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Wang B, Yang F, Wang W, Zhao F, Sun X. TurboID-mediated proximity labeling technologies to identify virus co-receptors. Front Cell Infect Microbiol 2024; 14:1371837. [PMID: 38994005 PMCID: PMC11236563 DOI: 10.3389/fcimb.2024.1371837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024] Open
Abstract
Virus receptors determine the tissue tropism of viruses and have a certain relationship with the clinical outcomes caused by viral infection, which is of great importance for the identification of virus receptors to understand the infection mechanism of viruses and to develop entry inhibitor. Proximity labeling (PL) is a new technique for studying protein-protein interactions, but it has not yet been applied to the identification of virus receptors or co-receptors. Here, we attempt to identify co-receptor of SARS-CoV-2 by employing TurboID-catalyzed PL. The membrane protein angiotensin-converting enzyme 2 (ACE2) was employed as a bait and conjugated to TurboID, and a A549 cell line with stable expression of ACE2-TurboID was constructed. SARS-CoV-2 pseudovirus were incubated with ACE2-TurboID stably expressed cell lines in the presence of biotin and ATP, which could initiate the catalytic activity of TurboID and tag adjacent endogenous proteins with biotin. Subsequently, the biotinylated proteins were harvested and identified by mass spectrometry. We identified a membrane protein, AXL, that has been functionally shown to mediate SARS-CoV-2 entry into host cells. Our data suggest that PL could be used to identify co-receptors for virus entry.
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Affiliation(s)
- Bo Wang
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Fan Yang
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - Wuqian Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
- Jiaxing Maternity and Children Health Care Hospital, Affiliated Women and Children Hospital Jiaxing University, Jiaxing, Zhejiang, China
| | - Fei Zhao
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - Xiaofang Sun
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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2
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Sun Y, Huang ZL, Chen WX, Zhang YF, Lei HT, Huang QJ, Lun ZR, Qu LH, Zheng LL. GateView: A Multi-Omics Platform for Gene Feature Analysis of Virus Receptors within Human Normal Tissues and Tumors. Biomolecules 2024; 14:516. [PMID: 38785923 PMCID: PMC11118183 DOI: 10.3390/biom14050516] [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: 03/13/2024] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Viruses are obligate intracellular parasites that rely on cell surface receptor molecules to complete the first step of invading host cells. The experimental method for virus receptor screening is time-consuming, and receptor molecules have been identified for less than half of known viruses. This study collected known human viruses and their receptor molecules. Through bioinformatics analysis, common characteristics of virus receptor molecules (including sequence, expression, mutation, etc.) were obtained to study why these membrane proteins are more likely to become virus receptors. An in-depth analysis of the cataloged virus receptors revealed several noteworthy findings. Compared to other membrane proteins, human virus receptors generally exhibited higher expression levels and lower sequence conservation. These receptors were found in multiple tissues, with certain tissues and cell types displaying significantly higher expression levels. While most receptor molecules showed noticeable age-related variations in expression across different tissues, only a limited number of them exhibited gender-related differences in specific tissues. Interestingly, in contrast to normal tissues, virus receptors showed significant dysregulation in various types of tumors, particularly those associated with dsRNA and retrovirus receptors. Finally, GateView, a multi-omics platform, was established to analyze the gene features of virus receptors in human normal tissues and tumors. Serving as a valuable resource, it enables the exploration of common patterns among virus receptors and the investigation of virus tropism across different tissues, population preferences, virus pathogenicity, and oncolytic virus mechanisms.
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Affiliation(s)
| | | | | | | | | | | | | | - Liang-Hu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Y.S.); (Z.-L.H.); (W.-X.C.); (Y.-F.Z.); (H.-T.L.); (Q.-J.H.); (Z.-R.L.)
| | - Ling-Ling Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Y.S.); (Z.-L.H.); (W.-X.C.); (Y.-F.Z.); (H.-T.L.); (Q.-J.H.); (Z.-R.L.)
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3
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Valero-Rello A, Baeza-Delgado C, Andreu-Moreno I, Sanjuán R. Cellular receptors for mammalian viruses. PLoS Pathog 2024; 20:e1012021. [PMID: 38377111 PMCID: PMC10906839 DOI: 10.1371/journal.ppat.1012021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 03/01/2024] [Accepted: 02/02/2024] [Indexed: 02/22/2024] Open
Abstract
The interaction of viral surface components with cellular receptors and other entry factors determines key features of viral infection such as host range, tropism and virulence. Despite intensive research, our understanding of these interactions remains limited. Here, we report a systematic analysis of published work on mammalian virus receptors and attachment factors. We build a dataset twice the size of those available to date and specify the role of each factor in virus entry. We identify cellular proteins that are preferentially used as virus receptors, which tend to be plasma membrane proteins with a high propensity to interact with other proteins. Using machine learning, we assign cell surface proteins a score that predicts their ability to function as virus receptors. Our results also reveal common patterns of receptor usage among viruses and suggest that enveloped viruses tend to use a broader repertoire of alternative receptors than non-enveloped viruses, a feature that might confer them with higher interspecies transmissibility.
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Affiliation(s)
- Ana Valero-Rello
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, València, Spain
| | - Carlos Baeza-Delgado
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, València, Spain
| | - Iván Andreu-Moreno
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, València, Spain
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4
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Yang S, Lan T, Wei R, Zhang L, Lin L, Du H, Huang Y, Zhang G, Huang S, Shi M, Wang C, Wang Q, Li R, Han L, Tang D, Li H, Zhang H, Cui J, Lu H, Huang J, Luo Y, Li D, Wan QH, Liu H, Fang SG. Single-nucleus transcriptome inventory of giant panda reveals cellular basis for fitness optimization under low metabolism. BMC Biol 2023; 21:222. [PMID: 37858133 PMCID: PMC10588165 DOI: 10.1186/s12915-023-01691-2] [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: 02/19/2023] [Accepted: 08/25/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Energy homeostasis is essential for the adaptation of animals to their environment and some wild animals keep low metabolism adaptive to their low-nutrient dietary supply. Giant panda is such a typical low-metabolic mammal exhibiting species specialization of extremely low daily energy expenditure. It has low levels of basal metabolic rate, thyroid hormone, and physical activities, whereas the cellular bases of its low metabolic adaptation remain rarely explored. RESULTS In this study, we generate a single-nucleus transcriptome atlas of 21 organs/tissues from a female giant panda. We focused on the central metabolic organ (liver) and dissected cellular metabolic status by cross-species comparison. Adaptive expression mode (i.e., AMPK related) was prominently displayed in the hepatocyte of giant panda. In the highest energy-consuming organ, the heart, we found a possibly optimized utilization of fatty acid. Detailed cell subtype annotation of endothelial cells showed the uterine-specific deficiency of blood vascular subclasses, indicating a potential adaptation for a low reproductive energy expenditure. CONCLUSIONS Our findings shed light on the possible cellular basis and transcriptomic regulatory clues for the low metabolism in giant pandas and helped to understand physiological adaptation response to nutrient stress.
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Affiliation(s)
- Shangchen Yang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
| | - Rongping Wei
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Ling Zhang
- China Wildlife Conservation Association, Beijing, 100714, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8000, Aarhus, Denmark
| | - Hanyu Du
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yunting Huang
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Guiquan Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Shan Huang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengdong Wang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rengui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Lei Han
- College of Wildlife Resources, Northeast Forestry University, Harbin, 150040, China
| | - Dan Tang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hemin Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Jie Cui
- The Genome Synthesis and Editing Platform, BGI-Shenzhen, Shenzhen, 518120, China
| | - Haorong Lu
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jinrong Huang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8000, Aarhus, Denmark
| | - Desheng Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China.
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China.
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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5
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Zhang Z, Lu C, Mo B, Bai K, Ge XY, Deng L, Peng Y. Prediction of mammalian virus cross-species transmission based on host proteins. Microbiol Spectr 2023; 11:e0536822. [PMID: 37754753 PMCID: PMC10581197 DOI: 10.1128/spectrum.05368-22] [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: 01/06/2023] [Accepted: 08/04/2023] [Indexed: 09/28/2023] Open
Abstract
Most emerging viruses are spilled over from mammals. Understanding the mechanism of virus cross-species transmission and identifying zoonotic viruses before their emergence are critical for the prevention and control of newly emerging viruses. This study systematically investigated the host proteins associated with the cross-species transmission of mammalian viruses based on 1,271 pairs of virus-mammal interactions including 382 viruses from 33 viral families and 73 mammal species from 11 orders. Numerous host proteins were found to contribute to the cross-species transmission of mammalian viruses. Host proteins potentially contributing to virus cross-species transmission are specific to viral families, and few overlaps of such host proteins are observed in different viral families. Based on these host proteins, the random-forest (RF) models were built to predict the cross-species transmission potential of mammalian viruses. Moderate performance was obtained when using all viruses together. However, when modeling by viral family, the performance of the RF models varied much among viral families. In 13 viral families such as Flaviviridae, Retroviridae, and Poxviridae, the AUC of the RF model was greater than 0.8. Finally, the contribution of virus receptors to cross-species transmission was evaluated, and the virus receptor was found to have a minor effect in predicting the cross-species transmission of mammalian viruses. The study deepens our understanding of the mechanism of virus cross-species transmission and provides a framework for predicting the cross-species transmission of mammalian viruses. IMPORTANCE Emerging viruses pose serious threats to humans. Understanding the mechanism of virus cross-species transmission and identifying zoonotic viruses before their emergence are critical for the prevention and control of emerging viruses. This study systematically identified host factors associated with cross-species transmission of mammalian viruses and further built machine-learning models for predicting cross-species transmission of the viruses based on host factors including virus receptors. The study not only deepens our understanding of the mechanism of virus cross-species transmission but also provides a framework for predicting the cross-species transmission of mammalian viruses based on host factors.
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Affiliation(s)
- Zheng Zhang
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, Hunan, China
- Hunan Engineering and Technology Research Center for Agricultural Big Data Analysis & Decision-making, College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Congyu Lu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, Hunan, China
| | - Bocheng Mo
- Hunan Engineering and Technology Research Center for Agricultural Big Data Analysis & Decision-making, College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Kehan Bai
- Hunan Juyoubiotech Co., Ltd, Changsha, Hunan, China
| | - Xing-Yi Ge
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, Hunan, China
| | - Li Deng
- Department of Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, Hunan, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, Hunan, China
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6
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Assou S, Ahmed E, Morichon L, Nasri A, Foisset F, Bourdais C, Gros N, Tieo S, Petit A, Vachier I, Muriaux D, Bourdin A, De Vos J. The Transcriptome Landscape of the In Vitro Human Airway Epithelium Response to SARS-CoV-2. Int J Mol Sci 2023; 24:12017. [PMID: 37569398 PMCID: PMC10418806 DOI: 10.3390/ijms241512017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Airway-liquid interface cultures of primary epithelial cells and of induced pluripotent stem-cell-derived airway epithelial cells (ALI and iALI, respectively) are physiologically relevant models for respiratory virus infection studies because they can mimic the in vivo human bronchial epithelium. Here, we investigated gene expression profiles in human airway cultures (ALI and iALI models), infected or not with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), using our own and publicly available bulk and single-cell transcriptome datasets. SARS-CoV-2 infection significantly increased the expression of interferon-stimulated genes (IFI44, IFIT1, IFIT3, IFI35, IRF9, MX1, OAS1, OAS3 and ISG15) and inflammatory genes (NFKBIA, CSF1, FOSL1, IL32 and CXCL10) by day 4 post-infection, indicating activation of the interferon and immune responses to the virus. Extracellular matrix genes (ITGB6, ITGB1 and GJA1) were also altered in infected cells. Single-cell RNA sequencing data revealed that SARS-CoV-2 infection damaged the respiratory epithelium, particularly mature ciliated cells. The expression of genes encoding intercellular communication and adhesion proteins was also deregulated, suggesting a mechanism to promote shedding of infected epithelial cells. These data demonstrate that ALI/iALI models help to explain the airway epithelium response to SARS-CoV-2 infection and are a key tool for developing COVID-19 treatments.
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Affiliation(s)
- Said Assou
- IRMB, University of Montpellier, INSERM, CHU Montpellier, 34295 Montpellier, France; (E.A.); (L.M.); (A.N.); (F.F.); (C.B.); (J.D.V.)
| | - Engi Ahmed
- IRMB, University of Montpellier, INSERM, CHU Montpellier, 34295 Montpellier, France; (E.A.); (L.M.); (A.N.); (F.F.); (C.B.); (J.D.V.)
- Department of Respiratory Diseases, CHU Montpellier, Arnaud de Villeneuve Hospital, INSERM, 34000 Montpellier, France; (A.P.); (I.V.)
- PhyMedExp, University of Montpellier, INSERM U1046, CNRS UMR 9214, 34090 Montpellier, France
| | - Lisa Morichon
- IRMB, University of Montpellier, INSERM, CHU Montpellier, 34295 Montpellier, France; (E.A.); (L.M.); (A.N.); (F.F.); (C.B.); (J.D.V.)
- CEMIPAI, Université de Montpellier, CNRS UAR3725, 34090 Montpellier, France; (N.G.); (D.M.)
| | - Amel Nasri
- IRMB, University of Montpellier, INSERM, CHU Montpellier, 34295 Montpellier, France; (E.A.); (L.M.); (A.N.); (F.F.); (C.B.); (J.D.V.)
| | - Florent Foisset
- IRMB, University of Montpellier, INSERM, CHU Montpellier, 34295 Montpellier, France; (E.A.); (L.M.); (A.N.); (F.F.); (C.B.); (J.D.V.)
| | - Carine Bourdais
- IRMB, University of Montpellier, INSERM, CHU Montpellier, 34295 Montpellier, France; (E.A.); (L.M.); (A.N.); (F.F.); (C.B.); (J.D.V.)
| | - Nathalie Gros
- CEMIPAI, Université de Montpellier, CNRS UAR3725, 34090 Montpellier, France; (N.G.); (D.M.)
| | - Sonia Tieo
- CEFE, University of Montpellier, CNRS, EPHE, IRD, 34090 Montpellier, France;
| | - Aurelie Petit
- Department of Respiratory Diseases, CHU Montpellier, Arnaud de Villeneuve Hospital, INSERM, 34000 Montpellier, France; (A.P.); (I.V.)
- PhyMedExp, University of Montpellier, INSERM U1046, CNRS UMR 9214, 34090 Montpellier, France
| | - Isabelle Vachier
- Department of Respiratory Diseases, CHU Montpellier, Arnaud de Villeneuve Hospital, INSERM, 34000 Montpellier, France; (A.P.); (I.V.)
- PhyMedExp, University of Montpellier, INSERM U1046, CNRS UMR 9214, 34090 Montpellier, France
| | - Delphine Muriaux
- CEMIPAI, Université de Montpellier, CNRS UAR3725, 34090 Montpellier, France; (N.G.); (D.M.)
- IRIM, Université de Montpellier, CNRS UMR9004, 34090 Montpellier, France
| | - Arnaud Bourdin
- Department of Respiratory Diseases, CHU Montpellier, Arnaud de Villeneuve Hospital, INSERM, 34000 Montpellier, France; (A.P.); (I.V.)
- PhyMedExp, University of Montpellier, INSERM U1046, CNRS UMR 9214, 34090 Montpellier, France
| | - John De Vos
- IRMB, University of Montpellier, INSERM, CHU Montpellier, 34295 Montpellier, France; (E.A.); (L.M.); (A.N.); (F.F.); (C.B.); (J.D.V.)
- Department of Cell and Tissue Engineering, University of Montpellier, CHU Montpellier, 34090 Montpellier, France
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7
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Ding P, Wang H, Zhu J, An F, Xu J, Ding X, Luo L, Wu W, Qin Q, Wei Y, Zhao W, Lv Z, Li H, Zhu Y, Li M, Zhang W, Zhang Y, Ou Z, Liu H, Hua Y. Viral receptor profiles of masked palm civet revealed by single-cell transcriptomics. J Genet Genomics 2022; 49:1072-1075. [PMID: 35490934 DOI: 10.1016/j.jgg.2022.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/31/2022] [Accepted: 04/11/2022] [Indexed: 12/29/2022]
Affiliation(s)
- Peiwen Ding
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Haoyu Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Jiacheng Zhu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Fuyu An
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong 510520, China
| | - Jinqian Xu
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong 510520, China
| | - Xiangning Ding
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Lihua Luo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Weiying Wu
- Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brian Medicine, and the MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310012, China
| | - Qiuyu Qin
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, China
| | - Yanan Wei
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, China
| | - Wandong Zhao
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, China
| | - Zhiyuan Lv
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, China
| | - Haimeng Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yixin Zhu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Meiling Li
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Wensheng Zhang
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Yanan Zhang
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, Guangdong 518000, China.
| | - Zhihua Ou
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, Guangdong 518083, China.
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China.
| | - Yan Hua
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong 510520, China.
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8
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Bani Hani A, Abu Tarboush N, Bani Ali M, Alabhoul F, Alansari F, Abuhani A, Al-Kawak M, Shamoun B, Albdour S, Abu Abeeleh M, Ahram M. Serum ACE2 Level is Associated With Severe SARS-CoV-2 Infection: A Cross-Sectional Observational Study. Biomark Insights 2022; 17:11772719221125123. [PMID: 36156891 PMCID: PMC9500304 DOI: 10.1177/11772719221125123] [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: 03/04/2022] [Accepted: 08/24/2022] [Indexed: 01/08/2023] Open
Abstract
Objectives: Angiotensin-converting enzyme 2 (ACE2) represents the primary receptor for SARS-CoV-2 to enter endothelial cells, causing coronavirus disease of 2019 (COVID-19). In this study, we investigate the association between circulating ACE2 levels with the severity of COVID-19. Methods: Serum ACE2 levels were measured in 144 COVID-19-positive subjects at hospital admission, and 123 COVID-19-negative control subjects. The association between ACE2 and clinical outcomes was analyzed. Results: About 144 COVID-19 patients and 123 healthy controls data were analyzed, the mean age of patients was 62 years and 50% of them were males. The mean age of the control group was 55 years and 63% were males. ACE-II level was measured and compared between COVID-19 patients and controls and revealed no significant differences (P > .05). ACE-II level was measured in COVID-19 patients and compared between different patient’s subgroups, ACE II level was not dependent on gender, smoking, ACE intake, or comorbidities (P > .05), and was significantly correlated with cardiovascular diseases (CVS) (P-value = .046) ICU admission (P-value = .0007) and Death (P-value = .0082). Conclusion: There was no significant difference between the COVID-19 and Control group, however, ACE2 serum level was significantly higher in patients with COVID-19 who were critically ill or non-survivors, its increased level is also associated with length of stay. Elevated ACE2 level is associated with the severity of COVID-19 disease, and it has the potential to be a predictor of the severity of the disease.
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Affiliation(s)
- Amjad Bani Hani
- Department of General Surgery, School of Medicine, The University of Jordan, Amman, Jordan
| | - Nafez Abu Tarboush
- Department of Biochemistry and Physiology, School of Medicine, The University of Jordan, Amman, Jordan
| | - Mo'ath Bani Ali
- Department of Medicine, School of Medicine, The University of Jordan, Amman, Jordan
| | - Fahad Alabhoul
- Department of Biochemistry and Physiology, School of Medicine, The University of Jordan, Amman, Jordan
| | - Fahad Alansari
- Department of Biochemistry and Physiology, School of Medicine, The University of Jordan, Amman, Jordan
| | - Ahmad Abuhani
- Department of Biochemistry and Physiology, School of Medicine, The University of Jordan, Amman, Jordan
| | - Mustafa Al-Kawak
- Department of Biochemistry and Physiology, School of Medicine, The University of Jordan, Amman, Jordan
| | - Badea'a Shamoun
- Department of Anesthesia and Critical Care, Prince Hamza Hospital, Amman, Jordan
| | - Suzan Albdour
- Department of Biochemistry and Physiology, School of Medicine, The University of Jordan, Amman, Jordan
| | - Mahmoud Abu Abeeleh
- Department of General Surgery, School of Medicine, The University of Jordan, Amman, Jordan
| | - Mamoun Ahram
- Department of General Surgery, School of Medicine, The University of Jordan, Amman, Jordan
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9
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Chen D, Ou Z, Zhu J, Wang H, Ding P, Luo L, Ding X, Sun C, Lan T, Sahu SK, Wu W, Yuan Y, Wu W, Qiu J, Zhu Y, Yue Q, Jia Y, Wei Y, Qin Q, Li R, Zhao W, Lv Z, Pu M, Lv B, Yang S, Chang A, Wei X, Chen F, Yang T, Wei Z, Yang F, Zhang P, Guo G, Li Y, Hua Y, Liu H. Screening of cell-virus, cell-cell, gene-gene crosstalk among animal kingdom at single cell resolution. Clin Transl Med 2022; 12:e886. [PMID: 35917402 PMCID: PMC9345398 DOI: 10.1002/ctm2.886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The exact animal origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains obscure and understanding its host range is vital for preventing interspecies transmission. METHODS Herein, we applied single-cell sequencing to multiple tissues of 20 species (30 data sets) and integrated them with public resources (45 data sets covering 26 species) to expand the virus receptor distribution investigation. While the binding affinity between virus and receptor is essential for viral infectivity, understanding the receptor distribution could predict the permissive organs and tissues when infection occurs. RESULTS Based on the transcriptomic data, the expression profiles of receptor or associated entry factors for viruses capable of causing respiratory, blood, and brain diseases were described in detail. Conserved cellular connectomes and regulomes were also identified, revealing fundamental cell-cell and gene-gene cross-talks from reptiles to humans. CONCLUSIONS Overall, our study provides a resource of the single-cell atlas of the animal kingdom which could help to identify the potential host range and tissue tropism of viruses and reveal the host-virus co-evolution.
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Affiliation(s)
- Dongsheng Chen
- BGI‐ShenzhenShenzhenChina,Suzhou Institute of Systems MedicineSuzhouJiangsuChina
| | - Zhihua Ou
- BGI‐ShenzhenShenzhenChina,Shenzhen Key Laboratory of Unknown Pathogen IdentificationBGI‐ShenzhenShenzhenChina
| | - Jiacheng Zhu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Haoyu Wang
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Peiwen Ding
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Lihua Luo
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Xiangning Ding
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Chengcheng Sun
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | | | | | - Weiying Wu
- The MOE Frontier Science Center for Brain Research and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouChina
| | - Yuting Yuan
- Department of Physiology, School of Basic Medical SciencesBinzhou Medical UniversityYantaiChina
| | - Wendi Wu
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Jiaying Qiu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yixin Zhu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Qizhen Yue
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Yi Jia
- BGI‐ShenzhenShenzhenChina
| | - Yanan Wei
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Qiuyu Qin
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Runchu Li
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Wandong Zhao
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Zhiyuan Lv
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Mingyi Pu
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | | | - Shangchen Yang
- College of Life SciencesZhejiang UniversityHangzhouChina
| | | | | | | | - Tao Yang
- China National GeneBankShenzhenChina
| | | | - Fan Yang
- China National GeneBankShenzhenChina
| | - Peijing Zhang
- Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouChina
| | - Guoji Guo
- Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouChina
| | | | - Yan Hua
- Guangdong Provincial Key Laboratory of SilvicultureProtection and UtilizationGuangdong Academy of ForestryGuangzhouChina
| | - Huan Liu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
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10
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Ye S, Lu C, Qiu Y, Zheng H, Ge X, Wu A, Xia Z, Jiang T, Zhu H, Peng Y. An atlas of human viruses provides new insights into diversity and tissue tropism of human viruses. Bioinformatics 2022; 38:3087-3093. [PMID: 35435220 DOI: 10.1093/bioinformatics/btac275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Viruses continue to threaten human health. Yet, the complete viral species carried by humans and their infection characteristics have not been fully revealed. RESULTS This study curated an atlas of human viruses from public databases and literature, and built the Human Virus Database (HVD). The HVD contains 1,131 virus species of 54 viral families which were more than twice the number of the human-infecting virus species reported in previous studies. These viruses were identified in human samples including 68 human tissues, the excreta and body fluid. The viral diversity in humans was age-dependent with a peak in the infant and a valley in the teenager. The tissue tropism of viruses was found to be associated with several factors including the viral group (DNA, RNA or reverse-transcribing viruses), enveloped or not, viral genome length and GC content, viral receptors and the virus-interacting proteins. Finally, the tissue tropism of DNA viruses was predicted using a random-forest algorithm with a middle performance. Overall, the study not only provides a valuable resource for further studies of human viruses, but also deepens our understanding towards the diversity and tissue tropism of human viruses. AVAILABILITY The HVD is available at http://computationalbiology.cn/humanVirusBase/#/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sifan Ye
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Congyu Lu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Ye Qiu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Heping Zheng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Xingyi Ge
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Aiping Wu
- Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Zanxian Xia
- Department of Cell Biology, Hunan Key Laboratory of Animal Models for Human Diseases and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410013, China
| | - Taijiao Jiang
- Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Haizhen Zhu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
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11
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Forni D, Sironi M, Cagliani R. Evolutionary history of type II transmembrane serine proteases involved in viral priming. Hum Genet 2022; 141:1705-1722. [PMID: 35122525 PMCID: PMC8817155 DOI: 10.1007/s00439-022-02435-y] [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: 10/11/2021] [Accepted: 01/15/2022] [Indexed: 11/24/2022]
Abstract
Type II transmembrane serine proteases (TTSPs) are a family of trypsin-like membrane-anchored serine proteases that play key roles in the regulation of some crucial processes in physiological conditions, including cardiac function, digestion, cellular iron homeostasis, epidermal differentiation, and immune responses. However, some of them, in particular TTSPs expressed in the human airways, were identified as host factors that promote the proteolytic activation and spread of respiratory viruses such as influenza virus, human metapneumovirus, and coronaviruses, including SARS-CoV-2. Given their involvement in viral priming, we hypothesized that members of the TTSP family may represent targets of positive selection, possibly as the result of virus-driven pressure. Thus, we investigated the evolutionary history of sixteen TTSP genes in mammals. Evolutionary analyses indicate that most of the TTSP genes that have a verified role in viral proteolytic activation present signals of pervasive positive selection, suggesting that viral infections represent a selective pressure driving the evolution of these proteases. We also evaluated genetic diversity in human populations and we identified targets of balancing selection in TMPRSS2 and TMPRSS4. This scenario may be the result of an ancestral and still ongoing host–pathogen arms race. Overall, our results provide evolutionary information about candidate functional sites and polymorphic positions in TTSP genes.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842, Bosisio Parini, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842, Bosisio Parini, Italy.
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12
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Chen D, Tan C, Ding P, Luo L, Zhu J, Jiang X, Ou Z, Ding X, Lan T, Zhu Y, Jia Y, Wei Y, Li R, Qin Q, Sun C, Zhao W, Lv Z, Wang H, Wu W, Yuan Y, Pu M, Li Y, Zhang Y, Chang A, Guo G, Bai Y, Jin X, Liu H. VThunter: a database for single-cell screening of virus target cells in the animal kingdom. Nucleic Acids Res 2022; 50:D934-D942. [PMID: 34634807 PMCID: PMC8728219 DOI: 10.1093/nar/gkab894] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/11/2021] [Accepted: 10/05/2021] [Indexed: 01/22/2023] Open
Abstract
Viral infectious diseases are a devastating and continuing threat to human and animal health. Receptor binding is the key step for viral entry into host cells. Therefore, recognizing viral receptors is fundamental for understanding the potential tissue tropism or host range of these pathogens. The rapid advancement of single-cell RNA sequencing (scRNA-seq) technology has paved the way for studying the expression of viral receptors in different tissues of animal species at single-cell resolution, resulting in huge scRNA-seq datasets. However, effectively integrating or sharing these datasets among the research community is challenging, especially for laboratory scientists. In this study, we manually curated up-to-date datasets generated in animal scRNA-seq studies, analyzed them using a unified processing pipeline, and comprehensively annotated 107 viral receptors in 142 viruses and obtained accurate expression signatures in 2 100 962 cells from 47 animal species. Thus, the VThunter database provides a user-friendly interface for the research community to explore the expression signatures of viral receptors. VThunter offers an informative and convenient resource for scientists to better understand the interactions between viral receptors and animal viruses and to assess viral pathogenesis and transmission in species. Database URL: https://db.cngb.org/VThunter/.
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Affiliation(s)
- Dongsheng Chen
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cong Tan
- BGI-Shenzhen, Shenzhen 518083, China
| | - Peiwen Ding
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lihua Luo
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiacheng Zhu
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaosen Jiang
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihua Ou
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiangning Ding
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianming Lan
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixin Zhu
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Jia
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yanan Wei
- BGI-Shenzhen, Shenzhen 518083, China
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Runchu Li
- BGI-Shenzhen, Shenzhen 518083, China
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Qiuyu Qin
- BGI-Shenzhen, Shenzhen 518083, China
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Chengcheng Sun
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wandong Zhao
- BGI-Shenzhen, Shenzhen 518083, China
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Zhiyuan Lv
- BGI-Shenzhen, Shenzhen 518083, China
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Haoyu Wang
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wendi Wu
- BGI-Shenzhen, Shenzhen 518083, China
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Yuting Yuan
- BGI-Shenzhen, Shenzhen 518083, China
- Department of Physiology, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Mingyi Pu
- BGI-Shenzhen, Shenzhen 518083, China
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | | | - Yanan Zhang
- BGI-Shenzhen, Shenzhen 518083, China
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen, 518055, China
| | | | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Bai
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen 518083, China
- School of Medicine, South China University of Technology, Guangzhou 510006, Guangdong, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Huan Liu
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Jayawardena N, Miles LA, Burga LN, Rudin C, Wolf M, Poirier JT, Bostina M. N-Linked Glycosylation on Anthrax Toxin Receptor 1 Is Essential for Seneca Valley Virus Infection. Viruses 2021; 13:v13050769. [PMID: 33924774 PMCID: PMC8145208 DOI: 10.3390/v13050769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 01/12/2023] Open
Abstract
Seneca Valley virus (SVV) is a picornavirus with potency in selectively infecting and lysing cancerous cells. The cellular receptor for SVV mediating the selective tropism for tumors is anthrax toxin receptor 1 (ANTXR1), a type I transmembrane protein expressed in tumors. Similar to other mammalian receptors, ANTXR1 has been shown to harbor N-linked glycosylation sites in its extracellular vWA domain. However, the exact role of ANTXR1 glycosylation on SVV attachment and cellular entry was unknown. Here we show that N-linked glycosylation in the ANTXR1 vWA domain is necessary for SVV attachment and entry. In our study, tandem mass spectrometry analysis of recombinant ANTXR1-Fc revealed the presence of complex glycans at N166, N184 in the vWA domain, and N81 in the Fc domain. Symmetry-expanded cryo-EM reconstruction of SVV-ANTXR1-Fc further validated the presence of N166 and N184 in the vWA domain. Cell blocking, co-immunoprecipitation, and plaque formation assays confirmed that deglycosylation of ANTXR1 prevents SVV attachment and subsequent entry. Overall, our results identified N-glycosylation in ANTXR1 as a necessary post-translational modification for establishing stable interactions with SVV. We anticipate our findings will aid in selecting patients for future cancer therapeutics, where screening for both ANTXR1 and its glycosylation could lead to an improved outcome from SVV therapy.
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Affiliation(s)
- Nadishka Jayawardena
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand; (N.J.); (L.N.B.)
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - Linde A. Miles
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Laura N. Burga
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand; (N.J.); (L.N.B.)
| | - Charles Rudin
- Druckenmiller Center for Lung Cancer Research and Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
- Correspondence: (M.W.); (J.T.P.); (M.B.)
| | - John T. Poirier
- Druckenmiller Center for Lung Cancer Research and Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
- Correspondence: (M.W.); (J.T.P.); (M.B.)
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand; (N.J.); (L.N.B.)
- Otago Micro and Nano Imaging Centre, University of Otago, Dunedin 9016, New Zealand
- Correspondence: (M.W.); (J.T.P.); (M.B.)
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14
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Zhu L, Yan C, Duan G. Prediction of Virus-Receptor Interactions Based on Improving Similarities. J Comput Biol 2021; 28:650-659. [PMID: 33481654 DOI: 10.1089/cmb.2020.0544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Viral infectious diseases have been seriously threatening human health. The receptor binding is the first step of viral infection. Predicting virus-receptor interactions will be helpful for the interaction mechanism of viruses and receptors, and further find some effective ways of preventing and treating viral infectious diseases so as to reduce the morbidity and mortality caused by viruses. Some computation algorithms have been proposed for identifying potential virus-receptor interactions. However, a common problem in those methods is the presence of noise in the similarity network. A new computational model (Network Enhancement and the Regularized Least Squares [NERLS]) is proposed to predict virus-receptor interactions based on improving similarities by Network Enhancement (NE). NERLS integrates the virus sequence similarity, the receptor sequence similarity and known virus-receptor interactions. We compute the virus sequence similarity and known virus-receptor interactions to construct the virus similarity network. The receptor similarity network is constructed by the Gaussian interaction profile kernel similarity and the receptor sequence similarity. To obtain the final virus similarity network and the final receptor similarity network, NE is, respectively, applied for reducing the noise of the virus similarity network and the receptor similarity network. Finally, NERLS employs the regularized least squares to predict interactions of viruses and receptors. The experiment results show that NERLS achieves the area under curve value of 0.893 and 0.921 in 10-fold cross-validation and leave-one-out cross-validation, respectively, which is consistently superior to four related methods [which include Initial interaction scores method via the neighbors and the Laplacian regularized Least Square (IILLS), Bi-random walk on a heterogeneous network (BRWH), Laplacian regularized least squares classifier (LapRLS), and Collaborative matrix factorization (CMF)]. Furthermore, a case study also demonstrates that NERLS effectively predicts potential virus-receptor interactions.
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Affiliation(s)
- Lingzhi Zhu
- School of Computer Science and Engineering, Central South University, Changsha, China.,School of Computer and Information Science, Hunan Institute of Technology, Hengyang, China
| | - Cheng Yan
- School of Computer Science and Engineering, Central South University, Changsha, China.,School of Computer and Information, Qiannan Normal University for Nationalities, Duyun, China
| | - Guihua Duan
- School of Computer Science and Engineering, Central South University, Changsha, China
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15
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Zhang Z, Yu F, Zou Y, Qiu Y, Wu A, Jiang T, Peng Y. Phage protein receptors have multiple interaction partners and high expressions. Bioinformatics 2020; 36:2975-2979. [PMID: 32096819 DOI: 10.1093/bioinformatics/btaa123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/07/2020] [Accepted: 02/18/2020] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION Receptors on host cells play a critical role in viral infection. How phages select receptors is still unknown. RESULTS Here, we manually curated a high-quality database named phageReceptor, including 427 pairs of phage-host receptor interactions, 341 unique viral species or sub-species and 69 bacterial species. Sugars and proteins were most widely used by phages as receptors. The receptor usage of phages in Gram-positive bacteria was different from that in Gram-negative bacteria. Most protein receptors were located on the outer membrane. The phage protein receptors (PPRs) were highly diverse in their structures, and had little sequence identity and no common protein domain with mammalian virus receptors. Further functional characterization of PPRs in Escherichia coli showed that they had larger node degrees and betweennesses in the protein-protein interaction network, and higher expression levels, than other outer membrane proteins, plasma membrane proteins or other intracellular proteins. These findings were consistent with what observed for mammalian virus receptors reported in previous studies, suggesting that viral protein receptors tend to have multiple interaction partners and high expressions. The study deepens our understanding of virus-host interactions. AVAILABILITY AND IMPLEMENTATION phageReceptor is publicly available from: http://www.computationalbiology.cn/phageReceptor/index.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zheng Zhang
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Fen Yu
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Yuanqiang Zou
- Changsha Qiangze Biotech Co., Ltd, Changsha 410000, China
| | - Ye Qiu
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu 215123, China
| | - Taijiao Jiang
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu 215123, China
| | - Yousong Peng
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
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16
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Khodadadi E, Maroufi P, Khodadadi E, Esposito I, Ganbarov K, Espsoito S, Yousefi M, Zeinalzadeh E, Kafil HS. Study of combining virtual screening and antiviral treatments of the Sars-CoV-2 (Covid-19). Microb Pathog 2020; 146:104241. [PMID: 32387389 PMCID: PMC7199731 DOI: 10.1016/j.micpath.2020.104241] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023]
Abstract
The recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 and causing the respiratory tract disease COVID-19 has reached worldwide resonance and a global effort is being undertaken to characterize the molecular features and evolutionary origins of this virus. Therefore, rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people's lives and preventing epidemics. Additionally, general treatments, coronavirus-specific treatments, and antiviral treatments useful in fighting COVID-19 are addressed. This review sets out to shed light on the SARS-CoV-2 and host receptor recognition, a crucial factor for successful virus infection and taking immune-informatics approaches to identify B- and T-cell epitopes for surface glycoprotein of SARS-CoV-2. A variety of improved or new approaches also have been developed. It is anticipated that this will assist researchers and clinicians in developing better techniques for timely and effective detection of coronavirus infection. Moreover, the genomic sequence of the virus responsible for COVID-19, as well as the experimentally determined three-dimensional structure of the Main protease (Mpro) is available. The reported structure of the target Mpro was described in this review to identify potential drugs for COVID-19 using virtual high throughput screening.
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Affiliation(s)
- Ehsaneh Khodadadi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Parham Maroufi
- Department of Orthopedy, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Ehsan Khodadadi
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
| | | | | | | | - Mehdi Yousefi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Elham Zeinalzadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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17
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Gagliardi I, Patella G, Michael A, Serra R, Provenzano M, Andreucci M. COVID-19 and the Kidney: From Epidemiology to Clinical Practice. J Clin Med 2020; 9:E2506. [PMID: 32759645 PMCID: PMC7464116 DOI: 10.3390/jcm9082506] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 02/06/2023] Open
Abstract
The new respiratory infectious disease coronavirus disease 2019 (COVID-19) that originated in Wuhan, China, in December 2019 and caused by a new strain of zoonotic coronavirus, named severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), to date has killed over 630,000 people and infected over 15,000,000 worldwide. Most of the deceased patients had pre-existing comorbidities; over 20% had chronic kidney disease (CKD). Furthermore, although SARS-CoV-2 infection is characterized mainly by diffuse alveolar damage and acute respiratory failure, acute kidney injury (AKI) has developed in a high percentage of cases. As AKI has been shown to be associated with worse prognosis, we believe that the impact of SARS-CoV-2 on the kidney should be investigated. This review sets out to describe the main renal aspects of SARS-CoV-2 infection and the role of the virus in the development and progression of kidney damage. In this article, attention is focused on the epidemiology, etiology and pathophysiological mechanisms of kidney damage, histopathology, clinical features in nephropathic patients (CKD, hemodialysis, peritoneal dialysis, AKI, transplantation) and prevention and containment strategies. Although there remains much more to be learned with regards to this disease, nonetheless it is our hope that this review will aid in the understanding and management of SARS-CoV-2 infection.
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Affiliation(s)
- Ida Gagliardi
- Renal Unit, Department of Health Sciences, Magna Graecia University, 88100 Catanzaro, Italy; (I.G.); (G.P.); (A.M.); (M.P.)
| | - Gemma Patella
- Renal Unit, Department of Health Sciences, Magna Graecia University, 88100 Catanzaro, Italy; (I.G.); (G.P.); (A.M.); (M.P.)
| | - Ashour Michael
- Renal Unit, Department of Health Sciences, Magna Graecia University, 88100 Catanzaro, Italy; (I.G.); (G.P.); (A.M.); (M.P.)
| | - Raffaele Serra
- Interuniversity Center of Phlebolymphology (CIFL), International Research and Educational Program in Clinical and Experimental Biotechnology, Headquarters, Magna Graecia University, 88100 Catanzaro, Italy;
| | - Michele Provenzano
- Renal Unit, Department of Health Sciences, Magna Graecia University, 88100 Catanzaro, Italy; (I.G.); (G.P.); (A.M.); (M.P.)
| | - Michele Andreucci
- Renal Unit, Department of Health Sciences, Magna Graecia University, 88100 Catanzaro, Italy; (I.G.); (G.P.); (A.M.); (M.P.)
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18
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Host-Virus Arms Races Drive Elevated Adaptive Evolution in Viral Receptors. J Virol 2020; 94:JVI.00684-20. [PMID: 32493827 DOI: 10.1128/jvi.00684-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/01/2020] [Indexed: 02/02/2023] Open
Abstract
Viral receptors are the cell surface proteins that are hijacked by viruses to initialize their infections. Viral receptors are subject to two conflicting directional forces, namely, negative selection due to functional constraints and positive selection due to host-virus arms races. It remains largely obscure whether negative pleiotropy limits the rate of adaptation in viral receptors. Here, we perform evolutionary analyses of 96 viral receptor genes in primates and find that 41 out of 96 viral receptors experienced adaptive evolution. Many positively selected residues in viral receptors are located at the virus-receptor interfaces. Compared with control proteins, viral receptors exhibit significantly elevated rate of adaptation. Further analyses of genetic polymorphisms in human populations reveal signals of positive selection and balancing selection for 53 and 5 viral receptors, respectively. Moreover, we find that 49 viral receptors experienced different selection pressures in different human populations, indicating that viruses represent an important driver of local adaptation in humans. Our findings suggest that diverse viruses, many of which have not been known to infect nonhuman primates, have maintained antagonistic associations with primates for millions of years, and the host-virus conflicts drive accelerated adaptive evolution in viral receptors.IMPORTANCE Viruses hijack cellular proteins, termed viral receptors, to assist their entry into host cells. While viral receptors experience negative selection to maintain their normal functions, they also undergo positive selection due to an everlasting evolutionary arms race between viruses and hosts. A complete picture on how viral receptors evolve under two conflicting forces is still lacking. In this study, we systematically analyzed the evolution of 96 viral receptors in primates and human populations. We found around half of viral receptors underwent adaptive evolution and exhibit significantly elevated rates of adaptation compared to control genes in primates. We also found signals of past natural selection for 58 viral receptors in human populations. Interestingly, 49 viral receptors experienced different selection pressures in different human populations, indicating that viruses represent an important driver of local adaptation in humans. Our results suggest that host-virus arms races drive accelerated adaptive evolution in viral receptors.
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19
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Zhang Z, Ye S, Wu A, Jiang T, Peng Y. Prediction of the Receptorome for the Human-Infecting Virome. Virol Sin 2020; 36:133-140. [PMID: 32725480 PMCID: PMC7385468 DOI: 10.1007/s12250-020-00259-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/01/2020] [Indexed: 11/26/2022] Open
Abstract
The virus receptors are key for the viral infection of host cells. Identification of the virus receptors is still challenging at present. Our previous study has shown that human virus receptor proteins have some unique features including high N-glycosylation level, high number of interaction partners and high expression level. Here, a random-forest model was built to identify human virus receptorome from human cell membrane proteins with an accepted accuracy based on the combination of the unique features of human virus receptors and protein sequences. A total of 1424 human cell membrane proteins were predicted to constitute the receptorome of the human-infecting virome. In addition, the combination of the random-forest model with protein–protein interactions between human and viruses predicted in previous studies enabled further prediction of the receptors for 693 human-infecting viruses, such as the enterovirus, norovirus and West Nile virus. Finally, the candidate alternative receptors of the SARS-CoV-2 were also predicted in this study. As far as we know, this study is the first attempt to predict the receptorome for the human-infecting virome and would greatly facilitate the identification of the receptors for viruses.
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Affiliation(s)
- Zheng Zhang
- Bioinformatics Center of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Sifan Ye
- Bioinformatics Center of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Taijiao Jiang
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yousong Peng
- Bioinformatics Center of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China.
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20
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Qi F, Qian S, Zhang S, Zhang Z. Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses. Biochem Biophys Res Commun 2020. [PMID: 32199615 DOI: 10.1016/j.bbrc.2020.03.044pmid:32199615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The new coronavirus (SARS-CoV-2) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by SARS-CoV-2 to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. SARS-CoV-2 may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell co-expression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins. Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted "CellPhoneDB" analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.
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Affiliation(s)
- Furong Qi
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China
| | - Shen Qian
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center and Institute of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Zheng Zhang
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China; The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, China.
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21
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Qi F, Qian S, Zhang S, Zhang Z. Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses. Biochem Biophys Res Commun 2020. [PMID: 32199615 DOI: 10.1016/j.bbrc.2020.03.044medicine] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
The new coronavirus (SARS-CoV-2) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by SARS-CoV-2 to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. SARS-CoV-2 may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell co-expression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins. Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted "CellPhoneDB" analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.
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Affiliation(s)
- Furong Qi
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China
| | - Shen Qian
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center and Institute of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Zheng Zhang
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China; The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, China.
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22
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Qi F, Qian S, Zhang S, Zhang Z. Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses. Biochem Biophys Res Commun 2020; 526:135-140. [PMID: 32199615 PMCID: PMC7156119 DOI: 10.1016/j.bbrc.2020.03.044] [Citation(s) in RCA: 710] [Impact Index Per Article: 177.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 03/08/2020] [Indexed: 11/26/2022]
Abstract
The new coronavirus (SARS-CoV-2) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by SARS-CoV-2 to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. SARS-CoV-2 may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell co-expression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins. Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted "CellPhoneDB" analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.
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Affiliation(s)
- Furong Qi
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China
| | - Shen Qian
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center and Institute of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Zheng Zhang
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, 518100, China; The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, China.
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23
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Identification of Virus-Receptor Interactions Based on Network Enhancement and Similarity. BIOINFORMATICS RESEARCH AND APPLICATIONS 2020. [DOI: 10.1007/978-3-030-57821-3_33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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24
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Yan C, Duan G, Wu FX, Wang J. IILLS: predicting virus-receptor interactions based on similarity and semi-supervised learning. BMC Bioinformatics 2019; 20:651. [PMID: 31881820 PMCID: PMC6933616 DOI: 10.1186/s12859-019-3278-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background Viral infectious diseases are the serious threat for human health. The receptor-binding is the first step for the viral infection of hosts. To more effectively treat human viral infectious diseases, the hidden virus-receptor interactions must be discovered. However, current computational methods for predicting virus-receptor interactions are limited. Result In this study, we propose a new computational method (IILLS) to predict virus-receptor interactions based on Initial Interaction scores method via the neighbors and the Laplacian regularized Least Square algorithm. IILLS integrates the known virus-receptor interactions and amino acid sequences of receptors. The similarity of viruses is calculated by the Gaussian Interaction Profile (GIP) kernel. On the other hand, we also compute the receptor GIP similarity and the receptor sequence similarity. Then the sequence similarity is used as the final similarity of receptors according to the prediction results. The 10-fold cross validation (10CV) and leave one out cross validation (LOOCV) are used to assess the prediction performance of our method. We also compare our method with other three competing methods (BRWH, LapRLS, CMF). Conlusion The experiment results show that IILLS achieves the AUC values of 0.8675 and 0.9061 with the 10-fold cross validation and leave-one-out cross validation (LOOCV), respectively, which illustrates that IILLS is superior to the competing methods. In addition, the case studies also further indicate that the IILLS method is effective for the virus-receptor interaction prediction.
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Affiliation(s)
- Cheng Yan
- School of Computer Science and Engineering, Central South University, 932 South Lushan Rd, ChangSha, 410083, China.,School of Computer and Information,Qiannan Normal University for Nationalities, Longshan Road, DuYun, 558000, China
| | - Guihua Duan
- School of Computer Science and Engineering, Central South University, 932 South Lushan Rd, ChangSha, 410083, China.
| | - Fang-Xiang Wu
- Biomedical Engineering and Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SKS7N5A9, Canada
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, 932 South Lushan Rd, ChangSha, 410083, China
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