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Wang M, Bo Z, Zhang C, Guo M, Wu Y, Zhang X. Deciphering the Genetic Variation: A Comparative Analysis of Parental and Attenuated Strains of the QXL87 Vaccine for Infectious Bronchitis. Animals (Basel) 2024; 14:1784. [PMID: 38929403 PMCID: PMC11200882 DOI: 10.3390/ani14121784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The QXL87 live attenuated vaccine strain for infectious bronchitis represents the first approved QX type (GI-19 lineage) vaccine in China. This strain was derived from the parental strain CK/CH/JS/2010/12 through continuous passage in SPF chicken embryos. To elucidate the molecular mechanism behind its attenuation, whole-genome sequencing was conducted on both the parental and attenuated strains. Analysis revealed 145 nucleotide mutations in the attenuated strain, leading to 48 amino acid mutations in various proteins, including Nsp2 (26), Nsp3 (14), Nsp4 (1), S (4), 3a (1), E (1), and N (1). Additionally, a frameshift mutation caused by a single base insertion in the ORFX resulted in a six-amino-acid extension. Subsequent comparison of post-translational modification sites, protein structure, and protein-protein binding sites between the parental and attenuated strains identified three potential virulence genes: Nsp2, Nsp3, and S. The amino acid mutations in these proteins not only altered their conformation but also affected the distribution of post-translational modification sites and protein-protein interaction sites. Furthermore, three potential functional mutation sites-P106S, A352T, and L472F, all located in the Nsp2 protein-were identified through PROVEAN, PolyPhen, and I-Mutant. Overall, our findings suggest that Nsp2, Nsp3, and S proteins may play a role in modulating IBV pathogenicity, with a particular focus on the significance of the Nsp2 protein. This study contributes to our understanding of the molecular mechanisms underlying IBV attenuation and holds promise for the development of safer live attenuated IBV vaccines using reverse genetic approaches.
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Affiliation(s)
- Mengmeng Wang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Zongyi Bo
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Chengcheng Zhang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Mengjiao Guo
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Yantao Wu
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Xiaorong Zhang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
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Qamar F, Sharif Z, Idrees J, Wasim A, Haider S, Salman S. SARS-CoV-2-induced phosphorylation and its pharmacotherapy backed by artificial intelligence and machine learning. Future Sci OA 2024; 10:FSO917. [PMID: 38827795 PMCID: PMC11140666 DOI: 10.2144/fsoa-2023-0112] [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: 06/16/2023] [Accepted: 10/04/2023] [Indexed: 06/05/2024] Open
Abstract
Aims: To investigate the role of phosphorylation in SARS-CoV-2 infection, potential therapeutic targets and its harmful genetic sequences. Materials & Methods: Data mining techniques were employed to identify upregulated kinases responsible for proteomic changes induced by SARS-CoV-2. Spike and nucleocapsid proteins' sequences were analyzed using predictive tools, including SNAP2, MutPred2, PhD-SNP, SNPs&Go, MetaSNP, Predict-SNP and PolyPhen-2. Missense variants were identified using ensemble-based algorithms and homology/structure-based models like SIFT, PROVEAN, Predict-SNP and MutPred-2. Results: Eight missense variants were identified in viral sequences. Four damaging variants were found, with SNPs&Go and PolyPhen-2. Promising therapeutic candidates, including gilteritinib, pictilisib, sorafenib, RO5126766 and omipalisib, were identified. Conclusion: This research offers insights into SARS-CoV-2 pathogenicity, highlighting potential treatments and harmful variants in viral proteins.
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Affiliation(s)
- Fouzia Qamar
- Department of Biology, Lahore Garrison University, Lahore-54000, Punjab, Pakistan
| | - Zubair Sharif
- Faculty of Medical Laboratory Sciences, Superior University, Lahore-54000, Punjab, Pakistan
| | - Jawaria Idrees
- Khyber Pakhtunkhwa Education Monitoring Authority, Khyber-Pakhtunkhwa, Peshawar-25000, Pakistan
| | - Asif Wasim
- Department of Pharmacy, CECOS University of IT & Emerging Sciences, Peshawar-25000, Khyber Pakhtunkhwa, Peshawar, Pakistan
| | - Sana Haider
- Department of Pharmacy, CECOS University of IT & Emerging Sciences, Peshawar-25000, Khyber Pakhtunkhwa, Peshawar, Pakistan
| | - Saad Salman
- Department of Pharmacy, CECOS University of IT & Emerging Sciences, Peshawar-25000, Khyber Pakhtunkhwa, Peshawar, Pakistan
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Yin Q, Liu W, Jiang Y, Feng Q, Wang X, Dou H, Liu Z, He F, Fan Y, Jiao B, Jiao B. Comprehensive genomic analysis of the SARS-CoV-2 Omicron variant BA.2.76 in Jining City, China, 2022. BMC Genomics 2024; 25:378. [PMID: 38632523 PMCID: PMC11022347 DOI: 10.1186/s12864-024-10246-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
OBJECTIVE This study aims to analyze the molecular characteristics of the novel coronavirus (SARS-CoV-2) Omicron variant BA.2.76 in Jining City, China. METHODS Whole-genome sequencing was performed on 87 cases of SARS-CoV-2 infection. Evolutionary trees were constructed using bioinformatics software to analyze sequence homology, variant sites, N-glycosylation sites, and phosphorylation sites. RESULTS All 87 SARS-CoV-2 whole-genome sequences were classified under the evolutionary branch of the Omicron variant BA.2.76. Their similarity to the reference strain Wuhan-Hu-1 ranged from 99.72 to 99.74%. In comparison to the reference strain Wuhan-Hu-1, the 87 sequences exhibited 77-84 nucleotide differences and 27 nucleotide deletions. A total of 69 amino acid variant sites, 9 amino acid deletions, and 1 stop codon mutation were identified across 18 proteins. Among them, the spike (S) protein exhibited the highest number of variant sites, and the ORF8 protein showed a Q27 stop mutation. Multiple proteins displayed variations in glycosylation and phosphorylation sites. CONCLUSION SARS-CoV-2 continues to evolve, giving rise to new strains with enhanced transmission, stronger immune evasion capabilities, and reduced pathogenicity. The application of high-throughput sequencing technologies in the epidemic prevention and control of COVID-19 provides crucial insights into the evolutionary and variant characteristics of the virus at the genomic level, thereby holding significant implications for the prevention and control of the COVID-19 pandemic.
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Affiliation(s)
- Qiang Yin
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Wei Liu
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Yajuan Jiang
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Qiang Feng
- Department of Laboratory, Rencheng Center for Disease Control and Prevention, Jining, China
| | - Xiaoyu Wang
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Huixin Dou
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Zanzan Liu
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Feifei He
- Computer Information Technology, Northern Arizona University, Arizona, USA
| | - Yingying Fan
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
| | - Baihai Jiao
- Department of Medicine, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA.
| | - Boyan Jiao
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
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Kim HY, Jeong KM, Kim SH, Choi YJ, Kang HG, Jung H, Min K, Kim HM, Jeong HJ. Modulating effect of Eunkyo-san on expression of inflammatory cytokines and angiotensin-converting enzyme 2 in human mast cells. In Vitro Cell Dev Biol Anim 2024; 60:195-208. [PMID: 38228999 DOI: 10.1007/s11626-024-00847-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
Eunkyo-san is widely used in the treatment of severe respiratory infections. Mast cells not only serve as host cells for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but also they also exacerbate Coronavirus disease in 2019 (COVID-19) by causing a cytokine storm. Here we investigated whether Eunkyo-san and its active compound naringenin regulate the expression of inflammatory cytokines and factors connected to viral infection in activated human mast cell line, HMC-1 cells. Eunkyo-san and naringenin significantly reduced levels of inflammatory cytokines including interleukin (IL)-1β, IL-6, IL-8, thymic stromal lymphopoietin, and tumor necrosis factor-α without impacting cytotoxicity. Eunkyo-san and naringenin reduced levels of factors connected to SARS-CoV-2 infection such as angiotensin-converting enzyme 2 (ACE2, SARS-CoV-2 receptor), transmembrane protease/serine subfamily member 2, and tryptase in activated HMC-1 cells. Treatment with Eunkyo-san and naringenin considerably reduced expression levels of ACE2 transcription factor, AP-1 (C-JUN and C-FOS) by blocking phosphatidylinositide-3-kinase and c-Jun NH2-terminal kinases signaling pathways. In addition, Eunkyo-san and naringenin effectively suppressed activation of signal transducer and activator of transcription 3, nuclear translocation of nuclear factor-κB, and activation of caspase-1 in activated HMC-1 cells. Furthermore, Eunkyo-san and naringenin reduced expression of ACE2 mRNA in two activated mast cell lines, RBL-2H3 and IC-2 cells. The overall study findings showed that Eunkyo-san diminished the expression levels of inflammatory cytokines and ACE2, and these findings imply that Eunkyo-san is able to effectively mitigating the cytokine storm brought on by SARS-CoV-2 infection.
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Affiliation(s)
- Hee-Yun Kim
- Biochip Research Center, Hoseo University, Asan, 31499, Republic of Korea
| | - Kyung-Min Jeong
- Division of Food and Pharmaceutical Engineering, Hoseo University, Asan, 31499, Republic of Korea
| | - Seung-Hwan Kim
- Division of Food and Pharmaceutical Engineering, Hoseo University, Asan, 31499, Republic of Korea
| | - Yu-Jin Choi
- Division of Food and Pharmaceutical Engineering, Hoseo University, Asan, 31499, Republic of Korea
| | - Ho-Geun Kang
- Department of Bio-Convergence System, Graduate School, Hoseo University, Asan, 31499, Republic of Korea
| | - Hanchul Jung
- Department of Science in Korean Medicine, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Kyunghwon Min
- Department of Science in Korean Medicine, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Hyung-Min Kim
- Department of Science in Korean Medicine, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea.
| | - Hyun-Ja Jeong
- Biochip Research Center, Hoseo University, Asan, 31499, Republic of Korea.
- Division of Food and Pharmaceutical Engineering, Hoseo University, Asan, 31499, Republic of Korea.
- Department of Bio-Convergence System, Graduate School, Hoseo University, Asan, 31499, Republic of Korea.
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Pham NT, Phan LT, Seo J, Kim Y, Song M, Lee S, Jeon YJ, Manavalan B. Advancing the accuracy of SARS-CoV-2 phosphorylation site detection via meta-learning approach. Brief Bioinform 2023; 25:bbad433. [PMID: 38058187 PMCID: PMC10753650 DOI: 10.1093/bib/bbad433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 12/08/2023] Open
Abstract
The worldwide appearance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has generated significant concern and posed a considerable challenge to global health. Phosphorylation is a common post-translational modification that affects many vital cellular functions and is closely associated with SARS-CoV-2 infection. Precise identification of phosphorylation sites could provide more in-depth insight into the processes underlying SARS-CoV-2 infection and help alleviate the continuing COVID-19 crisis. Currently, available computational tools for predicting these sites lack accuracy and effectiveness. In this study, we designed an innovative meta-learning model, Meta-Learning for Serine/Threonine Phosphorylation (MeL-STPhos), to precisely identify protein phosphorylation sites. We initially performed a comprehensive assessment of 29 unique sequence-derived features, establishing prediction models for each using 14 renowned machine learning methods, ranging from traditional classifiers to advanced deep learning algorithms. We then selected the most effective model for each feature by integrating the predicted values. Rigorous feature selection strategies were employed to identify the optimal base models and classifier(s) for each cell-specific dataset. To the best of our knowledge, this is the first study to report two cell-specific models and a generic model for phosphorylation site prediction by utilizing an extensive range of sequence-derived features and machine learning algorithms. Extensive cross-validation and independent testing revealed that MeL-STPhos surpasses existing state-of-the-art tools for phosphorylation site prediction. We also developed a publicly accessible platform at https://balalab-skku.org/MeL-STPhos. We believe that MeL-STPhos will serve as a valuable tool for accelerating the discovery of serine/threonine phosphorylation sites and elucidating their role in post-translational regulation.
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Affiliation(s)
- Nhat Truong Pham
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Le Thi Phan
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Jimin Seo
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Yeonwoo Kim
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Minkyung Song
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Young-Jun Jeon
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Balachandran Manavalan
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
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Jiang S, Yang H, Sun Z, Zhang Y, Li Y, Li J. The basis of complications in the context of SARS-CoV-2 infection: Pathological activation of ADAM17. Biochem Biophys Res Commun 2023; 679:37-46. [PMID: 37666046 DOI: 10.1016/j.bbrc.2023.08.063] [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: 07/20/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
The virulence of SARS-CoV-2 decreases with increasing infectivity, the primary approaches for antiviral treatments will be preventing or minimizing the complications resulting from virus infection. ADAM metallopeptidase domain 17 (ADAM17) activation by SARS-CoV-2 infection has a dual effect on the development of the disease: increased release of inflammatory cytokines and dysregulation of Angiotensin converting enzyme II (ACE2) on cell surfaces, inflammatory cytokine infiltration and loss of ACE2 protective function lead to a significant increase in the incidence of related complications. Importantly, pathologically activated ADAM17 showed superior features than S protein in regulating ACE2 expression and participating in the intra cellular replication of SARS-CoV-2. In short, SARS-CoV-2 elicits only a limited immune response when it promotes its own replication and pathogenicity through ADAM17. Therefore, the pathological activation of ADAM17 may also represent a diminished innate antiviral defense and an altered strategy of SARS-CoV-2 infection. In this review, we summarized recent advances in our understanding of the pathophysiology of ADAM17, with a focus on the new findings that SARS-CoV-2 affects ADAM17 expression through Furin protein converting enzyme and Mitogen-activated protein kinase (MAPK) pathway, and raises the hypothesis that SARS-CoV-2 may mediates the pathological activation of ADAM17 by hijacking the actin regulatory pathway, and discussed the underlying biological principles.
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Affiliation(s)
| | - Hao Yang
- Zunyi Medical University Guizhou, China
| | | | - Yi Zhang
- Zunyi Medical University Guizhou, China
| | - Yan Li
- Zunyi Medical University Guizhou, China
| | - Jida Li
- Zunyi Medical University Guizhou, China; Key Laboratory of Maternal & Child Health and Exposure Science of Guizhou Higher Education Institutes, Zunyi, Guizhou, China.
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Di Primio C, Quaranta P, Mignanelli M, Siano G, Bimbati M, Scarlatti A, Piazza CR, Spezia PG, Perrera P, Basolo F, Poma AM, Costa M, Pistello M, Cattaneo A. Severe acute respiratory syndrome coronavirus 2 infection leads to Tau pathological signature in neurons. PNAS NEXUS 2023; 2:pgad282. [PMID: 37731949 PMCID: PMC10508204 DOI: 10.1093/pnasnexus/pgad282] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/07/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023]
Abstract
COVID-19 has represented an issue for global health since its outbreak in March 2020. It is now evident that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection results in a wide range of long-term neurological symptoms and is worryingly associated with the aggravation of Alzheimer's disease. Little is known about the molecular basis of these manifestations. Here, several strain variants were used to infect SH-SY5Y neuroblastoma cells and K18-hACE C57BL/6J mice. The Tau phosphorylation profile and aggregation propensity upon infection were investigated on cellular extracts, subcellular fractions, and brain tissue. The viral proteins spike, nucleocapsid, and membrane were overexpressed in SH-SY5Y cells, and the direct interaction and effect on Tau phosphorylation were checked using immunoblot experiments. Upon infection, Tau is phosphorylated at several pathological epitopes associated with Alzheimer's disease and other tauopathies. Moreover, this event increases Tau's propensity to form insoluble aggregates and alters its subcellular localization. Our data support the hypothesis that SARS-CoV-2 infection in the central nervous system triggers downstream effects altering Tau function, eventually leading to the impairment of neuronal function.
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Affiliation(s)
- Cristina Di Primio
- Institute of Neuroscience, Italian National Research Council (CNR), Pisa 56124, Italy
| | - Paola Quaranta
- Institute of Neuroscience, Italian National Research Council (CNR), Pisa 56124, Italy
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa 56100, Italy
| | - Marianna Mignanelli
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore di Pisa, Pisa 56126, Italy
| | - Giacomo Siano
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore di Pisa, Pisa 56126, Italy
| | - Matteo Bimbati
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore di Pisa, Pisa 56126, Italy
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Arianna Scarlatti
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore di Pisa, Pisa 56126, Italy
| | - Carmen Rita Piazza
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa 56100, Italy
- Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
| | - Piero Giorgio Spezia
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa 56100, Italy
| | - Paola Perrera
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa 56100, Italy
| | - Fulvio Basolo
- Department of Surgical, Medical and Molecular Pathology, University Hospital of Pisa, Pisa 56124, Italy
| | - Anello Marcello Poma
- Department of Surgical, Medical and Molecular Pathology, University Hospital of Pisa, Pisa 56124, Italy
| | - Mario Costa
- Institute of Neuroscience, Italian National Research Council (CNR), Pisa 56124, Italy
| | - Mauro Pistello
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa 56100, Italy
- Virology Unit, Pisa University Hospital, Pisa 56100, Italy
| | - Antonino Cattaneo
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore di Pisa, Pisa 56126, Italy
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Guichard A, Lu S, Kanca O, Bressan D, Huang Y, Ma M, Sanz Juste S, Andrews JC, Jay KL, Sneider M, Schwartz R, Huang MC, Bei D, Pan H, Ma L, Lin WW, Auradkar A, Bhagwat P, Park S, Wan KH, Ohsako T, Takano-Shimizu T, Celniker SE, Wangler MF, Yamamoto S, Bellen HJ, Bier E. A comprehensive Drosophila resource to identify key functional interactions between SARS-CoV-2 factors and host proteins. Cell Rep 2023; 42:112842. [PMID: 37480566 PMCID: PMC10962759 DOI: 10.1016/j.celrep.2023.112842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/18/2023] [Accepted: 07/05/2023] [Indexed: 07/24/2023] Open
Abstract
Development of effective therapies against SARS-CoV-2 infections relies on mechanistic knowledge of virus-host interface. Abundant physical interactions between viral and host proteins have been identified, but few have been functionally characterized. Harnessing the power of fly genetics, we develop a comprehensive Drosophila COVID-19 resource (DCR) consisting of publicly available strains for conditional tissue-specific expression of all SARS-CoV-2 encoded proteins, UAS-human cDNA transgenic lines encoding established host-viral interacting factors, and GAL4 insertion lines disrupting fly homologs of SARS-CoV-2 human interacting proteins. We demonstrate the utility of the DCR to functionally assess SARS-CoV-2 genes and candidate human binding partners. We show that NSP8 engages in strong genetic interactions with several human candidates, most prominently with the ATE1 arginyltransferase to induce actin arginylation and cytoskeletal disorganization, and that two ATE1 inhibitors can reverse NSP8 phenotypes. The DCR enables parallel global-scale functional analysis of SARS-CoV-2 components in a prime genetic model system.
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Affiliation(s)
- Annabel Guichard
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Daniel Bressan
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA; Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Yan Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Sara Sanz Juste
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA; Department of Epigenetics & Molecular Carcinogenesis at MD Anderson, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan C Andrews
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Kristy L Jay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Marketta Sneider
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Ruth Schwartz
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Mei-Chu Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Danqing Bei
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Hongling Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Liwen Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Wen-Wen Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Pranjali Bhagwat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Soo Park
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kenneth H Wan
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Takashi Ohsako
- Advanced Technology Center, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Toshiyuki Takano-Shimizu
- Kyoto Drosophila Stock Center and Faculty of Applied Biology, Kyoto Institute of Technology, Kyoto 616-8354, Japan
| | - Susan E Celniker
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego (UCSD), La Jolla, CA 92093, USA; Tata Institute for Genetics and Society - UCSD, La Jolla, CA 92093, USA.
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9
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El-Arabey AA, Abdalla M, Rashad Abd-Allah A, Marenga H, Modafer Y, Aloufi AS. Molecular dynamic and bioinformatic studies of metformin-induced ACE2 phosphorylation in the presence of different SARS-CoV-2 S protein mutations. Saudi J Biol Sci 2023; 30:103699. [PMID: 37292255 PMCID: PMC10238124 DOI: 10.1016/j.sjbs.2023.103699] [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: 05/04/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/10/2023] Open
Abstract
The SARS-CoV-2 infection activates host kinases and causes high phosphorylation in both the host and the virus. There were around 70 phosphorylation sites found in SARS-CoV-2 viral proteins. Besides, almost 15,000 host phosphorylation sites were found in SARS-CoV-2-infected cells. COVID-19 is thought to enter cells via the well-known receptor Angiotensin-Converting Enzyme 2 (ACE2) and the serine protease TMPRSS2. Substantially, the COVID-19 infection doesn't induce phosphorylation of the ACE2 receptor at Serin-680(s680). Metformin's numerous pleiotropic properties and extensive use in medicine including COVID-19, have inspired experts to call it the "aspirin of the twenty-first century". Metformin's impact on COVID-19 has been verified in clinical investigations via ACE2 receptor phosphorylation at s680. In the infection of COVID-19, sodium-dependent transporters including the major neutral amino acid (B0AT1) is regulated by ACE2. The structure of B0AT1 complexing with the COVID-19 receptor ACE2 enabled significant progress in the creation of mRNA vaccines. We aimed to study the impact of the interaction of the phosphorylation form of ACE2-s680 with wild-type (WT) and different mutations of SARS-CoV-2 infection such as delta, omicron, and gamma (γ) on their entrance of host cells as well as the regulation of B0AT1by the SARS-CoV-2 receptor ACE2. Interestingly, compared to WT SARS-CoV-2, ACE2 receptor phosphorylation at s680 produces conformational alterations in all types of SARS-CoV-2. Furthermore, our results showed for the first time that this phosphorylation significantly influences ACE2 sites K625, K676, and R678, which are key mediators for ACE2-B0AT1 complex.
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Affiliation(s)
- Amr Ahmed El-Arabey
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo 11751, Egypt
| | - Mohnad Abdalla
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jinan 250022, China
| | - Adel Rashad Abd-Allah
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo 11751, Egypt
| | - Hanin.S. Marenga
- Department of Pharmaceutical chemistry, College of pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Yosra Modafer
- Department of Biology, Faculty of Science, Jazan university, Jazan 45142, Saudi Arabia
| | - Abeer S. Aloufi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
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10
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Zhang G, Tang Q, Feng P, Chen W. IPs-GRUAtt: An attention-based bidirectional gated recurrent unit network for predicting phosphorylation sites of SARS-CoV-2 infection. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:28-35. [PMID: 36908648 PMCID: PMC9968446 DOI: 10.1016/j.omtn.2023.02.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has generated tremendous concern and poses a serious threat to international public health. Phosphorylation is a common post-translational modification affecting many essential cellular processes and is inextricably linked to SARS-CoV-2 infection. Hence, accurate identification of phosphorylation sites will be helpful to understand the mechanisms of SARS-CoV-2 infection and mitigate the ongoing COVID-19 pandemic. In the present study, an attention-based bidirectional gated recurrent unit network, called IPs-GRUAtt, was proposed to identify phosphorylation sites in SARS-CoV-2-infected host cells. Comparative results demonstrated that IPs-GRUAtt surpassed both state-of-the-art machine-learning methods and existing models for identifying phosphorylation sites. Moreover, the attention mechanism made IPs-GRUAtt able to extract the key features from protein sequences. These results demonstrated that the IPs-GRUAtt is a powerful tool for identifying phosphorylation sites. For facilitating its academic use, a freely available online web server for IPs-GRUAtt is provided at http://cbcb.cdutcm.edu.cn/phosphory/.
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Affiliation(s)
- Guiyang Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qiang Tang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Pengmian Feng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Wei Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.,State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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11
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Maginnis MS. β-arrestins and G protein-coupled receptor kinases in viral entry: A graphical review. Cell Signal 2023; 102:110558. [PMID: 36509265 PMCID: PMC9811579 DOI: 10.1016/j.cellsig.2022.110558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Viruses rely on host-cell machinery in order to invade host cells and carry out a successful infection. G-protein coupled receptor (GPCR)-mediated signaling pathways are master regulators of cellular physiological processing and are an attractive target for viruses to rewire cells during infection. In particular, the GPCR-associated scaffolding proteins β-arrestins and GPCR signaling effectors G-protein receptor kinases (GRKs) have been identified as key cellular factors that mediate viral entry and orchestrate signaling pathways that reprogram cells for viral replication. Interestingly, a broad range of viruses have been identified to activate and/or require GPCR-mediated pathways for infection, including polyomaviruses, flaviviruses, influenza virus, and SARS-CoV-2, demonstrating that these viruses may have conserved mechanisms of host-cell invasion. Thus, GPCR-mediated pathways highlight an attractive target for the development of broad antiviral therapies.
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Affiliation(s)
- Melissa S Maginnis
- Molecular and Biomedical Sciences, The University of Maine, Orono, ME 04469, United States of America; Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, ME 04469, United States of America.
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12
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Molecular Dynamics Simulations to Decipher the Role of Phosphorylation of SARS-CoV-2 Nonstructural Proteins (nsps) in Viral Replication. Viruses 2022; 14:v14112436. [PMID: 36366534 PMCID: PMC9693435 DOI: 10.3390/v14112436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Protein phosphorylation is a post-translational modification that enables various cellular activities and plays essential roles in protein interactions. Phosphorylation is an important process for the replication of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). To shed more light on the effects of phosphorylation, we used an ensemble of neural networks to predict potential kinases that might phosphorylate SARS-CoV-2 nonstructural proteins (nsps) and molecular dynamics (MD) simulations to investigate the effects of phosphorylation on nsps structure, which could be a potential inhibitory target to attenuate viral replication. Eight target candidate sites were found as top-ranked phosphorylation sites of SARS-CoV-2. During the process of molecular dynamics (MD) simulation, the root-mean-square deviation (RMSD) analysis was used to measure conformational changes in each nsps. Root-mean-square fluctuation (RMSF) was employed to measure the fluctuation in each residue of 36 systems considered, allowing us to evaluate the most flexible regions. These analysis shows that there are significant structural deviations in the residues namely nsp1 THR 72, nsp2 THR 73, nsp3 SER 64, nsp4 SER 81, nsp4 SER 455, nsp5 SER284, nsp6 THR 238, and nsp16 SER 132. The identified list of residues suggests how phosphorylation affects SARS-CoV-2 nsps function and stability. This research also suggests that kinase inhibitors could be a possible component for evaluating drug binding studies, which are crucial in therapeutic discovery research.
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13
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Jain S, Rego S, Park S, Liu Y, Parn S, Savsani K, Perlin DS, Dakshanamurthy S. RNASeq profiling of COVID19-infected patients identified an EIF2AK2 inhibitor as a potent SARS-CoV-2 antiviral. Clin Transl Med 2022; 12:e1098. [PMID: 36321336 PMCID: PMC9627224 DOI: 10.1002/ctm2.1098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/03/2022] [Accepted: 10/13/2022] [Indexed: 12/05/2022] Open
Affiliation(s)
- Sidharth Jain
- Lombardi Comprehensive Cancer CenterGeorgetown University Medical CenterWashington DCDistrict of Columbia20057USA,Georgetown CollegeGeorgetown UniversityWashington DCDistrict of Columbia20057USA
| | - Samantha Rego
- Georgetown CollegeGeorgetown UniversityWashington DCDistrict of Columbia20057USA
| | - Steven Park
- Center for Discovery and InnovationHackensack Meridian HealthNew Jersey07110USA
| | - Yiran Liu
- Department of Biochemistry & Molecular BiologyGeorgetown University Medical CenterWashington DCDistrict of Columbia20057USA
| | - Simone Parn
- College of Arts & ScienceUniversity of the District of ColumbiaWashington DCDistrict of Columbia20008USA
| | - Kush Savsani
- College of Humanities and SciencesVirginia Commonwealth UniversityRichmondVirginia23284USA
| | - David S. Perlin
- Center for Discovery and InnovationHackensack Meridian HealthNew Jersey07110USA
| | - Sivanesan Dakshanamurthy
- Lombardi Comprehensive Cancer CenterGeorgetown University Medical CenterWashington DCDistrict of Columbia20057USA
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14
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Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the pathogen responsible for the coronavirus disease 2019 (COVID-19) pandemic. Of particular interest for this topic are the signaling cascades that regulate cell survival and death, two opposite cell programs whose control is hijacked by viral infections. The AKT and the Unfolded Protein Response (UPR) pathways, which maintain cell homeostasis by regulating these two programs, have been shown to be deregulated during SARS-CoVs infection as well as in the development of cancer, one of the most important comorbidities in relation to COVID-19. Recent evidence revealed two way crosstalk mechanisms between the AKT and the UPR pathways, suggesting that they might constitute a unified homeostatic control system. Here, we review the role of the AKT and UPR pathways and their interaction in relation to SARS-CoV-2 infection as well as in tumor onset and progression. Feedback regulation between AKT and UPR pathways emerges as a master control mechanism of cell decision making in terms of survival or death and therefore represents a key potential target for developing treatments for both viral infection and cancer. In particular, drug repositioning, the investigation of existing drugs for new therapeutic purposes, could significantly reduce time and costs compared to de novo drug discovery.
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15
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Stamoula E, Sarantidi E, Dimakopoulos V, Ainatzoglou A, Dardalas I, Papazisis G, Kontopoulou K, Anagnostopoulos AK. Serum Proteome Signatures of Anti-SARS-CoV-2 Vaccinated Healthcare Workers in Greece Associated with Their Prior Infection Status. Int J Mol Sci 2022; 23:ijms231710153. [PMID: 36077551 PMCID: PMC9456361 DOI: 10.3390/ijms231710153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Over the course of the pandemic, proteomics, being in the frontline of anti-COVID-19 research, has massively contributed to the investigation of molecular pathogenic properties of the virus. However, data on the proteome on anti-SARS-CoV-2 vaccinated individuals remain scarce. This study aimed to identify the serum proteome characteristics of anti-SARS-CoV-2 vaccinated individuals who had previously contracted the virus and comparatively assess them against those of virus-naïve vaccine recipients. Blood samples of n = 252 individuals, out of whom n = 35 had been previously infected, were collected in the "G. Gennimatas" General Hospital of Thessaloniki, from 4 January 2021 to 31 August 2021. All participants received the BNT162b2 mRNA COVID-19 vaccine (Pfizer/BioNTech). A label-free quantitative proteomics LC-MS/MS approach was undertaken, and the identified proteins were analyzed using the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes) databases as well as processed by bioinformatics tools. Titers of total RBD-specific IgGs against SARS-CoV-2 were also determined using the SARS-CoV-2 IgG II Quant assay. A total of 47 proteins were significantly differentially expressed, the majority of which were down-regulated in sera of previously infected patients compared to virus-naïve controls. Several pathways were affected supporting the crucial role of the humoral immune response in the protection against SARS-CoV-2 infection provided by COVID-19 vaccination. Overall, our comprehensive proteome profiling analysis contributes novel knowledge of the mechanisms of immune response induced by anti-SARS-CoV-2 vaccination and identified protein signatures reflecting the immune status of vaccine recipients.
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Affiliation(s)
- Eleni Stamoula
- Department of Biotechnology, Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- Department of Clinical Pharmacology, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Eleana Sarantidi
- Department of Biotechnology, Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Vasilis Dimakopoulos
- Department of Biotechnology, Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Alexandra Ainatzoglou
- Department of Clinical Pharmacology, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Ioannis Dardalas
- Department of Clinical Pharmacology, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Georgios Papazisis
- Department of Clinical Pharmacology, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
- Clinical Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | | | - Athanasios K. Anagnostopoulos
- Department of Biotechnology, Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- Correspondence:
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16
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Liu J, Chen Y, Nie L, Liang X, Huang W, Li R. In silico analysis and preclinical findings uncover potential targets of anti-cervical carcinoma and COVID-19 in laminarin, a promising nutraceutical. Front Pharmacol 2022; 13:955482. [PMID: 36016559 PMCID: PMC9395986 DOI: 10.3389/fphar.2022.955482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/04/2022] [Indexed: 12/03/2022] Open
Abstract
Until today, the coronavirus disease 2019 (COVID-19) pandemic has caused 6,043,094 deaths worldwide, and most of the mortality cases have been related to patients with long-term diseases, especially cancer. Autophagy is a cellular process for material degradation. Recently, studies demonstrated the association of autophagy with cancer development and immune disorder, suggesting autophagy as a possible target for cancer and immune therapy. Laminarin is a polysaccharide commonly found in brown algae and has been reported to have pharmaceutic roles in treating human diseases, including cancers. In the present report, we applied network pharmacology with systematic bioinformatic analysis, including gene ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, reactome pathway analysis, and molecular docking to determine the pharmaceutic targets of laminarin against COVID-19 and cervical cancer via the autophagic process. Our results showed that the laminarin would target ten genes: CASP8, CFTR, DNMT1, HPSE, KCNH2, PIK3CA, PIK3R1, SERPINE1, TLR4, and VEGFA. The enrichment analysis suggested their involvement in cell death, immune responses, apoptosis, and viral infection. In addition, molecular docking further demonstrated the direct binding of laminarin to its target proteins, VEGFA, TLR4, CASP8, and PIK3R1. The present findings provide evidence that laminarin could be used as a combined therapy for treating patients with COVID-19 and cervical cancer.
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Affiliation(s)
- Jiaqi Liu
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin, China
| | - Yudong Chen
- Department of Gynecology, Guigang City People’s Hospital, The Eighth Affiliated Hospital of Guangxi Medical University, Guigang, China
| | - Litao Nie
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin, China
| | - Xiao Liang
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin, China
| | - Wenjun Huang
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin, China
- *Correspondence: Wenjun Huang, ; Rong Li,
| | - Rong Li
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin, China
- Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, China
- *Correspondence: Wenjun Huang, ; Rong Li,
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17
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Kakkanas A, Karamichali E, Koufogeorgou EI, Kotsakis SD, Georgopoulou U, Foka P. Targeting the YXXΦ Motifs of the SARS Coronaviruses 1 and 2 ORF3a Peptides by In Silico Analysis to Predict Novel Virus-Host Interactions. Biomolecules 2022; 12:1052. [PMID: 36008946 PMCID: PMC9405953 DOI: 10.3390/biom12081052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 02/08/2023] Open
Abstract
The emerging SARS-CoV and SARS-CoV-2 belong to the family of "common cold" RNA coronaviruses, and they are responsible for the 2003 epidemic and the current pandemic with over 6.3 M deaths worldwide. The ORF3a gene is conserved in both viruses and codes for the accessory protein ORF3a, with unclear functions, possibly related to viral virulence and pathogenesis. The tyrosine-based YXXΦ motif (Φ: bulky hydrophobic residue-L/I/M/V/F) was originally discovered to mediate clathrin-dependent endocytosis of membrane-spanning proteins. Many viruses employ the YXXΦ motif to achieve efficient receptor-guided internalisation in host cells, maintain the structural integrity of their capsids and enhance viral replication. Importantly, this motif has been recently identified on the ORF3a proteins of SARS-CoV and SARS-CoV-2. Given that the ORF3a aa sequence is not fully conserved between the two SARS viruses, we aimed to map in silico structural differences and putative sequence-driven alterations of regulatory elements within and adjacently to the YXXΦ motifs that could predict variations in ORF3a functions. Using robust bioinformatics tools, we investigated the presence of relevant post-translational modifications and the YXXΦ motif involvement in protein-protein interactions. Our study suggests that the predicted YXXΦ-related features may confer specific-yet to be discovered-functions to ORF3a proteins, significant to the new virus and related to enhanced propagation, host immune regulation and virulence.
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Affiliation(s)
- Athanassios Kakkanas
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Eirini Karamichali
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Efthymia Ioanna Koufogeorgou
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Stathis D. Kotsakis
- Laboratory of Bacteriology, Hellenic Pasteur Institute, 115-21 Athens, Greece;
| | - Urania Georgopoulou
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Pelagia Foka
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
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