and tissues, infected or uninfected with SARS-CoV-2, may reveal molecular mechanisms associated with COVID-19 development and severity in lung cancer patients. Here, we integrated transcriptome data of lung tumors from patients with small- or non-small cell lung cancer (SCLC and NSCLC) and normal lung and lung cancer cells infected with SARS-CoV-2. We aimed to characterize molecular mechanisms potentially associated with COVID-19 development and severity in lung cancer patients and to predict the SARS-CoV-2-host cell interactome. We found that the gene expression profiles of lung cell lines infected with SARS-CoV-2 resemble more primary lung tumors than non-malignant lung tissues. In addition, the transcriptomic-based interactome analysis of SCLC and NSCLC revealed increased expression of cancer genes BRCA1 and CENPF, whose proteins are known or predicted to interact with the SARS-CoV-2 spike glycoprotein and helicase, respectively. We also found that TRIB3, a gene coding a putative host-SARS-CoV-2 interacting protein associated with COVID-19 infection, is co-expressed with the up-regulated genes MTHFD2, ADM2, and GPT2 in all tested conditions. Our analysis identified biological processes such as amino acid metabolism and angiogenesis and 22 host mediators of SARS-CoV-2 infection and replication that may contribute to the development and severity of COVID-19 in lung cancers.
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Affiliation(s)
- S.S. Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - J.S. Oliveira
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - C.A.O. Biagi-Júnior
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil,Institute for Cancer Research (IPEC), Guarapuava, PR, Brazil
| | - W.A. Silva Jr
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil,Institute for Cancer Research (IPEC), Guarapuava, PR, Brazil
| | - P.P. Reis
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - O. Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil,Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil,Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo, SP, Brazil,Department of Pharmacy and Postgraduate Program of Health and Science, Federal University of Rio Grande do Norte (UFRN), Natal, RN, Brazil
| | - E.N. Hasimoto
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - P.P. Freire
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil,Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil,Corresponding authors at: Department of Immunology, Institute of Biomedical Sciences - University of São Paulo, Lineu Prestes Avenue, 1730 São Paulo, Brazil (P.P. Freire). Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), CEP: 18.618-689, Botucatu, São Paulo, Brazil (R.F. Carvalho)
| | - R.F. Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil,Lead Contact,Corresponding authors at: Department of Immunology, Institute of Biomedical Sciences - University of São Paulo, Lineu Prestes Avenue, 1730 São Paulo, Brazil (P.P. Freire). Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), CEP: 18.618-689, Botucatu, São Paulo, Brazil (R.F. Carvalho)
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Dhawan M, Saied AA, Mitra S, Alhumaydhi FA, Emran TB, Wilairatana P. Omicron variant (B.1.1.529) and its sublineages: What do we know so far amid the emergence of recombinant variants of SARS-CoV-2? Biomed Pharmacother 2022; 154:113522. [PMID: 36030585 PMCID: PMC9376347 DOI: 10.1016/j.biopha.2022.113522] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 12/19/2022] Open
Abstract
Since the start of the COVID-19 pandemic, numerous variants of SARS-CoV-2 have been reported worldwide. The advent of variants of concern (VOCs) raises severe concerns amid the serious containment efforts against COVID-19 that include physical measures, pharmacological repurposing, immunization, and genomic/community surveillance. Omicron variant (B.1.1.529) has been identified as a highly modified, contagious, and crucial variant among the five VOCs of SARS-CoV-2. The increased affinity of the spike protein (S-protein), and host receptor, angiotensin converting enzyme-2 (ACE-2), due to a higher number of mutations in the receptor-binding domain (RBD) of the S-protein has been proposed as the primary reason for the decreased efficacy of majorly available vaccines against the Omicron variant and the increased transmissible nature of the Omicron variant. Because of its significant competitive advantage, the Omicron variant and its sublineages swiftly surpassed other variants to become the dominant circulating lineages in a number of nations. The Omicron variant has been identified as a prevalent strain in the United Kingdom and South Africa. Furthermore, the emergence of recombinant variants through the conjunction of the Omicron variant with other variants or by the mixing of the Omicron variant's sublineages/subvariants poses a major threat to humanity. This raises various issues and hazards regarding the Omicron variant and its sublineages, such as an Omicron variant breakout in susceptible populations among fully vaccinated persons. As a result, understanding the features and genetic implications of this variant is crucial. Hence, we explained in depth the evolution and features of the Omicron variant and analyzed the repercussions of spike mutations on infectiousness, dissemination ability, viral entry mechanism, and immune evasion. We also presented a viewpoint on feasible strategies for precluding and counteracting any future catastrophic emergence and spread of the omicron variant and its sublineages that could result in a detrimental wave of COVID-19 cases.
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Affiliation(s)
- Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, Punjab, India; Trafford College, Altrincham, Manchester WA14 5PQ, UK.
| | - AbdulRahman A Saied
- National Food Safety Authority (NFSA), Aswan Branch, Aswan 81511, Egypt; Ministry of Tourism and Antiquities, Aswan Office, Aswan 81511, Egypt
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh.
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand.
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