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Nakajima KI, Inagaki T, Espera JM, Izumiya Y. Kaposi's sarcoma-associated herpesvirus (KSHV) LANA prevents KSHV episomes from degradation. J Virol 2024; 98:e0126823. [PMID: 38240588 PMCID: PMC10878079 DOI: 10.1128/jvi.01268-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/14/2023] [Indexed: 02/21/2024] Open
Abstract
Protein knockdown with an inducible degradation system is a powerful tool for studying proteins of interest in living cells. Here, we adopted the auxin-inducible degron (AID) approach to detail Kaposi's sarcoma-associated herpesvirus (KSHV) latency-associated nuclear antigen (LANA) function in latency maintenance and inducible viral lytic gene expression. We fused the mini-auxin-inducible degron (mAID) tag at the LANA N-terminus with KSHV bacterial artificial chromosome 16 recombination, and iSLK cells were stably infected with the recombinant KSHV encoding mAID-LANA. Incubation with 5-phenyl-indole-3-acetic acid, a derivative of natural auxin, rapidly degraded LANA within 1.5 h. In contrast to our hypothesis, depletion of LANA alone did not trigger lytic reactivation but rather decreased inducible lytic gene expression when we stimulated reactivation with a combination of ORF50 protein expression and sodium butyrate. Decreased overall lytic gene induction seemed to be associated with a rapid loss of KSHV genomes in the absence of LANA. The rapid loss of viral genomic DNA was blocked by a lysosomal inhibitor, chloroquine. Furthermore, siRNA-mediated knockdown of cellular innate immune proteins, cyclic AMP-GMP synthase (cGAS) and simulator of interferon genes (STING), and other autophagy-related genes rescued the degradation of viral genomic DNA upon LANA depletion. Reduction of the viral genome was not observed in 293FT cells that lack the expression of cGAS. These results suggest that LANA actively prevents viral genomic DNA from sensing by cGAS-STING signaling axis, adding novel insights into the role of LANA in latent genome maintenance.IMPORTANCESensing of pathogens' components is a fundamental cellular immune response. Pathogens have therefore evolved strategies to evade such cellular immune responses. KSHV LANA is a multifunctional protein and plays an essential role in maintaining the latent infection by tethering viral genomic DNA to the host chromosome. We adopted the inducible protein knockdown approach and found that depletion of LANA induced rapid degradation of viral genomic DNA, which is mediated by innate immune DNA sensors and autophagy pathway. These observations suggest that LANA may play a role in hiding KSHV episome from innate immune DNA sensors. Our study thus provides new insights into the role of LANA in latency maintenance.
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Affiliation(s)
- Ken-ichi Nakajima
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Tomoki Inagaki
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Jonna Magdallene Espera
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Yoshihiro Izumiya
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California, USA
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Izumiya Y, Algalil A, Espera JM, Miura H, Izumiya C, Inagaki T, Kumar A. Kaposi's sarcoma-associated herpesvirus terminal repeat regulates inducible lytic gene promoters. J Virol 2024; 98:e0138623. [PMID: 38240593 PMCID: PMC10878276 DOI: 10.1128/jvi.01386-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024] Open
Abstract
The Kaposi's sarcoma-associated herpesvirus (KSHV) genome consists of an approximately 140-kb unique coding region flanked by 30-40 copies of a 0.8-kb terminal repeat (TR) sequence. A gene enhancer recruits transcription-related enzymes by having arrays of transcription factor binding sites. Here, we show that KSHV TR possesses transcription regulatory function with latency-associated nuclear antigen (LANA). Cleavage under targets and release using nuclease demonstrated that TR fragments were occupied by LANA-interacting histone-modifying enzymes in naturally infected cells. The TR was enriched with histone H3K27 acetylation (H3K27Ac) and H3K4 tri-methylation (H3K4me3) modifications and also expressed nascent RNAs. The sites of H3K27Ac and H3K4me3 modifications were also conserved in the KSHV unique region among naturally infected primary effusion lymphoma cells. KSHV origin of lytic replication (Ori-Lyt) showed similar protein and histone modification occupancies with that of TR. In the Ori-Lyt region, the LANA and LANA-interacting proteins colocalized with an H3K27Ac-modified nucleosome along with paused RNA polymerase II. The KSHV transactivator KSHV replication and transcription activator (K-Rta) recruitment sites franked the LANA-bound nucleosome, and reactivation evicted the LANA-bound nucleosome. Including TR fragments in reporter plasmid enhanced inducible viral gene promoter activities independent of the orientations. In the presence of TR in reporter plasmids, K-Rta transactivation was drastically increased, while LANA acquired the promoter repression function. KSHV TR, therefore, functions as an enhancer for KSHV inducible genes. However, in contrast to cellular enhancers bound by multiple transcription factors, perhaps the KSHV enhancer is predominantly regulated by the LANA nuclear body.IMPORTANCEEnhancers are a crucial regulator of differential gene expression programs. Enhancers are the cis-regulatory sequences determining target genes' spatiotemporal and quantitative expression. Here, we show that Kaposi's sarcoma-associated herpesvirus (KSHV) terminal repeats fulfill the enhancer definition for KSHV inducible gene promoters. The KSHV enhancer is occupied by latency-associated nuclear antigen (LANA) and its interacting proteins, such as CHD4. Neighboring terminal repeat (TR) fragments to lytic gene promoters drastically enhanced KSHV replication and transcription activator and LANA transcription regulatory functions. This study, thus, proposes a new latency-lytic switch model in which TR accessibility to the KSHV gene promoters regulates viral inducible gene expression.
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Affiliation(s)
- Yoshihiro Izumiya
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Adhraa Algalil
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
- Midwestern University College of Dental Medicine, Glendale, Arizona, USA
| | - Jonna M. Espera
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Hiroki Miura
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Chie Izumiya
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Tomoki Inagaki
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Ashish Kumar
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
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Li X, Guo H, Yang J, Liu X, Li H, Yang W, Zhang L, Li Y, Wei W. Enterovirus D68 3C protease antagonizes type I interferon signaling by cleaving signal transducer and activator of transcription 1. J Virol 2024; 98:e0199423. [PMID: 38240591 PMCID: PMC10878094 DOI: 10.1128/jvi.01994-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024] Open
Abstract
Following the successful control of poliovirus, the re-emergence of respiratory enterovirus D68 (EV-D68), a prominent non-polio enterovirus, has become a serious public health concern worldwide. Host innate immune responses are the primary defense against EV-D68 invasion; however, the mechanism underlying viral evasion of the antiviral activity of interferons (IFN) remains unclear. In this study, we found that EV-D68 inhibited type I IFN signaling by cleaving signal transducer and activator of transcription 1 (STAT1), a crucial factor in cellular responses to interferons and other cytokines. We observed that the prototype and circulating EV-D68 strains conserved their ability to induce STAT1 cleavage and attenuate IFN signal transduction. Further investigation revealed that EV-D68 3C protease cleaves STAT1 at the 131Q residue. Interestingly, not all enterovirus-encoded 3C proteases exhibited this ability. EV-D68 and poliovirus 3C proteases efficiently induced STAT1 cleavage; whereas, 3C proteases from EV-A71, coxsackievirus A16, and echoviruses did not. STAT1 cleavage also abolished the nuclear translocation capacity of STAT1 in response to IFN stimulation to activate downstream signaling elements. Overall, these results suggest that STAT1, targeted by viral protease 3C, is utilized by EV-D68 to subvert the host's innate immune response.IMPORTANCEEnterovirus D68 (EV-D68) has significantly transformed over the past decade, evolving from a rare pathogen to a potential pandemic pathogen. The interferon (IFN) signaling pathway is an important defense mechanism and therapeutic target for the host to resist viral invasion. Previous studies have reported that the EV-D68 virus blocks or weakens immune recognition and IFN production in host cells through diverse strategies; however, the mechanisms of EV-D68 resistance to IFN signaling have not been fully elucidated. Our study revealed that EV-D68 relies on its own encoded protease, 3C, to directly cleave signal transducer and activator of transcription 1 (STAT1), a pivotal transduction component in the IFN signaling pathway, disrupting the IFN-mediated antiviral response. Previous studies on human enteroviruses have not documented direct cleavage of the STAT1 protein to evade cellular immune defenses. However, not all enteroviral 3C proteins can cleave STAT1. These findings highlight the diverse evolutionary strategies different human enteroviruses employ to evade host immunity.
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Affiliation(s)
- Xiaohan Li
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Haoran Guo
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Jiaxin Yang
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Xize Liu
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Huili Li
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Wanying Yang
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Lili Zhang
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Yan Li
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Wei Wei
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Translational Medicine, First Hospital, Jilin University, Changchun, Jilin, China
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Balint E, Feng E, Giles EC, Ritchie TM, Qian AS, Vahedi F, Montemarano A, Portillo AL, Monteiro JK, Trigatti BL, Ashkar AA. Bystander activated CD8 + T cells mediate neuropathology during viral infection via antigen-independent cytotoxicity. Nat Commun 2024; 15:896. [PMID: 38316762 PMCID: PMC10844499 DOI: 10.1038/s41467-023-44667-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 12/21/2023] [Indexed: 02/07/2024] Open
Abstract
Although many viral infections are linked to the development of neurological disorders, the mechanism governing virus-induced neuropathology remains poorly understood, particularly when the virus is not directly neuropathic. Using a mouse model of Zika virus (ZIKV) infection, we found that the severity of neurological disease did not correlate with brain ZIKV titers, but rather with infiltration of bystander activated NKG2D+CD8+ T cells. Antibody depletion of CD8 or blockade of NKG2D prevented ZIKV-associated paralysis, suggesting that CD8+ T cells induce neurological disease independent of TCR signaling. Furthermore, spleen and brain CD8+ T cells exhibited antigen-independent cytotoxicity that correlated with NKG2D expression. Finally, viral infection and inflammation in the brain was necessary but not sufficient to induce neurological damage. We demonstrate that CD8+ T cells mediate virus-induced neuropathology via antigen-independent, NKG2D-mediated cytotoxicity, which may serve as a therapeutic target for treatment of virus-induced neurological disease.
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Affiliation(s)
- Elizabeth Balint
- McMaster Immunology Research Centre, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Emily Feng
- McMaster Immunology Research Centre, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Elizabeth C Giles
- McMaster Immunology Research Centre, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Tyrah M Ritchie
- McMaster Immunology Research Centre, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Alexander S Qian
- Thrombosis and Atherosclerosis Research Institute, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton Health Sciences, Hamilton, ON, Canada
| | - Fatemeh Vahedi
- McMaster Immunology Research Centre, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Amelia Montemarano
- McMaster Immunology Research Centre, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Ana L Portillo
- McMaster Immunology Research Centre, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Jonathan K Monteiro
- McMaster Immunology Research Centre, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Bernardo L Trigatti
- Thrombosis and Atherosclerosis Research Institute, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton Health Sciences, Hamilton, ON, Canada
| | - Ali A Ashkar
- McMaster Immunology Research Centre, Department of Medicine, McMaster University, Hamilton, ON, Canada.
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Li S, Wang M, Van Sciver N, Szymula A, Tumuluri VS, George A, Ramachandran A, Raina K, Costa CN, Zhao B, Kazemian M, Simas JP, Kaye KM. Kaposi's sarcoma herpesvirus latency-associated nuclear antigen broadly regulates viral gene expression and is essential for lytic infection. PLoS Pathog 2024; 20:e1011907. [PMID: 38232124 PMCID: PMC10793894 DOI: 10.1371/journal.ppat.1011907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024] Open
Abstract
Kaposi's sarcoma herpesvirus (KSHV) is a leading cause of malignancy in AIDS and current therapies are limited. Like all herpesviruses, KSHV infection can be latent or lytic. KSHV latency-associated nuclear antigen (LANA) is essential for viral genome persistence during latent infection. LANA also maintains latency by antagonizing expression and function of the KSHV lytic switch protein, RTA. Here, we find LANA null KSHV is not capable of lytic replication, indicating a requirement for LANA. While LANA promoted both lytic and latent gene expression in cells partially permissive for lytic infection, it repressed expression in non-permissive cells. Importantly, forced RTA expression in non-permissive cells led to induction of lytic infection and LANA switched to promote, rather than repress, most lytic viral gene expression. When basal viral gene expression levels were high, LANA promoted expression, but repressed expression at low basal levels unless RTA expression was forcibly induced. LANA's effects were broad, but virus gene specific, extending to an engineered, recombinant viral GFP under control of host EF1α promoter, but not to host EF1α. Together, these results demonstrate that, in addition to its essential role in genome maintenance, LANA broadly regulates viral gene expression, and is required for high levels of lytic gene expression during lytic infection. Strategies that target LANA are expected to abolish KSHV infection.
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Affiliation(s)
- Shijun Li
- Departments of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mengbo Wang
- Department of Computer Science, Purdue University, West Lafayette, Indiana
| | - Nicholas Van Sciver
- Departments of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Agnieszka Szymula
- Departments of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Vinayak Sadasivam Tumuluri
- Departments of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Athira George
- Departments of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Akshaya Ramachandran
- Departments of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Komal Raina
- Departments of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Catarina N. Costa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, Lisboa, Portugal
- Universidade Católica Portuguesa, Católica Medical School, Católica Biomedical Research, Palma de Cima, Portugal
| | - Bo Zhao
- Departments of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Majid Kazemian
- Department of Computer Science, Purdue University, West Lafayette, Indiana
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - J. Pedro Simas
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, Lisboa, Portugal
- Universidade Católica Portuguesa, Católica Medical School, Católica Biomedical Research, Palma de Cima, Portugal
| | - Kenneth M. Kaye
- Departments of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Song JH, Mun SH, Yang H, Kwon YS, Kim SR, Song MY, Ham Y, Choi HJ, Baek WJ, Cho S, Ko HJ. Antiviral Mechanisms of Saucerneol from Saururus chinensis against Enterovirus A71, Coxsackievirus A16, and Coxsackievirus B3: Role of Mitochondrial ROS and the STING/TKB-1/IRF3 Pathway. Viruses 2023; 16:16. [PMID: 38275951 PMCID: PMC10821076 DOI: 10.3390/v16010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Enterovirus A71 (EV71), coxsackievirus A16 (CVA16), and coxsackievirus B3 (CVB3) are pathogenic members of the Picornaviridae family that cause a range of diseases, including severe central nervous system complications, myocarditis, and pancreatitis. Despite the considerable public health impact of these viruses, no approved antiviral treatments are currently available. In the present study, we confirmed the potential of saucerneol, a compound derived from Saururus chinensis, as an antiviral agent against EV71, CVA16, and CVB3. In the in vivo model, saucerneol effectively suppressed CVB3 replication in the pancreas and alleviated virus-induced pancreatitis. The antiviral activity of saucerneol is associated with increased mitochondrial ROS (mROS) production. In vitro inhibition of mROS generation diminishes the antiviral efficacy of saucerneol. Moreover, saucerneol treatment enhanced the phosphorylation of STING, TBK-1, and IRF3 in EV71- and CVA16-infected cells, indicating that its antiviral effects were mediated through the STING/TBK-1/IRF3 antiviral pathway, which was activated by increased mROS production. Saucerneol is a promising natural antiviral agent against EV71, CVA16, and CVB3 and has potential against virus-induced pancreatitis and myocarditis. Further studies are required to assess its safety and efficacy, which is essential for the development of effective antiviral strategies against these viruses.
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Affiliation(s)
- Jae-Hyoung Song
- Department of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea; (J.-H.S.); (S.-H.M.); (H.Y.); (M.-y.S.)
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Seo-Hyeon Mun
- Department of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea; (J.-H.S.); (S.-H.M.); (H.Y.); (M.-y.S.)
| | - Heejung Yang
- Department of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea; (J.-H.S.); (S.-H.M.); (H.Y.); (M.-y.S.)
| | - Yong Soo Kwon
- Department of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea; (J.-H.S.); (S.-H.M.); (H.Y.); (M.-y.S.)
| | - Seong-Ryeol Kim
- Division of Acute Viral Diseases, Centers for Emerging Virus Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Republic of Korea;
| | - Min-young Song
- Department of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea; (J.-H.S.); (S.-H.M.); (H.Y.); (M.-y.S.)
| | - Youngwook Ham
- Nucleic Acid Therapeutics Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, Republic of Korea;
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (KUST), Daejeon 34113, Republic of Korea
| | - Hwa-Jung Choi
- Department of Beauty Art, Youngsan University, 142 Bansong Beltway, Busan 48015, Republic of Korea; (H.-J.C.); (W.-J.B.)
| | - Won-Jin Baek
- Department of Beauty Art, Youngsan University, 142 Bansong Beltway, Busan 48015, Republic of Korea; (H.-J.C.); (W.-J.B.)
| | - Sungchan Cho
- Nucleic Acid Therapeutics Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28116, Republic of Korea;
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (KUST), Daejeon 34113, Republic of Korea
| | - Hyun-Jeong Ko
- Department of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea; (J.-H.S.); (S.-H.M.); (H.Y.); (M.-y.S.)
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
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Viktorova EG, Gabaglio S, Moghimi S, Zimina A, Wynn BG, Sztul E, Belov GA. The development of resistance to an inhibitor of a cellular protein reveals a critical interaction between the enterovirus protein 2C and a small GTPase Arf1. PLoS Pathog 2023; 19:e1011673. [PMID: 37721955 PMCID: PMC10538752 DOI: 10.1371/journal.ppat.1011673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/28/2023] [Accepted: 09/08/2023] [Indexed: 09/20/2023] Open
Abstract
The cellular protein GBF1, an activator of Arf GTPases (ArfGEF: Arf guanine nucleotide exchange factor), is recruited to the replication organelles of enteroviruses through interaction with the viral protein 3A, and its ArfGEF activity is required for viral replication, however how GBF1-dependent Arf activation supports the infection remains enigmatic. Here, we investigated the development of resistance of poliovirus, a prototype enterovirus, to increasing concentrations of brefeldin A (BFA), an inhibitor of GBF1. High level of resistance required a gradual accumulation of multiple mutations in the viral protein 2C. The 2C mutations conferred BFA resistance even in the context of a 3A mutant previously shown to be defective in the recruitment of GBF1 to replication organelles, and in cells depleted of GBF1, suggesting a GBF1-independent replication mechanism. Still, activated Arfs accumulated on the replication organelles of this mutant even in the presence of BFA, its replication was inhibited by a pan-ArfGEF inhibitor LM11, and the BFA-resistant phenotype was compromised in Arf1-knockout cells. Importantly, the mutations strongly increased the interaction of 2C with the activated form of Arf1. Analysis of other enteroviruses revealed a particularly strong interaction of 2C of human rhinovirus 1A with activated Arf1. Accordingly, the replication of this virus was significantly less sensitive to BFA than that of poliovirus. Thus, our data demonstrate that enterovirus 2Cs may behave like Arf1 effector proteins and that GBF1 but not Arf activation can be dispensable for enterovirus replication. These findings have important implications for the development of host-targeted anti-viral therapeutics.
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Affiliation(s)
- Ekaterina G. Viktorova
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Samuel Gabaglio
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Seyedehmahsa Moghimi
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Anna Zimina
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Bridge G. Wynn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham; Birmingham, Alabama, United States of America
| | - Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham; Birmingham, Alabama, United States of America
| | - George A. Belov
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
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López-Astacio RA, Adu OF, Goetschius DJ, Lee H, Weichert WS, Wasik BR, Frueh SP, Alford BK, Voorhees IEH, Flint JF, Saddoris S, Goodman LB, Holmes EC, Hafenstein SL, Parrish CR. Viral Capsid, Antibody, and Receptor Interactions: Experimental Analysis of the Antibody Escape Evolution of Canine Parvovirus. J Virol 2023; 97:e0009023. [PMID: 37199627 PMCID: PMC10308881 DOI: 10.1128/jvi.00090-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/23/2023] [Indexed: 05/19/2023] Open
Abstract
Canine parvovirus (CPV) is a small nonenveloped single-stranded DNA virus that causes serious diseases in dogs worldwide. The original strain of the virus (CPV-2) emerged in dogs during the late 1970s due to a host range switch of a virus similar to the feline panleukopenia virus that infected another host. The virus that emerged in dogs had altered capsid receptor and antibody binding sites, with some changes affecting both functions. Further receptor and antibody binding changes arose when the virus became better adapted to dogs or to other hosts. Here, we used in vitro selection and deep sequencing to reveal how two antibodies with known interactions select for escape mutations in CPV. The antibodies bound two distinct epitopes, and one largely overlapped the host receptor binding site. We also generated mutated antibody variants with altered binding structures. Viruses were passaged with wild-type (WT) or mutated antibodies, and their genomes were deep sequenced during the selective process. A small number of mutations were detected only within the capsid protein gene during the first few passages of selection, and most sites remained polymorphic or were slow to go to fixation. Mutations arose both within and outside the antibody binding footprints on the capsids, and all avoided the transferrin receptor type 1 binding footprint. Many selected mutations matched those that have arisen in the natural evolution of the virus. The patterns observed reveal the mechanisms by which these variants have been selected in nature and provide a better understanding of the interactions between antibody and receptor selections. IMPORTANCE Antibodies protect animals against infection by many different viruses and other pathogens, and we are gaining new information about the epitopes that induce antibody responses against viruses and the structures of the bound antibodies. However, less is known about the processes of antibody selection and antigenic escape and the constraints that apply in this system. Here, we used an in vitro model system and deep genome sequencing to reveal the mutations that arose in the virus genome during selection by each of two monoclonal antibodies or their mutated variants. High-resolution structures of each of the Fab:capsid complexes revealed their binding interactions. The wild-type antibodies or their mutated variants allowed us to examine how changes in antibody structure influence the mutational selection patterns seen in the virus. The results shed light on the processes of antibody binding, neutralization escape, and receptor binding, and they likely have parallels for many other viruses.
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Affiliation(s)
- Robert A. López-Astacio
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Oluwafemi F. Adu
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Daniel J. Goetschius
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Hyunwook Lee
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Wendy S. Weichert
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Brian R. Wasik
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Simon P. Frueh
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- Department for Veterinary Sciences, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Brynn K. Alford
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Ian E. H. Voorhees
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Joseph F. Flint
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Sarah Saddoris
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Laura B. Goodman
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Susan L. Hafenstein
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Colin R. Parrish
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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9
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Kang J, Huang M, Li J, Zhang K, Zhu C, Liu S, Zhou Z, Wang T, Wang Z. Enterovirus D68 VP3 Targets the Interferon Regulatory Factor 7 To Inhibit Type I Interferon Response. Microbiol Spectr 2023; 11:e0413822. [PMID: 37125923 PMCID: PMC10269600 DOI: 10.1128/spectrum.04138-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/09/2023] [Indexed: 05/02/2023] Open
Abstract
Enterovirus D68 (EV-D68) is a globally emerging pathogen causing severe respiratory illnesses mainly in children. The protease from EV-D68 could impair type I interferon (IFN-I) production. However, the role of the EV-D68 structural protein in antagonizing host antiviral responses remains largely unknown. We showed that the EV-D68 structural protein VP3 interacted with IFN regulatory factor 7 (IRF7), and this interaction suppressed the phosphorylation and nuclear translocation of IRF7 and then repressed the transcription of IFN. Furthermore, VP3 inhibited the TNF receptor associated factor 6 (TRAF6)-induced ubiquitination of IRF7 by competitive interaction with IRF7. IRF7Δ305-503 showed much weaker interaction ability to VP3, and VP3Δ41-50 performed weaker interaction ability with IRF7. The VP3 from enterovirus A71 (EV-A71) and coxsackievirus A16 (CV-A16) was also found to interact with the IRF7 protein. These results indicate that the enterovirus structural protein VP3 plays a pivotal role in subverting host innate immune responses and may be a potential target for antiviral drug research. IMPORTANCE EV-D68 is a globally emerging pathogen that causes severe respiratory illnesses. Here, we report that EV-D68 inhibits innate immune responses by targeting IRF7. Further investigations revealed that the structural protein VP3 inhibited the TRAF6-induced ubiquitination of IRF7 by competitive interaction with IRF7. These results indicate that the control of IRF7 by VP3 may be a mechanism by which EV-D68 represses IFN-I production.
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Affiliation(s)
- Jun Kang
- School of Life Sciences, Tianjin University, Tianjin, China
- Institute of Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, China
| | - Mengqian Huang
- School of Life Sciences, Tianjin University, Tianjin, China
- Institute of Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, China
| | - Jinyu Li
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Keke Zhang
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Cheng Zhu
- School of Life Sciences, Tianjin University, Tianjin, China
- Institute of Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, China
| | - Sihua Liu
- School of Life Sciences, Tianjin University, Tianjin, China
- Institute of Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, China
| | - Zhenwei Zhou
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Tao Wang
- School of Life Sciences, Tianjin University, Tianjin, China
- Institute of Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, China
| | - Zhiyun Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
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10
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Weng KF, Tee HK, Tseligka ED, Cagno V, Mathez G, Rosset S, Nagamine CM, Sarnow P, Kirkegaard K, Tapparel C. Variant enterovirus A71 found in immune-suppressed patient binds to heparan sulfate and exhibits neurotropism in B-cell-depleted mice. Cell Rep 2023; 42:112389. [PMID: 37058406 PMCID: PMC10590055 DOI: 10.1016/j.celrep.2023.112389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 01/30/2023] [Accepted: 03/29/2023] [Indexed: 04/15/2023] Open
Abstract
Enterovirus A71 (EV-A71) causes hand, foot, and mouth disease outbreaks with neurological complications and deaths. We previously isolated an EV-A71 variant in the stool, cerebrospinal fluid, and blood of an immunocompromised patient who had a leucine-to-arginine substitution on the VP1 capsid protein, resulting in increased heparin sulfate binding. We show here that this mutation increases the virus's pathogenicity in orally infected mice with depleted B cells, which mimics the patient's immune status, and increases susceptibility to neutralizing antibodies. However, a double mutant with even greater heparin sulfate affinity is not pathogenic, suggesting that increased heparin sulfate affinity may trap virions in peripheral tissues and reduce neurovirulence. This research sheds light on the increased pathogenicity of variant with heparin sulfate (HS)-binding ability in individuals with decreased B cell immunity.
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Affiliation(s)
- Kuo-Feng Weng
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Han Kang Tee
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Eirini D Tseligka
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Valeria Cagno
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Gregory Mathez
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Stéphane Rosset
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Claude M Nagamine
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter Sarnow
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karla Kirkegaard
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caroline Tapparel
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland.
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11
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Bennett SJ, Yalcin D, Privatt SR, Ngalamika O, Lidenge SJ, West JT, Wood C. Antibody epitope profiling of the KSHV LANA protein using VirScan. PLoS Pathog 2022; 18:e1011033. [PMID: 36534707 PMCID: PMC9810164 DOI: 10.1371/journal.ppat.1011033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/03/2023] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
The humoral antibody response against Kaposi sarcoma-associated herpesvirus (KSHV) in infected individuals has been characterized demonstrating the latency-associated nuclear antigen (LANA) as the most antigenic KSHV protein. Despite the antigenicity of the protein, specific LANA epitopes have not been systematically characterized. Here, we utilized a bacteriophage T7 library, which displays 56-amino acid KSHV LANA peptides with 28-amino acid overlap (VirScan), to define those epitopes in LANA targeted by antibodies from a cohort of 62 sub-Saharan African Kaposi sarcoma (KS) patients and 22 KSHV-infected asymptomatic controls. Intra- and inter-patient breadth and magnitude of the anti-LANA responses were quantified at the peptide and amino acid levels. From these data, we derived a detailed epitope annotation of the entire LANA protein, with a high-resolution focus on the N- and C-termini. Overall, the central repeat region was highly antigenic, but the responses to this region could not be confidently mapped due to its high variability. The highly conserved N-terminus was targeted with low breadth and magnitude. In a minority of individuals, antibodies specific to the nuclear localization sequence and a portion of the proline-rich regions of the N-terminus were evident. In contrast, the first half of the conserved C-terminal domain was consistently targeted with high magnitude. Unfortunately, this region was not included in LANA partial C-terminal crystal structures, however, it was predicted to adopt predominantly random-coil structure. Coupled with functional and secondary structure domain predictions, VirScan revealed fine resolution epitope mapping of the N- and C-terminal domains of LANA that is consistent with previous antigenicity studies and may prove useful to correlate KSHV humoral immunity with pathogenesis.
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Affiliation(s)
- Sydney J. Bennett
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Dicle Yalcin
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Sara R. Privatt
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Owen Ngalamika
- Dermatology and Venereology Section, University Teaching Hospital, University of Zambia School of Medicine, Lusaka, Zambia
| | - Salum J. Lidenge
- Ocean Road Cancer Institute, Dar es Salaam, Tanzania
- Department of Clinical Oncology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - John T. West
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Charles Wood
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
- * E-mail:
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12
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Margolin E, Allen JD, Verbeek M, Chapman R, Meyers A, van Diepen M, Ximba P, Motlou T, Moore PL, Woodward J, Strasser R, Crispin M, Williamson AL, Rybicki EP. Augmenting glycosylation-directed folding pathways enhances the fidelity of HIV Env immunogen production in plants. Biotechnol Bioeng 2022; 119:2919-2937. [PMID: 35781691 PMCID: PMC9544252 DOI: 10.1002/bit.28169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/25/2022]
Abstract
Heterologous glycoprotein production relies on host glycosylation-dependent folding. When the biosynthetic machinery differs from the usual expression host, there is scope to remodel the assembly pathway to enhance glycoprotein production. Here we explore the integration of chaperone coexpression with glyco-engineering to improve the production of a model HIV-1 envelope antigen. Calreticulin was coexpressed to support protein folding together with Leishmania major STT3D oligosaccharyltransferase, to improve glycan occupancy, RNA interference to suppress the formation of truncated glycans, and Nicotiana benthamiana plants lacking α1,3-fucosyltransferase and β1,2-xylosyltransferase was used as an expression host to prevent plant-specific complex N-glycans forming. This approach reduced the formation of undesired aggregates, which predominated in the absence of glyco-engineering. The resulting antigen also exhibited increased glycan occupancy, albeit to a slightly lower level than the equivalent mammalian cell-produced protein. The antigen was decorated almost exclusively with oligomannose glycans, which were less processed compared with the mammalian protein. Immunized rabbits developed comparable immune responses to the plant-produced and mammalian cell-derived antigens, including the induction of autologous neutralizing antibodies when the proteins were used to boost DNA and modified vaccinia Ankara virus-vectored vaccines. This study demonstrates that engineering glycosylation-directed folding offers a promising route to enhance the production of complex viral glycoproteins in plants.
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Affiliation(s)
- Emmanuel Margolin
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Matthew Verbeek
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Ros Chapman
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ann Meyers
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Michiel van Diepen
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Phindile Ximba
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Thopisang Motlou
- National Institute for Communicable Diseases of the National Health Laboratory Service, Centre for HIV and STIs, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L Moore
- National Institute for Communicable Diseases of the National Health Laboratory Service, Centre for HIV and STIs, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, Durban, South Africa
| | - Jeremy Woodward
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Anna-Lise Williamson
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Edward P Rybicki
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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13
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Peters CE, Schulze-Gahmen U, Eckhardt M, Jang GM, Xu J, Pulido EH, Bardine C, Craik CS, Ott M, Gozani O, Verba KA, Hüttenhain R, Carette JE, Krogan NJ. Structure-function analysis of enterovirus protease 2A in complex with its essential host factor SETD3. Nat Commun 2022; 13:5282. [PMID: 36075902 PMCID: PMC9453702 DOI: 10.1038/s41467-022-32758-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/16/2022] [Indexed: 01/07/2023] Open
Abstract
Enteroviruses cause a number of medically relevant and widespread human diseases with no approved antiviral therapies currently available. Host-directed therapies present an enticing option for this diverse genus of viruses. We have previously identified the actin histidine methyltransferase SETD3 as a critical host factor physically interacting with the viral protease 2A. Here, we report the 3.5 Å cryo-EM structure of SETD3 interacting with coxsackievirus B3 2A at two distinct interfaces, including the substrate-binding surface within the SET domain. Structure-function analysis revealed that mutations of key residues in the SET domain resulted in severely reduced binding to 2A and complete protection from enteroviral infection. Our findings provide insight into the molecular basis of the SETD3-2A interaction and a framework for the rational design of host-directed therapeutics against enteroviruses.
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Affiliation(s)
- Christine E Peters
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ursula Schulze-Gahmen
- Gladstone Institute of Virology, The J. David Gladstone Institutes, San Francisco, CA, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Manon Eckhardt
- QBI Coronavirus Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, The J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Gwendolyn M Jang
- QBI Coronavirus Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, The J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Jiewei Xu
- QBI Coronavirus Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, The J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Ernst H Pulido
- QBI Coronavirus Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, The J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Conner Bardine
- QBI Coronavirus Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Charles S Craik
- QBI Coronavirus Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Melanie Ott
- Gladstone Institute of Virology, The J. David Gladstone Institutes, San Francisco, CA, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Kliment A Verba
- QBI Coronavirus Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
| | - Ruth Hüttenhain
- QBI Coronavirus Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, The J. David Gladstone Institutes, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Nevan J Krogan
- QBI Coronavirus Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, The J. David Gladstone Institutes, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
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14
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Yang X, Aloise C, van Vliet ALW, Zwaagstra M, Lyoo H, Cheng A, van Kuppeveld FJM. Proteolytic Activities of Enterovirus 2A Do Not Depend on Its Interaction with SETD3. Viruses 2022; 14:v14071360. [PMID: 35891342 PMCID: PMC9318592 DOI: 10.3390/v14071360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 11/28/2022] Open
Abstract
Enterovirus 2Apro is a protease that proteolytically processes the viral polyprotein and cleaves several host proteins to antagonize host responses during enteroviral infection. Recently, the host protein actin histidine methyltransferase SET domain containing 3 (SETD3) was identified to interact with 2Apro and to be essential for virus replication. The role of SETD3 and its interaction with 2Apro remain unclear. In this study, we investigated the potential involvement of SETD3 in several functions of 2Apro. For this, we introduced the 2Apro from coxsackievirus B3 (CVB3) in a mutant of encephalomyocarditis virus (EMCV) containing an inactivated Leader protein (EMCV-Lzn) that is unable to shut down host mRNA translation, to trigger nucleocytoplasmic transport disorder (NCTD), and to suppress stress granule (SG) formation and type I interferon (IFN) induction. Both in wt HeLa cells and in HeLa SETD3 knockout (SETD3KO) cells, the virus containing active 2Apro (EMCV-2Apro) efficiently cleaved eukaryotic translation initiation factor 4 gamma (eIF4G) to shut off host mRNA translation, cleaved nucleoporins to trigger NCTD, and actively suppressed SG formation and IFN gene transcription, arguing against a role of SETD3 in these 2Apro-mediated functions. Surprisingly, we observed that the catalytic activity of enteroviral 2A is not crucial for triggering NCTD, as a virus containing an inactive 2Apro (EMCV-2Am) induced NCTD in both wt and SETD3KO cells, albeit delayed, challenging the idea that the NCTD critically depends on nucleoporin cleavage by this protease. Taken together, our results do not support a role of SETD3 in the proteolytic activities of enterovirus 2Apro.
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Affiliation(s)
- Xiaoyao Yang
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (X.Y.); (C.A.); (A.L.W.v.V.); (M.Z.); (H.L.)
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Chiara Aloise
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (X.Y.); (C.A.); (A.L.W.v.V.); (M.Z.); (H.L.)
| | - Arno L. W. van Vliet
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (X.Y.); (C.A.); (A.L.W.v.V.); (M.Z.); (H.L.)
| | - Marleen Zwaagstra
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (X.Y.); (C.A.); (A.L.W.v.V.); (M.Z.); (H.L.)
| | - Heyrhyoung Lyoo
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (X.Y.); (C.A.); (A.L.W.v.V.); (M.Z.); (H.L.)
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (A.C.); (F.J.M.v.K.)
| | - Frank J. M. van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (X.Y.); (C.A.); (A.L.W.v.V.); (M.Z.); (H.L.)
- Correspondence: (A.C.); (F.J.M.v.K.)
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15
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Li Y, Liu M, Yan Y, Wang Z, Dai Q, Yang X, Guo X, Li W, Chen X, Cao R, Zhong W. Molnupiravir and Its Active Form, EIDD-1931, Show Potent Antiviral Activity against Enterovirus Infections In Vitro and In Vivo. Viruses 2022; 14:v14061142. [PMID: 35746614 PMCID: PMC9227765 DOI: 10.3390/v14061142] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 02/04/2023] Open
Abstract
Enterovirus infections can cause hand, foot, and mouth disease (HFDM), aseptic meningitis, encephalitis, myocarditis, and acute flaccid myelitis, leading to death of infants and young children. However, no specific antiviral drug is currently available for the treatment of this type of infection. The Unites States and United Kingdom health authorities recently approved a new antiviral drug, molnupiravir, for the treatment of COVID-19. In this study, we reported that molnupiravir (EIDD-2801) and its active form, EIDD-1931, have broad-spectrum anti-enterovirus potential. Our data showed that EIDD-1931 could significantly reduce the production of EV-A71 progeny virus and the expression of EV-A71 viral protein at non-cytotoxic concentrations. The results of the time-of-addition assay suggest that EIDD-1931 acts at the post-entry step, which is in accordance with its antiviral mechanism. The intraperitoneal administration of EIDD-1931 and EIDD-2801 protected 1-day-old ICR suckling mice from lethal EV-A71 challenge by reducing the viral load in various tissues of the infected mice. The pharmacokinetics analysis indicated that the plasma drug concentration overwhelmed the EC50 for enteroviruses, suggesting the clinical potential of molnupiravir against enteroviruses. Thus, molnupiravir along with its active form, EIDD-1931, may be a promising drug candidate against enterovirus infections.
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Affiliation(s)
- Yuexiang Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.L.); (M.L.); (Y.Y.); (Z.W.); (Q.D.); (X.Y.); (X.G.); (W.L.)
| | - Miaomiao Liu
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.L.); (M.L.); (Y.Y.); (Z.W.); (Q.D.); (X.Y.); (X.G.); (W.L.)
| | - Yunzheng Yan
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.L.); (M.L.); (Y.Y.); (Z.W.); (Q.D.); (X.Y.); (X.G.); (W.L.)
| | - Zhuang Wang
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.L.); (M.L.); (Y.Y.); (Z.W.); (Q.D.); (X.Y.); (X.G.); (W.L.)
- Institute of Medical Research, Northwestern Polytechnical University, Xi’an 710072, China;
| | - Qingsong Dai
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.L.); (M.L.); (Y.Y.); (Z.W.); (Q.D.); (X.Y.); (X.G.); (W.L.)
| | - Xiaotong Yang
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.L.); (M.L.); (Y.Y.); (Z.W.); (Q.D.); (X.Y.); (X.G.); (W.L.)
| | - Xiaojia Guo
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.L.); (M.L.); (Y.Y.); (Z.W.); (Q.D.); (X.Y.); (X.G.); (W.L.)
| | - Wei Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.L.); (M.L.); (Y.Y.); (Z.W.); (Q.D.); (X.Y.); (X.G.); (W.L.)
| | - Xingjuan Chen
- Institute of Medical Research, Northwestern Polytechnical University, Xi’an 710072, China;
| | - Ruiyuan Cao
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.L.); (M.L.); (Y.Y.); (Z.W.); (Q.D.); (X.Y.); (X.G.); (W.L.)
- Correspondence: (R.C.); (W.Z.); Tel.: +86-10-66930673 (R.C.); +86-10-66932624 (W.Z.)
| | - Wu Zhong
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China; (Y.L.); (M.L.); (Y.Y.); (Z.W.); (Q.D.); (X.Y.); (X.G.); (W.L.)
- Correspondence: (R.C.); (W.Z.); Tel.: +86-10-66930673 (R.C.); +86-10-66932624 (W.Z.)
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16
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Kumar A, Lyu Y, Yanagihashi Y, Chantarasrivong C, Majerciak V, Salemi M, Wang KH, Inagaki T, Chuang F, Davis RR, Tepper CG, Nakano K, Izumiya C, Shimoda M, Nakajima KI, Merleev A, Zheng ZM, Campbell M, Izumiya Y. KSHV episome tethering sites on host chromosomes and regulation of latency-lytic switch by CHD4. Cell Rep 2022; 39:110788. [PMID: 35545047 PMCID: PMC9153692 DOI: 10.1016/j.celrep.2022.110788] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/11/2022] [Accepted: 04/14/2022] [Indexed: 12/25/2022] Open
Abstract
Kaposi sarcoma-associated herpesvirus (KSHV) establishes a latent infection in the cell nucleus, but where KSHV episomal genomes are tethered and the mechanisms underlying KSHV lytic reactivation are unclear. Here, we study the nuclear microenvironment of KSHV episomes and show that the KSHV latency-lytic replication switch is regulated via viral long non-coding (lnc)RNA-CHD4 (chromodomain helicase DNA binding protein 4) interaction. KSHV episomes localize with CHD4 and ADNP proteins, components of the cellular ChAHP complex. The CHD4 and ADNP proteins occupy the 5'-region of the highly inducible lncRNAs and terminal repeats of the KSHV genome together with latency-associated nuclear antigen (LANA). Viral lncRNA binding competes with CHD4 DNA binding, and KSHV reactivation sequesters CHD4 from the KSHV genome, which is also accompanied by detachment of KSHV episomes from host chromosome docking sites. We propose a model in which robust KSHV lncRNA expression determines the latency-lytic decision by regulating LANA/CHD4 binding to KSHV episomes.
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Affiliation(s)
- Ashish Kumar
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA
| | - Yuanzhi Lyu
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA
| | | | | | - Vladimir Majerciak
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Michelle Salemi
- Genome Center, Proteomics Core, Genome and Biomedical Sciences Facility, UC Davis, Davis, CA 95616, USA
| | - Kang-Hsin Wang
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA
| | - Tomoki Inagaki
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA
| | - Frank Chuang
- Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA
| | - Ryan R Davis
- Department of Pathology and Laboratory Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA
| | - Clifford G Tepper
- Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA; Viral Oncology and Pathogen-Associated Malignancies Initiative, UC Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Kazushi Nakano
- Lifescience Division, Lifematics, Osaka, Osaka 541-0046, Japan
| | - Chie Izumiya
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA
| | - Michiko Shimoda
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA; Viral Oncology and Pathogen-Associated Malignancies Initiative, UC Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Ken-Ichi Nakajima
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA
| | - Alexander Merleev
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Mel Campbell
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA.
| | - Yoshihiro Izumiya
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA; Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA; Viral Oncology and Pathogen-Associated Malignancies Initiative, UC Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA.
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17
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Sadanari H, Takemoto M, Ishida T, Otagiri H, Daikoku T, Murayama T, Kusano S. The Interferon-Inducible Human PLSCR1 Protein Is a Restriction Factor of Human Cytomegalovirus. Microbiol Spectr 2022; 10:e0134221. [PMID: 35138119 PMCID: PMC8826943 DOI: 10.1128/spectrum.01342-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/19/2022] [Indexed: 11/20/2022] Open
Abstract
Human phospholipid scramblase 1 (PLSCR1) is strongly expressed in response to interferon (IFN) treatment and viral infection, and it has been suggested to play an important role in IFN-dependent antiviral responses. In this study, we showed that the levels of human cytomegalovirus (HCMV) plaque formation in OUMS-36T-3 (36T-3) cells with high basal expression of PLSCR1 were significantly lower than those in human embryonic lung (HEL) cells with low basal expression of PLSCR1. In addition, the levels of HCMV plaque formation and replication in PLSCR1-knockout (KO) 36T-3 cells were significantly higher than those in parental 36T-3 cells and were comparable to those in HEL cells. Furthermore, compared to that in PLSCR1-KO cells, the expression of HCMV major immediate early (MIE) proteins was repressed and/or delayed in parental 36T-3 cells after HCMV infection. We also showed that PLSCR1 expression decreased the levels of the cAMP-responsive element (CRE)-binding protein (CREB)•HCMV immediate early protein 2 (IE2) and CREB-binding protein (CBP)•IE2 complexes, which have been suggested to play important roles in the IE2-mediated transactivation of the viral early promoter through interactions with CREB, CBP, and IE2. Interestingly, PLSCR1 expression repressed CRE- and HCMV MIE promoter-regulated reporter gene activities. These observations reveal, for the first time, that PLSCR1 negatively regulates HCMV replication by repressing the transcription from viral MIE and early promoters, and that PLSCR1 expression may contribute to the IFN-mediated suppression of HCMV infection. IMPORTANCE Because several IFN-stimulated genes (ISGs) have been reported to suppress HCMV replication, HCMV replication is thought to be regulated by an IFN-mediated host defense mechanism, but the mechanism remains unclear. PLSCR1 expression is induced in response to viral infection and IFN treatment, and PLSCR1 has been reported to play an important role in IFN-dependent antiviral responses. Here, we demonstrate that HCMV plaque formation and major immediate early (MIE) gene expression are significantly increased in PLSCR1-KO human fibroblast cells. PLSCR1 reduces levels of the CREB•IE2 and CBP•IE2 complexes, which have been suggested to play important roles in HCMV replication through its interactions with CREB, CBP, and IE2. In addition, PLSCR1 expression represses transcription from the HCMV MIE promoter. Our results indicate that PLSCR1 plays important roles in the suppression of HCMV replication in the IFN-mediated host defense system.
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Affiliation(s)
- Hidetaka Sadanari
- Department of Pharmaceutical Life Sciences, Faculty of Pharmaceutical Sciences, Hokuriku University, Ishikawa, Japan
| | - Masaya Takemoto
- Research Center for Pharmaceutical Education, Faculty of Pharmaceutical Sciences, Hokuriku University, Ishikawa, Japan
| | - Tomoki Ishida
- Department of Pharmaceutical Life Sciences, Faculty of Pharmaceutical Sciences, Hokuriku University, Ishikawa, Japan
| | - Hikaru Otagiri
- Department of Pharmaceutical Life Sciences, Faculty of Pharmaceutical Sciences, Hokuriku University, Ishikawa, Japan
| | - Tohru Daikoku
- Department of Pharmaceutical Life Sciences, Faculty of Pharmaceutical Sciences, Hokuriku University, Ishikawa, Japan
| | - Tsugiya Murayama
- Department of Pharmaceutical Life Sciences, Faculty of Pharmaceutical Sciences, Hokuriku University, Ishikawa, Japan
| | - Shuichi Kusano
- Division of Biological Information Technology, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
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18
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Petrovan V, Rathakrishnan A, Islam M, Goatley LC, Moffat K, Sanchez-Cordon PJ, Reis AL, Dixon LK. Role of African Swine Fever Virus Proteins EP153R and EP402R in Reducing Viral Persistence in Blood and Virulence in Pigs Infected with BeninΔDP148R. J Virol 2022; 96:e0134021. [PMID: 34643433 PMCID: PMC8754224 DOI: 10.1128/jvi.01340-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
The limited knowledge on the role of many of the approximately 170 proteins encoded by African swine fever virus restricts progress toward vaccine development. Previously, the DP148R gene was deleted from the genome of genotype I virulent Benin 97/1 isolate. This virus, BeninΔDP148R, induced transient moderate clinical signs after immunization and high levels of protection against challenge. However, the BeninΔDP148R virus and genome persisted in blood over a prolonged period. In the current study, deletion of either EP402R or EP153R genes individually or in combination from BeninΔDP148R genome was shown not to reduce virus replication in macrophages in vitro. However, deletion of EP402R dramatically reduced the period of infectious virus persistence in blood in immunized pigs from 28 to 14 days and virus genome from 59 to 14 days while maintaining high levels of protection against challenge. The additional deletion of EP153R (BeninΔDP148RΔEP153RΔEP402R) further attenuated the virus, and no viremia or clinical signs were observed postimmunization. This was associated with decreased protection and detection of moderate levels of challenge virus in blood. Interestingly, the deletion of EP153R alone from BeninΔDP148R did not result in further virus attenuation and did not reduce the period of virus persistence in blood. These results show that EP402R and EP153R have a synergistic role in reducing clinical signs and levels of virus in blood. IMPORTANCE African swine fever virus (ASFV) causes a disease of domestic pigs and wild boar which results in death of almost all infected animals. The disease has a high economic impact, and no vaccine is available. We investigated the role of two ASFV proteins, called EP402R and EP153R, in determining the levels and length of time virus persists in blood from infected pigs. EP402R causes ASFV particles and infected cells to bind to red blood cells. Deletion of the EP402R gene dramatically reduced virus persistence in blood but did not reduce the level of virus. Deletion of the EP153R gene alone did not reduce the period or level of virus persistence in blood. However, deleting both EP153R and EP402R resulted in undetectable levels of virus in blood and no clinical signs showing that the proteins act synergistically. Importantly, the infected pigs were protected following infection with the wild-type virus that kills pigs.
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Affiliation(s)
- Vlad Petrovan
- The Pirbright Institute, Pirbright, Woking, Surrey, UK
| | | | - Muneeb Islam
- The Pirbright Institute, Pirbright, Woking, Surrey, UK
| | | | - Katy Moffat
- The Pirbright Institute, Pirbright, Woking, Surrey, UK
| | | | - Ana L. Reis
- The Pirbright Institute, Pirbright, Woking, Surrey, UK
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19
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Niemeyer BF, Sanford B, Gibson JE, Berger JN, Oko LM, Medina E, Clambey ET, van Dyk LF. The gammaherpesvirus 68 viral cyclin facilitates expression of LANA. PLoS Pathog 2021; 17:e1010019. [PMID: 34780571 PMCID: PMC8629379 DOI: 10.1371/journal.ppat.1010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/29/2021] [Accepted: 10/08/2021] [Indexed: 11/29/2022] Open
Abstract
Gammaherpesviruses establish life-long infections within their host and have been shown to be the causative agents of devastating malignancies. Chronic infection within the host is mediated through cycles of transcriptionally quiescent stages of latency with periods of reactivation into detectable lytic and productive infection. The mechanisms that regulate reactivation from latency remain poorly understood. Previously, we defined a critical role for the viral cyclin in promoting reactivation from latency. Disruption of the viral cyclin had no impact on the frequency of cells containing viral genome during latency, yet it remains unclear whether the viral cyclin influences latently infected cells in a qualitative manner. To define the impact of the viral cyclin on properties of latent infection, we utilized a viral cyclin deficient variant expressing a LANA-beta-lactamase fusion protein (LANA::βla), to enumerate both the cellular distribution and frequency of LANA gene expression. Disruption of the viral cyclin did not affect the cellular distribution of latently infected cells, but did result in a significant decrease in the frequency of cells that expressed LANA::βla across multiple tissues and in both immunocompetent and immunodeficient hosts. Strikingly, whereas the cyclin-deficient virus had a reactivation defect in bulk culture, sort purified cyclin-deficient LANA::βla expressing cells were fully capable of reactivation. These data emphasize that the γHV68 latent reservoir is comprised of at least two distinct stages of infection characterized by differential LANA expression, and that a primary function of the viral cyclin is to promote LANA expression during latency, a state associated with ex vivo reactivation competence. Gammaherpesviruses are ubiquitous viruses with oncogenic potential that establish latency for the life of the host. These viruses can emerge from latency through reactivation, a process that is controlled by the immune system. Control of viral latency and reactivation is thought to be critical to prevent γHV-associated disease. This study focuses on a virally-encoded cyclin that is required for reactivation from latency. By characterizing how the viral cyclin influences latent infection in pure cell populations, we find that the viral cyclin has a vital role in promoting viral gene expression during latency. This work provides new insight into the function of a virally encoded cyclin in promoting reactivation from latency.
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Affiliation(s)
- Brian F. Niemeyer
- Immunology and Microbiology Department, University of Colorado Denver School of Medicine, Aurora, Colorado, United States of America
| | - Bridget Sanford
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Joy E. Gibson
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Jennifer N. Berger
- Immunology and Microbiology Department, University of Colorado Denver School of Medicine, Aurora, Colorado, United States of America
| | - Lauren M. Oko
- Immunology and Microbiology Department, University of Colorado Denver School of Medicine, Aurora, Colorado, United States of America
| | - Eva Medina
- Immunology and Microbiology Department, University of Colorado Denver School of Medicine, Aurora, Colorado, United States of America
| | - Eric T. Clambey
- Department of Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Linda F. van Dyk
- Immunology and Microbiology Department, University of Colorado Denver School of Medicine, Aurora, Colorado, United States of America
- * E-mail:
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20
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Abstract
Population screening played a substantial role in safely reopening the economy and avoiding new outbreaks of COVID-19. PCR-based pooled screening makes it possible to test the population with limited resources by pooling multiple individual samples. Our study compared different population-wide screening methods as transmission-mitigating interventions, including pooled PCR, individual PCR, and antigen screening. Incorporating testing-isolation process and individual-level viral load trajectories into an epidemic model, we further studied the impacts of testing-isolation on test sensitivities. Results show that the testing-isolation process could maintain a stable test sensitivity during the outbreak by removing most infected individuals, especially during the epidemic decline. Moreover, we compared the efficiency, accuracy, and cost of different screening methods during the pandemic. Our results show that PCR-based pooled screening is cost-effective in reversing the pandemic at low prevalence. When the prevalence is high, PCR-based pooled screening may not stop the outbreak. In contrast, antigen screening with sufficient frequency could reverse the epidemic, despite the high cost and the large numbers of false positives in the screening process.
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Affiliation(s)
- Jiali Yu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen, China
| | - Yiduo Huang
- Department of Civil and Environmental Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Zuo-Jun Shen
- College of Engineering, University of California Berkeley, Berkeley, CA, USA.
- Faculty of Engineering and Faculty of Business and Economics, University of Hong Kong, Hong Kong, China.
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21
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Ren X, Gelinas AD, Linehan M, Iwasaki A, Wang W, Janjic N, Pyle AM. Evolving A RIG-I Antagonist: A Modified DNA Aptamer Mimics Viral RNA. J Mol Biol 2021; 433:167227. [PMID: 34487794 DOI: 10.1016/j.jmb.2021.167227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/09/2021] [Accepted: 08/26/2021] [Indexed: 12/25/2022]
Abstract
Vertebrate organisms express a diversity of protein receptors that recognize and respond to the presence of pathogenic molecules, functioning as an early warning system for infection. As a result of mutation or dysregulated metabolism, these same innate immune receptors can be inappropriately activated, leading to inflammation and disease. One of the most important receptors for detection and response to RNA viruses is called RIG-I, and dysregulation of this protein is linked with a variety of disease states. Despite its central role in inflammatory responses, antagonists for RIG-I are underdeveloped. In this study, we use invitro selection from a pool of modified DNA aptamers to create a high affinity RIG-I antagonist. A high resolution crystal structure of the complex reveals molecular mimicry between the aptamer and the 5'-triphosphate terminus of viral ligands, which bind to the same amino acids within the CTD recognition platform of the RIG-I receptor. Our study suggests a powerful, generalizable strategy for generating immunomodulatory drugs and mechanistic tool compounds.
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MESH Headings
- Antigens, Viral/chemistry
- Antigens, Viral/metabolism
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/metabolism
- Binding Sites
- Cloning, Molecular
- Crystallography, X-Ray
- DEAD Box Protein 58/chemistry
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Humans
- Immunologic Factors/chemistry
- Immunologic Factors/metabolism
- Kinetics
- Models, Molecular
- Molecular Mimicry
- Mutation
- Nucleic Acid Conformation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- Receptors, Immunologic/chemistry
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- SELEX Aptamer Technique
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Affiliation(s)
- Xiaoming Ren
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Amy D Gelinas
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - Melissa Linehan
- Department of Immunobiology, Yale University, New Haven, CT 06519, USA
| | - Akiko Iwasaki
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA; Department of Immunobiology, Yale University, New Haven, CT 06519, USA
| | - Wenshuai Wang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Nebojsa Janjic
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA.
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.
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22
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Nitschel S, Zaeck LM, Potratz M, Nolden T, te Kamp V, Franzke K, Höper D, Pfaff F, Finke S. Point Mutations in the Glycoprotein Ectodomain of Field Rabies Viruses Mediate Cell Culture Adaptation through Improved Virus Release in a Host Cell Dependent and Independent Manner. Viruses 2021; 13:v13101989. [PMID: 34696419 PMCID: PMC8538267 DOI: 10.3390/v13101989] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/21/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
Molecular details of field rabies virus (RABV) adaptation to cell culture replication are insufficiently understood. A better understanding of adaptation may not only reveal requirements for efficient RABV replication in cell lines, but may also provide novel insights into RABV biology and adaptation-related loss of virulence and pathogenicity. Using two recombinant field rabies virus clones (rRABV Dog and rRABV Fox), we performed virus passages in three different cell lines to identify cell culture adaptive mutations. Ten passages were sufficient for the acquisition of adaptive mutations in the glycoprotein G and in the C-terminus of phosphoprotein P. Apart from the insertion of a glycosylation sequon via the mutation D247N in either virus, both acquired additional and cell line-specific mutations after passages on BHK (K425N) and MDCK-II (R346S or R350G) cells. As determined by virus replication kinetics, complementation, and immunofluorescence analysis, the major bottleneck in cell culture replication was the intracellular accumulation of field virus G protein, which was overcome after the acquisition of the adaptive mutations. Our data indicate that limited release of extracellular infectious virus at the plasma membrane is a defined characteristic of highly virulent field rabies viruses and we hypothesize that the observed suboptimal release of infectious virions is due to the inverse correlation of virus release and virulence in vivo.
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Affiliation(s)
- Sabine Nitschel
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology (IMVZ), 17493 Greifswald-Insel Riems, Germany; (S.N.); (L.M.Z.); (M.P.); (T.N.); (V.t.K.)
| | - Luca M. Zaeck
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology (IMVZ), 17493 Greifswald-Insel Riems, Germany; (S.N.); (L.M.Z.); (M.P.); (T.N.); (V.t.K.)
| | - Madlin Potratz
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology (IMVZ), 17493 Greifswald-Insel Riems, Germany; (S.N.); (L.M.Z.); (M.P.); (T.N.); (V.t.K.)
| | - Tobias Nolden
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology (IMVZ), 17493 Greifswald-Insel Riems, Germany; (S.N.); (L.M.Z.); (M.P.); (T.N.); (V.t.K.)
| | - Verena te Kamp
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology (IMVZ), 17493 Greifswald-Insel Riems, Germany; (S.N.); (L.M.Z.); (M.P.); (T.N.); (V.t.K.)
| | - Kati Franzke
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Infectiology (IMED), 17493 Greifswald-Insel Riems, Germany;
| | - Dirk Höper
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Diagnostic Virology (IVD), 17493 Greifswald-Insel Riems, Germany; (D.H.); (F.P.)
| | - Florian Pfaff
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Diagnostic Virology (IVD), 17493 Greifswald-Insel Riems, Germany; (D.H.); (F.P.)
| | - Stefan Finke
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology (IMVZ), 17493 Greifswald-Insel Riems, Germany; (S.N.); (L.M.Z.); (M.P.); (T.N.); (V.t.K.)
- Correspondence: ; Tel.: +49-38351-71283
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23
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Xu J, Liu X, Zhang X, Marshall B, Dong Z, Smith SB, Espinosa-Heidmann DG, Zhang M. Retinal and Choroidal Pathologies in Aged BALB/c Mice Following Systemic Neonatal Murine Cytomegalovirus Infection. Am J Pathol 2021; 191:1787-1804. [PMID: 34197777 PMCID: PMC8485058 DOI: 10.1016/j.ajpath.2021.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 11/30/2022]
Abstract
Although pathologies associated with acute virus infections have been extensively studied, the effects of long-term latent virus infections are less well understood. Human cytomegalovirus, which infects 50% to 80% of humans, is usually acquired during early life and persists in a latent state for the lifetime. The purpose of this study was to determine whether systemic murine cytomegalovirus (MCMV) infection acquired early in life disseminates to and becomes latent in the eye and if ocular MCMV can trigger in situ inflammation and occurrence of ocular pathology. This study found that neonatal infection of BALB/c mice with MCMV resulted in dissemination of virus to the eye, where it localized principally to choroidal endothelia and pericytes and less frequently to the retinal pigment epithelium (RPE) cells. MCMV underwent ocular latency, which was associated with expression of multiple virus genes and from which MCMV could be reactivated by immunosuppression. Latent ocular infection was associated with significant up-regulation of several inflammatory/angiogenic factors. Retinal and choroidal pathologies developed in a progressive manner, with deposits appearing at both basal and apical aspects of the RPE, RPE/choroidal atrophy, photoreceptor degeneration, and neovascularization. The pathologies induced by long-term ocular MCMV latency share features of previously described human ocular diseases, such as age-related macular degeneration.
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Affiliation(s)
- Jinxian Xu
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia; James and Jean Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Xinglou Liu
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia; James and Jean Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Xinyan Zhang
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia; James and Jean Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Brendan Marshall
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Zheng Dong
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia; Charlie Norwood Veterans Affairs Medical Center, Augusta, Georgia
| | - Sylvia B Smith
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia; James and Jean Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, Georgia; Department of Ophthamology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Diego G Espinosa-Heidmann
- James and Jean Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, Georgia; Department of Ophthamology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Ming Zhang
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia; James and Jean Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, Georgia.
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24
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Castillo-Esparza JF, Gómez-Lim MA. Transient Expression in Cytoplasm and Apoplast of Rotavirus VP6 Protein Fused to Anti-DEC205 Antibody in Nicotiana benthamiana and Nicotiana sylvestris. Mol Biotechnol 2021; 63:973-982. [PMID: 34146324 PMCID: PMC8214057 DOI: 10.1007/s12033-021-00359-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/14/2021] [Indexed: 11/29/2022]
Abstract
Rotavirus is the most common cause of severe diarrhea in infants and children worldwide and is responsible for about 215,000 deaths annually. Over 85% of these deaths originate in low-income/developing countries in Asia and Africa. Therefore, it is necessary to explore the development of vaccines that avoid the use of "living" viruses and furthermore, vaccines that have viral antigens capable of generating powerful heterotypic responses. Our strategy is based on the expression of the fusion of the anti-DEC205 single-chain variable fragment (scFv) coupled by an OLLAS tag to a viral protein (VP6) of Rotavirus in Nicotiana plants. It was possible to express transiently in N. benthamiana and N. sylvestris a recombinant protein consisting of the single chain variable fragment linked by an OLLAS tag to the VP6 protein. The presence of the recombinant protein, which had a molecular weight of approximately 75 kDa, was confirmed by immunodetection, in both plant species and in both cellular compartments (cytoplasm and apoplast) where it was expressed. In addition, the recombinant protein was modeled, and it was observed that some epitopes of interest are exposed on the surface, which could favor their immunogenic response.
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Affiliation(s)
- J Francisco Castillo-Esparza
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, 36824, Irapuato, Guanajuato, Mexico.
| | - Miguel A Gómez-Lim
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, 36824, Irapuato, Guanajuato, Mexico.
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25
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Fan Q, Miao C, Huang Y, Yue H, Wu A, Wu J, Wu J, Ma G. Hydroxypropyltrimethyl ammonium chloride chitosan-based hydrogel as the split H5N1 mucosal adjuvant: Structure-activity relationship. Carbohydr Polym 2021; 266:118139. [PMID: 34044953 DOI: 10.1016/j.carbpol.2021.118139] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/03/2021] [Accepted: 04/27/2021] [Indexed: 01/16/2023]
Abstract
In this study, 2-hydroxypropyltrimethyl ammonium chloride chitosan (HTCC)-based hydrogel was devised as a mucosal adjuvant for H5N1 vaccine. Aimed to investigate the structure activity relationship between HTCC hydrogel and immune response, we prepared a series of HTCC hydrogel with defined quaternization degrees (DQs, 0%, 21%, 41%, 60%, 80%). Results suggested that with DQ increasing, the positive charge and gelation time of HTCC hydrogel increased but the viscosity decreased. We applied in vivo imaging system and found that the moderate DQ 41% prolonged antigen residence time in nasal cavity, resulting in the most potent systemic responses (IgG, IgG1, IgG2a, HI). While, the lowest DQ 0% produced the best mucosal IgA antibody responses, most likely due to the closer contact with mucosa. Furthermore, the influence of animal gender was also discussed. These data add to the growing understanding of the relationship between physicochemical features of chitosan-based hydrogel and how they influence the immune responses.
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MESH Headings
- Adjuvants, Immunologic/administration & dosage
- Adjuvants, Immunologic/chemistry
- Adjuvants, Immunologic/pharmacology
- Administration, Intranasal
- Animals
- Antigens, Viral/immunology
- Antigens, Viral/metabolism
- Chitosan/administration & dosage
- Chitosan/analogs & derivatives
- Chitosan/chemistry
- Chitosan/pharmacology
- Female
- Hydrogels/administration & dosage
- Hydrogels/chemistry
- Hydrogels/pharmacology
- Immunity/drug effects
- Immunity, Mucosal/drug effects
- Influenza A Virus, H5N1 Subtype/drug effects
- Influenza A Virus, H5N1 Subtype/immunology
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/immunology
- Male
- Mice, Inbred BALB C
- Nasal Mucosa/virology
- Quaternary Ammonium Compounds/administration & dosage
- Quaternary Ammonium Compounds/chemistry
- Quaternary Ammonium Compounds/pharmacology
- Rats, Sprague-Dawley
- Sex Factors
- Structure-Activity Relationship
- Mice
- Rats
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Affiliation(s)
- Qingze Fan
- Department of Pharmacy, the Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, PR China; State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Chunyu Miao
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yilan Huang
- Department of Pharmacy, the Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, PR China
| | - Hua Yue
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Anguo Wu
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, PR China
| | - Jianming Wu
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, PR China
| | - Jie Wu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.
| | - Guanghui Ma
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.
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26
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Yuan M, Huang D, Lee CCD, Wu NC, Jackson AM, Zhu X, Liu H, Peng L, van Gils MJ, Sanders RW, Burton DR, Reincke SM, Prüss H, Kreye J, Nemazee D, Ward AB, Wilson IA. Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Science 2021; 373:818-823. [PMID: 34016740 PMCID: PMC8284396 DOI: 10.1126/science.abh1139] [Citation(s) in RCA: 241] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022]
Abstract
Neutralizing antibodies (nAbs) elicited against the receptor binding site (RBS) of the spike protein of wild-type severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are generally less effective against recent variants of concern. RBS residues Glu484, Lys417, and Asn501 are mutated in variants first described in South Africa (B.1.351) and Brazil (P.1). We analyzed their effects on angiotensin-converting enzyme 2 binding, as well as the effects of two of these mutations (K417N and E484K) on nAbs isolated from COVID-19 patients. Binding and neutralization of the two most frequently elicited antibody families (IGHV3-53/3-66 and IGHV1-2), which can both bind the RBS in alternative binding modes, are abrogated by K417N, E484K, or both. These effects can be structurally explained by their extensive interactions with RBS nAbs. However, nAbs to the more conserved, cross-neutralizing CR3022 and S309 sites were largely unaffected. The results have implications for next-generation vaccines and antibody therapies.
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MESH Headings
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antigenic Variation
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Antigens, Viral/metabolism
- Binding Sites
- Binding Sites, Antibody
- COVID-19/immunology
- COVID-19/virology
- Epitopes
- Humans
- Immune Evasion
- Mutation
- Protein Binding
- Protein Domains
- Receptors, Coronavirus/metabolism
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Abigail M Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marit J van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - S Momsen Reincke
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jakob Kreye
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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27
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Ju E, Li T, Ramos da Silva S, Markazi A, Gao SJ. Reversible switching of primary cells between normal and malignant state by oncogenic virus KSHV and CRISPR/Cas9-mediated targeting of a major viral latent protein. J Med Virol 2021; 93:5065-5075. [PMID: 33942339 PMCID: PMC9016784 DOI: 10.1002/jmv.27046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/11/2021] [Accepted: 04/23/2021] [Indexed: 11/10/2022]
Abstract
Viral infection has been implicated in the pathogenesis of a plethora of human diseases. Although antiviral therapies effectively confront the viral spread and infection, how to completely eradicate the viral genome from infected cells remains a challenge. In this study, we demonstrated the reversible switching of primary cells between normal and malignant states by an oncogenic virus Kaposi's sarcoma-associated herpesvirus (KSHV) and CRISPR/Cas9-mediated targeting of a major viral latent protein. Primary cells can be transformed into malignant status by infection of KSHV, while elimination of the KSHV genome from latent KSHV-infected cells reverses KSHV-transformed primary cells back to a "normal state" by CRISPR/Cas-mediated knockout of viral major latent gene LANA. As a proof of concept, we demonstrated efficient elimination of KSHV episome in KSHV-associated primary effusion lymphoma cells resulting in the induction of apoptosis by liposome-encapsulated CRISPR/Cas9 ribonucleoprotein complexes (Lipo/Cas9-LANAsgRNA). Our work illustrates CRISPR/Cas as a promising technology for eliminating oncogenic viruses from persistently infected cells by taking advantage of the genetic differences between viral and cellular genomes. Compared to traditional antiviral therapy, our study offer an approach for antagonizing human oncogenic virus-related cancers by directly targeting as well as clearing viral genomes.
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Affiliation(s)
- Enguo Ju
- Cancer Virology Program, UPMC Hillman Cancer Center, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tingting Li
- Cancer Virology Program, UPMC Hillman Cancer Center, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Suzane Ramos da Silva
- Cancer Virology Program, UPMC Hillman Cancer Center, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ashley Markazi
- Cancer Virology Program, UPMC Hillman Cancer Center, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Shou-Jiang Gao
- Cancer Virology Program, UPMC Hillman Cancer Center, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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28
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Nagler A, Kalaora S, Barbolin C, Gangaev A, Ketelaars SLC, Alon M, Pai J, Benedek G, Yahalom-Ronen Y, Erez N, Greenberg P, Yagel G, Peri A, Levin Y, Satpathy AT, Bar-Haim E, Paran N, Kvistborg P, Samuels Y. Identification of presented SARS-CoV-2 HLA class I and HLA class II peptides using HLA peptidomics. Cell Rep 2021; 35:109305. [PMID: 34166618 PMCID: PMC8185308 DOI: 10.1016/j.celrep.2021.109305] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/17/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
The human leukocyte antigen (HLA)-bound viral antigens serve as an immunological signature that can be selectively recognized by T cells. As viruses evolve by acquiring mutations, it is essential to identify a range of presented viral antigens. Using HLA peptidomics, we are able to identify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-derived peptides presented by highly prevalent HLA class I (HLA-I) molecules by using infected cells as well as overexpression of SARS-CoV-2 genes. We find 26 HLA-I peptides and 36 HLA class II (HLA-II) peptides. Among the identified peptides, some are shared between different cells and some are derived from out-of-frame open reading frames (ORFs). Seven of these peptides were previously shown to be immunogenic, and we identify two additional immunoreactive peptides by using HLA multimer staining. These results may aid the development of the next generation of SARS-CoV-2 vaccines based on presented viral-specific antigens that span several of the viral genes.
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Affiliation(s)
- Adi Nagler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shelly Kalaora
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Chaya Barbolin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Anastasia Gangaev
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, the Netherlands
| | - Steven L C Ketelaars
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, the Netherlands
| | - Michal Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Joy Pai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gil Benedek
- Tissue Typing and Immunogenetics Unit, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Noam Erez
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Polina Greenberg
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gal Yagel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Aviyah Peri
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- The de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Erez Bar-Haim
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Pia Kvistborg
- Tissue Typing and Immunogenetics Unit, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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29
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Belogiannis K, Florou VA, Fragkou PC, Ferous S, Chatzis L, Polyzou A, Lagopati N, Vassilakos D, Kittas C, Tzioufas AG, Tsiodras S, Sourvinos G, Gorgoulis VG. SARS-CoV-2 Antigenemia as a Confounding Factor in Immunodiagnostic Assays: A Case Study. Viruses 2021; 13:v13061143. [PMID: 34198719 PMCID: PMC8232125 DOI: 10.3390/v13061143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/11/2022] Open
Abstract
Humoral immunity has emerged as a vital immune component against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nevertheless, a subset of recovered Coronavirus Disease-2019 (COVID-19) paucisymptomatic/asymptomatic individuals do not generate an antibody response, constituting a paradox. We assumed that immunodiagnostic assays may operate under a competitive format within the context of antigenemia, potentially explaining this phenomenon. We present a case where persistent antigenemia/viremia was documented for at least 73 days post-symptom onset using ‘in-house’ methodology, and as it progressively declined, seroconversion took place late, around day 55, supporting our hypothesis. Thus, prolonged SARS-CoV-2 antigenemia/viremia could mask humoral responses, rendering, in certain cases, the phenomenon of ‘non-responders’ a misnomer.
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Affiliation(s)
- Konstantinos Belogiannis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, GR-11527 Athens, Greece; (K.B.); (V.A.F.); (A.P.); (N.L.); (D.V.); (C.K.)
| | - Venetia A. Florou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, GR-11527 Athens, Greece; (K.B.); (V.A.F.); (A.P.); (N.L.); (D.V.); (C.K.)
| | - Paraskevi C. Fragkou
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, GR-12462 Athens, Greece; (P.C.F.); (S.T.)
| | - Stefanos Ferous
- 2nd Medical Department, General Hospital of Athens G. Gennimatas, GR-11527 Athens, Greece;
| | - Loukas Chatzis
- Department of Pathophysiology, Athens School of Medicine, National and Kapodistrian University of Athens, GR-11527 Athens, Greece; (L.C.); (A.G.T.)
| | - Aikaterini Polyzou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, GR-11527 Athens, Greece; (K.B.); (V.A.F.); (A.P.); (N.L.); (D.V.); (C.K.)
| | - Nefeli Lagopati
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, GR-11527 Athens, Greece; (K.B.); (V.A.F.); (A.P.); (N.L.); (D.V.); (C.K.)
- Manchester Academic Health Sciences Centre, Division of Cancer Sciences, University of Manchester, Manchester M13 9NQ, UK
| | - Demetrios Vassilakos
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, GR-11527 Athens, Greece; (K.B.); (V.A.F.); (A.P.); (N.L.); (D.V.); (C.K.)
| | - Christos Kittas
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, GR-11527 Athens, Greece; (K.B.); (V.A.F.); (A.P.); (N.L.); (D.V.); (C.K.)
| | - Athanasios G. Tzioufas
- Department of Pathophysiology, Athens School of Medicine, National and Kapodistrian University of Athens, GR-11527 Athens, Greece; (L.C.); (A.G.T.)
| | - Sotirios Tsiodras
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, GR-12462 Athens, Greece; (P.C.F.); (S.T.)
| | - George Sourvinos
- Laboratory of Clinical Virology, Medical School, University of Crete, Crete, GR-71003 Heraklion, Greece
- Correspondence: (G.S.); (V.G.G.)
| | - Vassilis G. Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, GR-11527 Athens, Greece; (K.B.); (V.A.F.); (A.P.); (N.L.); (D.V.); (C.K.)
- Manchester Academic Health Sciences Centre, Division of Cancer Sciences, University of Manchester, Manchester M13 9NQ, UK
- Biomedical Research Foundation, Academy of Athens, GR-11527 Athens, Greece
- Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, GR-11527 Athens, Greece
- Correspondence: (G.S.); (V.G.G.)
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Guo X, Hou J, Yuan Z, Li H, Sang S. A novel paper biosensor based on Fe 3O 4@SiO 2-NH 2and MWCNTs for rapid detection of pseudorabies virus. Nanotechnology 2021; 32:355102. [PMID: 33975288 DOI: 10.1088/1361-6528/ac002a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
In this study, a novel paper biosensor based on Fe3O4@SiO2-NH2magnetic polymer microspheres and multi walled carbon nanotubes (MWCNTs) for rapid detection of pseudorabies virus (PRV) was first developed. Fe3O4@SiO2-NH2were functionalized with PRV antibody and doped in cellulose nitrate paper to fabricate the magnetic paper biosensor with good magnetic response and biocompatibility. Using MWCNTs to build conductive network of sensors, PRV antigen binds specifically to the immunomagnetic microspheres on the sensor, and the resulting immune complex changes the magnetic domain structure of the sensor and the structural gap of MWCNTs, causing the magnetic property and impedance change. TEM and EDS characterization proved that the biosensor was successfully doped with Fe3O4@SiO2-NH2and effectively recognized PRV. Under optimized conditions, the impedance variation was found to be linearly related to the logarithm value of PRV concentrations in the range of 10-1 mg ml-1, with the detection limit of 10 ng ml-1. This paper biosensor demonstrated advantages of portability, high sensitivity and specificity, providing a valuable method for early control of PRV.
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Affiliation(s)
- Xing Guo
- MicroNano System Research Center, Key Lab of Advanced Transducers and Intelligent Control System of the Ministry of Education & College of Information and Computer, Taiyuan University of Technology, Jinzhong 030600, Shanxi, People's Republic of China
| | - Jianru Hou
- MicroNano System Research Center, Key Lab of Advanced Transducers and Intelligent Control System of the Ministry of Education & College of Information and Computer, Taiyuan University of Technology, Jinzhong 030600, Shanxi, People's Republic of China
| | - Zhongyun Yuan
- MicroNano System Research Center, Key Lab of Advanced Transducers and Intelligent Control System of the Ministry of Education & College of Information and Computer, Taiyuan University of Technology, Jinzhong 030600, Shanxi, People's Republic of China
| | - Hongmei Li
- MicroNano System Research Center, Key Lab of Advanced Transducers and Intelligent Control System of the Ministry of Education & College of Information and Computer, Taiyuan University of Technology, Jinzhong 030600, Shanxi, People's Republic of China
| | - Shengbo Sang
- MicroNano System Research Center, Key Lab of Advanced Transducers and Intelligent Control System of the Ministry of Education & College of Information and Computer, Taiyuan University of Technology, Jinzhong 030600, Shanxi, People's Republic of China
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Diao B, Wang C, Wang R, Feng Z, Zhang J, Yang H, Tan Y, Wang H, Wang C, Liu L, Liu Y, Liu Y, Wang G, Yuan Z, Hou X, Ren L, Wu Y, Chen Y. Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 infection. Nat Commun 2021; 12:2506. [PMID: 33947851 DOI: 10.1101/2020.03.04.20031120] [Citation(s) in RCA: 192] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 03/23/2021] [Indexed: 05/20/2023] Open
Abstract
It is unclear whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can directly infect human kidney, thus leading to acute kidney injury (AKI). Here, we perform a retrospective analysis of clinical parameters from 85 patients with laboratory-confirmed coronavirus disease 2019 (COVID-19); moreover, kidney histopathology from six additional COVID-19 patients with post-mortem examinations was performed. We find that 27% (23/85) of patients exhibited AKI. The elderly patients and cases with comorbidities (hypertension and heart failure) are more prone to develop AKI. Haematoxylin & eosin staining shows that the kidneys from COVID-19 autopsies have moderate to severe tubular damage. In situ hybridization assays illustrate that viral RNA accumulates in tubules. Immunohistochemistry shows nucleocapsid and spike protein deposits in the tubules, and immunofluorescence double staining shows that both antigens are restricted to the angiotensin converting enzyme-II-positive tubules. SARS-CoV-2 infection triggers the expression of hypoxic damage-associated molecules, including DP2 and prostaglandin D synthase in infected tubules. Moreover, it enhances CD68+ macrophages infiltration into the tubulointerstitium, and complement C5b-9 deposition on tubules is also observed. These results suggest that SARS-CoV-2 directly infects human kidney to mediate tubular pathogenesis and AKI.
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Affiliation(s)
- Bo Diao
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
- Department of Medical Laboratory Center, General Hospital of Central Theater Command, Wuhan, Hubei Province, P. R. China
- Hubei Key Laboratory of Central Nervous System Tumor and Intervention, Wuhan, Hubei Province, P. R. China
| | - Chenhui Wang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Rongshuai Wang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
| | - Zeqing Feng
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Ji Zhang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Han Yang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Yingjun Tan
- Department of Medical Laboratory Center, General Hospital of Central Theater Command, Wuhan, Hubei Province, P. R. China
| | - Huiming Wang
- Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, P. R. China
| | - Changsong Wang
- Department of Pathology, 989th Hospital of PLA, Luoyang, Henan Province, P. R. China
| | - Liang Liu
- Hubei Chongxin Judicial Expertise Center, Wuhan, Hubei Province, P. R. China
| | - Ying Liu
- Department of Medical Laboratory Center, General Hospital of Central Theater Command, Wuhan, Hubei Province, P. R. China
| | - Yueping Liu
- Department of Medical Laboratory Center, General Hospital of Central Theater Command, Wuhan, Hubei Province, P. R. China
| | - Gang Wang
- Department of Medical Laboratory Center, General Hospital of Central Theater Command, Wuhan, Hubei Province, P. R. China
| | - Zilin Yuan
- Department of Medical Laboratory Center, General Hospital of Central Theater Command, Wuhan, Hubei Province, P. R. China
| | - Xiaotao Hou
- Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, Guangdong Province, P. R. China
| | - Liang Ren
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China.
| | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China.
| | - Yongwen Chen
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China.
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Haque M, Lei F, Xiong X, Ren Y, Peng HY, Wang L, Kumar A, Das JK, Song J. Stem Cell-Derived Viral Antigen-Specific T Cells Suppress HIV Replication and PD-1 Expression on CD4+ T Cells. Viruses 2021; 13:753. [PMID: 33923025 PMCID: PMC8146941 DOI: 10.3390/v13050753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 01/18/2023] Open
Abstract
The viral antigen (Ag)-specific CD8+ cytotoxic T lymphocytes (CTLs) derived from pluripotent stem cells (PSCs), i.e., PSC-CTLs, have the ability to suppress the human immunodeficiency virus (HIV) infection. After adoptive transfer, PSC-CTLs can infiltrate into the local tissues to suppress HIV replication. Nevertheless, the mechanisms by which the viral Ag-specific PSC-CTLs elicit the antiviral response remain to be fully elucidated. In this study, we generated the functional HIV-1 Gag epitope SL9-specific CTLs from the induced PSC (iPSCs), i.e., iPSC-CTLs, and investigated the suppression of SL9-specific iPSC-CTLs on viral replication and the protection of CD4+ T cells. A chimeric HIV-1, i.e., EcoHIV, was used to produce HIV replication in mice. We show that adoptive transfer of SL9-specific iPSC-CTLs greatly suppressed EcoHIV replication in the peritoneal macrophages and spleen in the animal model. Furthermore, we demonstrate that the adoptive transfer significantly reduced expression of PD-1 on CD4+ T cells in the spleen and generated persistent anti-HIV memory T cells. These results indicate that stem cell-derived viral Ag-specific CTLs can robustly accumulate in the local tissues to suppress HIV replication and prevent CD4+ T cell exhaustion through reduction of PD-1 expression.
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Affiliation(s)
- Mohammad Haque
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA; (M.H.); (X.X.); (Y.R.); (H.-Y.P.); (L.W.); (A.K.); (J.K.D.)
| | - Fengyang Lei
- Department of Ophthalmology, Harvard University School of Medicine, Boston, MA 02215, USA;
| | - Xiaofang Xiong
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA; (M.H.); (X.X.); (Y.R.); (H.-Y.P.); (L.W.); (A.K.); (J.K.D.)
| | - Yijie Ren
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA; (M.H.); (X.X.); (Y.R.); (H.-Y.P.); (L.W.); (A.K.); (J.K.D.)
| | - Hao-Yun Peng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA; (M.H.); (X.X.); (Y.R.); (H.-Y.P.); (L.W.); (A.K.); (J.K.D.)
| | - Liqing Wang
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA; (M.H.); (X.X.); (Y.R.); (H.-Y.P.); (L.W.); (A.K.); (J.K.D.)
| | - Anil Kumar
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA; (M.H.); (X.X.); (Y.R.); (H.-Y.P.); (L.W.); (A.K.); (J.K.D.)
| | - Jugal Kishore Das
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA; (M.H.); (X.X.); (Y.R.); (H.-Y.P.); (L.W.); (A.K.); (J.K.D.)
| | - Jianxun Song
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA; (M.H.); (X.X.); (Y.R.); (H.-Y.P.); (L.W.); (A.K.); (J.K.D.)
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33
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Griessl M, Renzaho A, Freitag K, Seckert CK, Reddehase MJ, Lemmermann NAW. Stochastic Episodes of Latent Cytomegalovirus Transcription Drive CD8 T-Cell "Memory Inflation" and Avoid Immune Evasion. Front Immunol 2021; 12:668885. [PMID: 33968074 PMCID: PMC8100209 DOI: 10.3389/fimmu.2021.668885] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/06/2021] [Indexed: 11/29/2022] Open
Abstract
Acute infection with murine cytomegalovirus (mCMV) is controlled by CD8+ T cells and develops into a state of latent infection, referred to as latency, which is defined by lifelong maintenance of viral genomes but absence of infectious virus in latently infected cell types. Latency is associated with an increase in numbers of viral epitope-specific CD8+ T cells over time, a phenomenon known as "memory inflation" (MI). The "inflationary" subset of CD8+ T cells has been phenotyped as KLRG1+CD62L- effector-memory T cells (iTEM). It is agreed upon that proliferation of iTEM requires repeated episodes of antigen presentation, which implies that antigen-encoding viral genes must be transcribed during latency. Evidence for this has been provided previously for the genes encoding the MI-driving antigenic peptides IE1-YPHFMPTNL and m164-AGPPRYSRI of mCMV in the H-2d haplotype. There exist two competing hypotheses for explaining MI-driving viral transcription. The "reactivation hypothesis" proposes frequent events of productive virus reactivation from latency. Reactivation involves a coordinated gene expression cascade from immediate-early (IE) to early (E) and late phase (L) transcripts, eventually leading to assembly and release of infectious virus. In contrast, the "stochastic transcription hypothesis" proposes that viral genes become transiently de-silenced in latent viral genomes in a stochastic fashion, not following the canonical IE-E-L temporal cascade of reactivation. The reactivation hypothesis, however, is incompatible with the finding that productive virus reactivation is exceedingly rare in immunocompetent mice and observed only under conditions of compromised immunity. In addition, the reactivation hypothesis fails to explain why immune evasion genes, which are regularly expressed during reactivation in the same cells in which epitope-encoding genes are expressed, do not prevent antigen presentation and thus MI. Here we show that IE, E, and L genes are transcribed during latency, though stochastically, not following the IE-E-L temporal cascade. Importantly, transcripts that encode MI-driving antigenic peptides rarely coincide with those that encode immune evasion proteins. As immune evasion can operate only in cis, that is, in a cell that simultaneously expresses antigenic peptides, the stochastic transcription hypothesis explains why immune evasion is not operative in latently infected cells and, therefore, does not interfere with MI.
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Affiliation(s)
| | | | | | | | | | - Niels A. W. Lemmermann
- Institute for Virology, Research Center for Immunotherapy (FZI) at the University Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
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Santana CM, Gauger P, Vetger A, Magstadt D, Kim DS, Shrestha D, Charavaryamath C, Rumbeiha WK. Ambient hydrogen sulfide exposure increases the severity of influenza A virus infection in swine. Arch Environ Occup Health 2021; 76:526-538. [PMID: 33750267 DOI: 10.1080/19338244.2021.1896986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Hydrogen sulfide (H2S) is common in concentrated pig feed operations from the decomposition of manure. Ambient H2S is a respiratory tract irritant and an environmental stressor for caretakers and pigs. Influenza A virus (IAV), a zoonotic pathogen, has caused prior pandemics. The effects of H2S or IAV alone on the respiratory system have been investigated, but their interaction has not. We hypothesized that exposure to environmentally-relevant H2S concentrations increases the pathogenicity of IAV infection in swine. Thirty-five, three-week old pigs of mixed sex were exposed to breathing air or H2S via inhalation 6 hours daily for 12 days. After 7 days, pigs were inoculated with H3N2 IAV (or a placebo). Results showed that ambient H2S increased the severity of respiratory distress and lung pathology. H2S also suppressed IL-IL-1β, IL-6 and IL-8 cytokine response in BALF and increased viral loads and nasal shedding.
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Affiliation(s)
- Cristina M Santana
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Phillip Gauger
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Amber Vetger
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Drew Magstadt
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Dong-Suk Kim
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Denusha Shrestha
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | | | - Wilson K Rumbeiha
- Department of Molecular Biosciences, University of California, Davis, CA, USA
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35
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Pramanik A, Gao Y, Patibandla S, Mitra D, McCandless MG, Fassero LA, Gates K, Tandon R, Ray PC. Aptamer Conjugated Gold Nanostar-Based Distance-Dependent Nanoparticle Surface Energy Transfer Spectroscopy for Ultrasensitive Detection and Inactivation of Corona Virus. J Phys Chem Lett 2021; 12:2166-2171. [PMID: 33629859 PMCID: PMC7927280 DOI: 10.1021/acs.jpclett.0c03570] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/16/2021] [Indexed: 05/25/2023]
Abstract
The ongoing outbreak of the coronavirus infection has killed more than 2 million people. Herein, we demonstrate that Rhodamine 6G (Rh-6G) dye conjugated DNA aptamer-attached gold nanostar (GNS)-based distance-dependent nanoparticle surface energy transfer (NSET) spectroscopy has the capability of rapid diagnosis of specific SARS-CoV-2 spike recombinant antigen or SARS-CoV-2 spike protein pseudotyped baculovirus within 10 min. Because Rh-6G-attached single-stand DNA aptamer wrapped the GNS, 99% dye fluorescence was quenched because of the NSET process. In the presence of spike antigen or virus, the fluorescence signal persists because of the aptamer-spike protein binding. Specifically, the limit of detection for the NSET assay has been determined to be 130 fg/mL for antigen and 8 particles/mL for virus. Finally, we have demonstrated that DNA aptamer-attached GNSs can stop virus infection by blocking the angiotensin-converting enzyme 2 (ACE2) receptor binding capability and destroying the lipid membrane of the virus.
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Affiliation(s)
- Avijit Pramanik
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
| | - Ye Gao
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
| | - Shamily Patibandla
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
| | - Dipanwita Mitra
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Martin G McCandless
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Lauren A Fassero
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Kalein Gates
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
| | - Ritesh Tandon
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Paresh Chandra Ray
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
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36
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Kim YJ, Kim Y, Kumar A, Kim CW, Toth Z, Cho NH, Lee HR. Kaposi's sarcoma-associated herpesvirus latency-associated nuclear antigen dysregulates expression of MCL-1 by targeting FBW7. PLoS Pathog 2021; 17:e1009179. [PMID: 33471866 PMCID: PMC7816990 DOI: 10.1371/journal.ppat.1009179] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/22/2020] [Indexed: 12/11/2022] Open
Abstract
Primary effusion lymphoma (PEL) is an aggressive B cell lymphoma that is etiologically linked to Kaposi’s sarcoma-associated herpesvirus (KSHV). Despite standard multi-chemotherapy treatment, PEL continues to cause high mortality. Thus, new strategies to control PEL are needed urgently. Here, we show that a phosphodegron motif within the KSHV protein, latency-associated nuclear antigen (LANA), specifically interacts with E3 ubiquitin ligase FBW7, thereby competitively inhibiting the binding of the anti-apoptotic protein MCL-1 to FBW7. Consequently, LANA-FBW7 interaction enhances the stability of MCL-1 by preventing its proteasome-mediated degradation, which inhibits caspase-3-mediated apoptosis in PEL cells. Importantly, MCL-1 inhibitors markedly suppress colony formation on soft agar and tumor growth of KSHV+PEL/BCBL-1 in a xenograft mouse model. These results strongly support the conclusion that high levels of MCL-1 expression enable the oncogenesis of PEL cells and thus, MCL-1 could be a potential drug target for KSHV-associated PEL. This work also unravels a mechanism by which an oncogenic virus perturbs a key component of the ubiquitination pathway to induce tumorigenesis. Primary effusion lymphoma (PEL), a highly aggressive B cell lymphoma, is associated with Kaposi’s sarcoma-associated herpesvirus (KSHV). However, the underlying mechanisms that govern the aggressiveness of KSHV-associated PEL are poorly understood. Here, we demonstrate that KSHV LANA interacts with cellular ubiquitin E3 ligase FBW7, sequestering MCL-1 from FBW7, which reduces MCL-1 ubiquitination. As such, LANA potently stabilizes and increases MCL-1 protein, leading to inhibition of caspase-3-mediated apoptosis in PEL cells. Furthermore, MCL-1 inhibitors efficiently blocked PEL progression in mouse xenograft model. These results suggest that LANA acts as a proto-oncogene via deregulating tumor suppressor FBW7, which upregulates anti-apoptotic MCL-1 expression. This study suggests drugs that target MCL-1 may serve as an effective therapy against KSHV+ PEL.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antigens, Viral/genetics
- Antigens, Viral/metabolism
- Apoptosis
- Cell Proliferation
- F-Box-WD Repeat-Containing Protein 7/genetics
- F-Box-WD Repeat-Containing Protein 7/metabolism
- Female
- Herpesvirus 8, Human/physiology
- Humans
- Lymphoma, Primary Effusion/genetics
- Lymphoma, Primary Effusion/metabolism
- Lymphoma, Primary Effusion/pathology
- Lymphoma, Primary Effusion/virology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Myeloid Cell Leukemia Sequence 1 Protein/genetics
- Myeloid Cell Leukemia Sequence 1 Protein/metabolism
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Phosphorylation
- Sarcoma, Kaposi/genetics
- Sarcoma, Kaposi/metabolism
- Sarcoma, Kaposi/pathology
- Sarcoma, Kaposi/virology
- Tumor Cells, Cultured
- Ubiquitination
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Yeong Jun Kim
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, South Korea
| | - Yuri Kim
- Department of Microbiology and Immunology, Seoul National University college of Medicine, Seoul, South Korea
| | - Abhishek Kumar
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, United States of America
| | - Chan Woo Kim
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, South Korea
| | - Zsolt Toth
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, United States of America
| | - Nam Hyuk Cho
- Department of Microbiology and Immunology, Seoul National University college of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Seoul National University college of Medicine, Seoul, South Korea
| | - Hye-Ra Lee
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, South Korea
- Department of Lab Medicine, College of Medicine, Korea University, Seoul, South Korea
- * E-mail:
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Antipova NV, Larionova TD, Siniavin AE, Nikiforova MA, Gushchin VA, Babichenko II, Volkov AV, Shakhparonov MI, Pavlyukov MS. Establishment of Murine Hybridoma Cells Producing Antibodies against Spike Protein of SARS-CoV-2. Int J Mol Sci 2020; 21:E9167. [PMID: 33271925 PMCID: PMC7731011 DOI: 10.3390/ijms21239167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/28/2020] [Accepted: 11/28/2020] [Indexed: 12/17/2022] Open
Abstract
In 2020 the world faced the pandemic of COVID-19 severe acute respiratory syndrome caused by a new type of coronavirus named SARS-CoV-2. To stop the spread of the disease, it is crucial to create molecular tools allowing the investigation, diagnoses and treatment of COVID-19. One of such tools are monoclonal antibodies (mAbs). In this study we describe the development of hybridoma cells that can produce mouse mAbs against receptor binding domain of SARS-CoV-2 spike (S) protein. These mAbs are able to specifically detect native and denatured S proteins in all tested applications, including immunoblotting, enzyme-linked immunosorbent assay, immunofluorescence staining of cells and immunohistochemical staining of paraffin embedded patients' tissue samples. In addition, we showed that the obtained mAbs can efficiently block SARS-CoV-2 infection in in vitro experiments. Finally, we determined the amino acid sequence of light and heavy chains of the mAbs. This information will allow the use of corresponding peptides to establish genetically engineered therapeutic antibodies. To date multiple mAbs against SARS-CoV-2 proteins have been established, however, bigger sets of various antibodies will allow the detection and neutralization of SARS-CoV-2, even if the virus acquires novel mutations.
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Affiliation(s)
- Nadezhda V. Antipova
- Department of Functioning of Living Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (N.V.A.); (T.D.L.); (A.E.S.); (M.I.S.)
- Institute of Medicine, Peoples’ Friendship University of Russia (RUDN University), 17198 Moscow, Russia;
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Tatyana D. Larionova
- Department of Functioning of Living Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (N.V.A.); (T.D.L.); (A.E.S.); (M.I.S.)
| | - Andrei E. Siniavin
- Department of Functioning of Living Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (N.V.A.); (T.D.L.); (A.E.S.); (M.I.S.)
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (M.A.N.); (V.A.G.)
| | - Maria A. Nikiforova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (M.A.N.); (V.A.G.)
| | - Vladimir A. Gushchin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (M.A.N.); (V.A.G.)
| | - Igor I. Babichenko
- Institute of Medicine, Peoples’ Friendship University of Russia (RUDN University), 17198 Moscow, Russia;
| | | | - Michail I. Shakhparonov
- Department of Functioning of Living Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (N.V.A.); (T.D.L.); (A.E.S.); (M.I.S.)
| | - Marat S. Pavlyukov
- Department of Functioning of Living Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (N.V.A.); (T.D.L.); (A.E.S.); (M.I.S.)
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38
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Villabruna N, Izquierdo Lara RW, Szarvas J, Koopmans MPG, de Graaf M. Phylogenetic Investigation of Norovirus Transmission between Humans and Animals. Viruses 2020; 12:v12111287. [PMID: 33182775 PMCID: PMC7698157 DOI: 10.3390/v12111287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 01/03/2023] Open
Abstract
Norovirus infections are a leading cause of acute gastroenteritis worldwide, affecting people of all ages. There are 10 norovirus genogroups (GI-GX) that infect humans and animals in a host-specific manner. New variants and genotypes frequently emerge, and their origin is not well understood. One hypothesis is that new human infections may be seeded from an animal reservoir, as human noroviruses have occasionally been detected in animal species. The majority of these sequences were identified as older GII.4 variants, but a variety of other GIIs and GIs have been detected as well. While these sequences share at least 94% nt similarity with human strains, most of them are >98% identical to human strains. The fact that these strains were detected in animals after they had been detected through human surveillance to be already circulating in humans suggests human-to-animal transmission.
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Affiliation(s)
- Nele Villabruna
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (N.V.); (R.W.I.L.); (M.P.G.K.)
| | - Ray W. Izquierdo Lara
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (N.V.); (R.W.I.L.); (M.P.G.K.)
| | - Judit Szarvas
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (N.V.); (R.W.I.L.); (M.P.G.K.)
| | - Miranda de Graaf
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (N.V.); (R.W.I.L.); (M.P.G.K.)
- Correspondence:
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39
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Stamatakis G, Samiotaki M, Mpakali A, Panayotou G, Stratikos E. Generation of SARS-CoV-2 S1 Spike Glycoprotein Putative Antigenic Epitopes in Vitro by Intracellular Aminopeptidases. J Proteome Res 2020; 19:4398-4406. [PMID: 32931291 PMCID: PMC7640968 DOI: 10.1021/acs.jproteome.0c00457] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Indexed: 12/20/2022]
Abstract
Presentation of antigenic peptides by MHCI is central to cellular immune responses against viral pathogens. While adaptive immune responses versus SARS-CoV-2 can be of critical importance to both recovery and vaccine efficacy, how protein antigens from this pathogen are processed to generate antigenic peptides is largely unknown. Here, we analyzed the proteolytic processing of overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein of SARS-CoV-2, by three key enzymes that generate antigenic peptides, aminopeptidases ERAP1, ERAP2, and IRAP. All enzymes generated shorter peptides with sequences suitable for binding onto HLA alleles, but with distinct specificity fingerprints. ERAP1 was the most efficient in generating peptides 8-11 residues long, the optimal length for HLA binding, while IRAP was the least efficient. The combination of ERAP1 with ERAP2 greatly limited the variability of peptide sequences produced. Less than 7% of computationally predicted epitopes were found to be produced experimentally, suggesting that aminopeptidase processing may constitute a significant filter to epitope presentation. These experimentally generated putative epitopes could be prioritized for SARS-CoV-2 immunogenicity studies and vaccine design. We furthermore propose that this in vitro trimming approach could constitute a general filtering method to enhance the prediction robustness for viral antigenic epitopes.
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Affiliation(s)
- George Stamatakis
- Biomedical
Sciences Research Center “Alexander Fleming”, 16672 Vari, Attica, Greece
| | - Martina Samiotaki
- Biomedical
Sciences Research Center “Alexander Fleming”, 16672 Vari, Attica, Greece
| | - Anastasia Mpakali
- National
Centre for Scientific Research “Demokritos”, 15310 Agia Paraskevi,
Attica, Greece
| | - George Panayotou
- Biomedical
Sciences Research Center “Alexander Fleming”, 16672 Vari, Attica, Greece
| | - Efstratios Stratikos
- National
Centre for Scientific Research “Demokritos”, 15310 Agia Paraskevi,
Attica, Greece
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40
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Bolaños-Martínez OC, Govea-Alonso DO, Cervantes-Torres J, Hernández M, Fragoso G, Sciutto-Conde E, Rosales-Mendoza S. Expression of immunogenic poliovirus Sabin type 1 VP proteins in transgenic tobacco. J Biotechnol 2020; 322:10-20. [PMID: 32659239 DOI: 10.1016/j.jbiotec.2020.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 11/24/2022]
Abstract
One of the milestones of vaccinology is the depletion of the global impact of Poliomyelitis. The current vaccines to deal with Polio comprise the Sabin and Salk formulations. The main limitation of the former is the use of attenuated viruses that can revert into pathogenic forms, whereas the latter is more expensive and induces no protection in the intestinal tract; the site of virus replication. Genetically engineered plants cope with such limitations. In addition, they offer a low-cost alternative for production, storage and delivery of vaccines. This technology has been narrowly applied in the development of Polio vaccines. Herein, we explored the ability of tobacco cells to express the immunogenic VP1, VP2, VP3, and VP4 Polio antigens, which are relevant for vaccine development. Evidence on the expression of the plant-made Polio VPs is presented and an immunogenicity assessment proved their capacity to induce local and systemic humoral responses when administered by subcutaneous and oral routes. The plant-made VPs will be useful in the development of low-cost vaccine formulations able to induce effective mucosal immunity without the risks associated to the use of attenuated viruses; therefore there is a potential for this technology to contribute toward Polio eradication.
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MESH Headings
- Animals
- Antibodies, Viral/analysis
- Antibodies, Viral/blood
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Antigens, Viral/metabolism
- Capsid Proteins/genetics
- Capsid Proteins/immunology
- Capsid Proteins/metabolism
- Feces/chemistry
- Male
- Mice
- Mice, Inbred BALB C
- Molecular Farming
- Plants, Genetically Modified/genetics
- Poliomyelitis/prevention & control
- Poliomyelitis/virology
- Poliovirus/genetics
- Poliovirus/immunology
- Poliovirus Vaccine, Oral/genetics
- Poliovirus Vaccine, Oral/immunology
- Poliovirus Vaccine, Oral/metabolism
- Nicotiana/genetics
- Vaccines, Subunit/genetics
- Vaccines, Subunit/immunology
- Vaccines, Subunit/metabolism
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Affiliation(s)
- Omayra C Bolaños-Martínez
- Laboratorio de Biofarmacéuticos Recombinantes, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, S.L.P, 78210, Mexico; Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí, S.L.P., 78210, Mexico; Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria s/n, Ciudad de México, 04650, Mexico
| | - Dania O Govea-Alonso
- Laboratorio de Biofarmacéuticos Recombinantes, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, S.L.P, 78210, Mexico; Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí, S.L.P., 78210, Mexico
| | - Jacquelynne Cervantes-Torres
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria s/n, Ciudad de México, 04650, Mexico
| | - Marisela Hernández
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria s/n, Ciudad de México, 04650, Mexico
| | - Gladis Fragoso
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria s/n, Ciudad de México, 04650, Mexico
| | - Edda Sciutto-Conde
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria s/n, Ciudad de México, 04650, Mexico.
| | - Sergio Rosales-Mendoza
- Laboratorio de Biofarmacéuticos Recombinantes, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, S.L.P, 78210, Mexico; Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí, S.L.P., 78210, Mexico.
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41
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Hussain A, Hasan A, Nejadi Babadaei MM, Bloukh SH, Chowdhury MEH, Sharifi M, Haghighat S, Falahati M. Targeting SARS-CoV2 Spike Protein Receptor Binding Domain by Therapeutic Antibodies. Biomed Pharmacother 2020; 130:110559. [PMID: 32768882 PMCID: PMC7395593 DOI: 10.1016/j.biopha.2020.110559] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/09/2020] [Accepted: 07/25/2020] [Indexed: 12/12/2022] Open
Abstract
As the number of people infected with the newly identified 2019 novel coronavirus (SARS-CoV2) is continuously increasing every day, development of potential therapeutic platforms is vital. Based on the comparatively high similarity of receptor-binding domain (RBD) in SARS-CoV2 and SARS-CoV, it seems crucial to assay the cross-reactivity of anti-SARS-CoV monoclonal antibodies (mAbs) with SARS-CoV2 spike (S)-protein. Indeed, developing mAbs targeting SARS-CoV2 S-protein RBD could show novel applications for rapid and sensitive development of potential epitope-specific vaccines (ESV). Herein, we present an overview on the discovery of new CoV followed by some explanation on the SARS-CoV2 S-protein RBD site. Furthermore, we surveyed the novel therapeutic mAbs for targeting S-protein RBD such as S230, 80R, F26G18, F26G19, CR3014, CR3022, M396, and S230.15. Afterwards, the mechanism of interaction of RBD and different mAbs were explained and it was suggested that one of the SARS-CoV-specific human mAbs, namely CR3022, could show the highest binding affinity with SARS-CoV2 S-protein RBD. Finally, some ongoing challenges and future prospects for rapid and sensitive advancement of therapeutic mAbs targeting S-protein RBD were discussed. In conclusion, it may be proposed that this review may pave the way for recognition of RBD and different mAbs to develop potential therapeutic ESV.
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MESH Headings
- Amino Acid Sequence
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antibody Affinity
- Antigen-Antibody Reactions
- Antigens, Viral/immunology
- Antigens, Viral/metabolism
- Betacoronavirus/immunology
- Binding Sites, Antibody
- COVID-19
- COVID-19 Vaccines
- Coronavirus/chemistry
- Coronavirus/immunology
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Epitopes/immunology
- Humans
- Models, Molecular
- Pandemics
- Phylogeny
- Pneumonia, Viral/immunology
- Protein Binding
- Protein Conformation
- Protein Domains
- SARS-CoV-2
- Sequence Alignment
- Sequence Homology, Amino Acid
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Viral Vaccines/immunology
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Affiliation(s)
- Arif Hussain
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha, 2713, Qatar; Biomedical Research Center, Qatar University, Doha, 2713, Qatar.
| | - Mohammad Mahdi Nejadi Babadaei
- Department of Molecular Genetics, Faculty of Biological Science, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Samir Haj Bloukh
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, PO Box 346, Ajman, United Arab Emirates
| | | | - Majid Sharifi
- Department of Nanotechnology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Setareh Haghighat
- Department of Microbiology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mojtaba Falahati
- Department of Nanotechnology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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42
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Galili U. Amplifying immunogenicity of prospective Covid-19 vaccines by glycoengineering the coronavirus glycan-shield to present α-gal epitopes. Vaccine 2020; 38:6487-6499. [PMID: 32907757 PMCID: PMC7437500 DOI: 10.1016/j.vaccine.2020.08.032] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/22/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022]
Abstract
The many carbohydrate chains on Covid-19 coronavirus SARS-CoV-2 and its S-protein form a glycan-shield that masks antigenic peptides and decreases uptake of inactivated virus or S-protein vaccines by APC. Studies on inactivated influenza virus and recombinant gp120 of HIV vaccines indicate that glycoengineering of glycan-shields to present α-gal epitopes (Galα1-3Galβ1-4GlcNAc-R) enables harnessing of the natural anti-Gal antibody for amplifying vaccine efficacy, as evaluated in mice producing anti-Gal. The α-gal epitope is the ligand for the natural anti-Gal antibody which constitutes ~1% of immunoglobulins in humans. Upon administration of vaccines presenting α-gal epitopes, anti-Gal binds to these epitopes at the vaccination site and forms immune complexes with the vaccines. These immune complexes are targeted for extensive uptake by APC as a result of binding of the Fc portion of immunocomplexed anti-Gal to Fc receptors on APC. This anti-Gal mediated effective uptake of vaccines by APC results in 10-200-fold higher anti-viral immune response and in 8-fold higher survival rate following challenge with a lethal dose of live influenza virus, than same vaccines lacking α-gal epitopes. It is suggested that glycoengineering of carbohydrate chains on the glycan-shield of inactivated SARS-CoV-2 or on S-protein vaccines, for presenting α-gal epitopes, will have similar amplifying effects on vaccine efficacy. α-Gal epitope synthesis on coronavirus vaccines can be achieved with recombinant α1,3galactosyltransferase, replication of the virus in cells with high α1,3galactosyltransferase activity as a result of stable transfection of cells with several copies of the α1,3galactosyltransferase gene (GGTA1), or by transduction of host cells with replication defective adenovirus containing this gene. In addition, recombinant S-protein presenting multiple α-gal epitopes on the glycan-shield may be produced in glycoengineered yeast or bacteria expression systems containing the corresponding glycosyltransferases. Prospective Covid-19 vaccines presenting α-gal epitopes may provide better protection than vaccines lacking this epitope because of increased uptake by APC.
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MESH Headings
- Animals
- Antibodies, Viral/biosynthesis
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Antigens, Viral/metabolism
- Betacoronavirus/drug effects
- Betacoronavirus/immunology
- Betacoronavirus/pathogenicity
- COVID-19
- COVID-19 Vaccines
- Coronavirus Infections/genetics
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/virology
- Dendritic Cells/drug effects
- Dendritic Cells/immunology
- Dendritic Cells/virology
- Genetic Engineering
- HIV Core Protein p24/chemistry
- HIV Core Protein p24/genetics
- HIV Core Protein p24/immunology
- HIV Envelope Protein gp120/chemistry
- HIV Envelope Protein gp120/genetics
- HIV Envelope Protein gp120/immunology
- Humans
- Immunogenicity, Vaccine
- Macrophages/drug effects
- Macrophages/immunology
- Macrophages/virology
- Mice
- Pandemics/prevention & control
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/virology
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/immunology
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Trisaccharides/chemistry
- Trisaccharides/immunology
- Viral Vaccines/administration & dosage
- Viral Vaccines/biosynthesis
- Viral Vaccines/genetics
- Viral Vaccines/immunology
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Affiliation(s)
- Uri Galili
- Department of Medicine, Rush Medical School, Chicago, IL, USA.
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43
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Chang D, Hackett WE, Zhong L, Wan XF, Zaia J. Measuring Site-specific Glycosylation Similarity between Influenza a Virus Variants with Statistical Certainty. Mol Cell Proteomics 2020; 19:1533-1545. [PMID: 32601173 PMCID: PMC8143645 DOI: 10.1074/mcp.ra120.002031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/26/2020] [Indexed: 12/30/2022] Open
Abstract
Influenza A virus (IAV) mutates rapidly, resulting in antigenic drift and poor year-to-year vaccine effectiveness. One challenge in designing effective vaccines is that genetic mutations frequently cause amino acid variations in IAV envelope protein hemagglutinin (HA) that create new N-glycosylation sequons; resulting N-glycans cause antigenic shielding, allowing viral escape from adaptive immune responses. Vaccine candidate strain selection currently involves correlating antigenicity with HA protein sequence among circulating strains, but quantitative comparison of site-specific glycosylation information may likely improve the ability to design vaccines with broader effectiveness against evolving strains. However, there is poor understanding of the influence of glycosylation on immunodominance, antigenicity, and immunogenicity of HA, and there are no well-tested methods for comparing glycosylation similarity among virus samples. Here, we present a method for statistically rigorous quantification of similarity between two related virus strains that considers the presence and abundance of glycopeptide glycoforms. We demonstrate the strength of our approach by determining that there was a quantifiable difference in glycosylation at the protein level between WT IAV HA from A/Switzerland/9715293/2013 (SWZ13) and a mutant strain of SWZ13, even though no N-glycosylation sequons were changed. We determined site-specifically that WT and mutant HA have varying similarity at the glycosylation sites of the head domain, reflecting competing pressures to evade host immune response while retaining viral fitness. To our knowledge, our results are the first to quantify changes in glycosylation state that occur in related proteins of considerable glycan heterogeneity. Our results provide a method for understanding how changes in glycosylation state are correlated with variations in protein sequence, which is necessary for improving IAV vaccine strain selection. Understanding glycosylation will be especially important as we find new expression vectors for vaccine production, as glycosylation state depends greatly on the host species.
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Affiliation(s)
- Deborah Chang
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - William E Hackett
- Boston University Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Lei Zhong
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi, USA
| | - Xiu-Feng Wan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi, USA; MU Center for Research on Influenza Systems Biology (CRISB), University of Missouri, Columbia, Missouri, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA; Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, Missouri, USA; Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA; MU Institute for Data Science & Informatics, University of Missouri, Columbia, Missouri, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA; Boston University Bioinformatics Program, Boston University, Boston, Massachusetts, USA.
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44
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Brooks BD, Closmore A, Yang J, Holland M, Cairns T, Cohen GH, Bailey-Kellogg C. Characterizing Epitope Binding Regions of Entire Antibody Panels by Combining Experimental and Computational Analysis of Antibody: Antigen Binding Competition. Molecules 2020; 25:molecules25163659. [PMID: 32796656 PMCID: PMC7464469 DOI: 10.3390/molecules25163659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 11/16/2022] Open
Abstract
Vaccines and immunotherapies depend on the ability of antibodies to sensitively and specifically recognize particular antigens and specific epitopes on those antigens. As such, detailed characterization of antibody-antigen binding provides important information to guide development. Due to the time and expense required, high-resolution structural characterization techniques are typically used sparingly and late in a development process. Here, we show that antibody-antigen binding can be characterized early in a process for whole panels of antibodies by combining experimental and computational analyses of competition between monoclonal antibodies for binding to an antigen. Experimental "epitope binning" of monoclonal antibodies uses high-throughput surface plasmon resonance to reveal which antibodies compete, while a new complementary computational analysis that we call "dock binning" evaluates antibody-antigen docking models to identify why and where they might compete, in terms of possible binding sites on the antigen. Experimental and computational characterization of the identified antigenic hotspots then enables the refinement of the competitors and their associated epitope binding regions on the antigen. While not performed at atomic resolution, this approach allows for the group-level identification of functionally related monoclonal antibodies (i.e., communities) and identification of their general binding regions on the antigen. By leveraging extensive epitope characterization data that can be readily generated both experimentally and computationally, researchers can gain broad insights into the basis for antibody-antigen recognition in wide-ranging vaccine and immunotherapy discovery and development programs.
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Affiliation(s)
- Benjamin D. Brooks
- Department of Biomedical Sciences, Rocky Vista University, Ivins, UT 84738, USA
- Inovan Inc., Fargo, ND 58102, USA
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
- Correspondence: ; Tel.: +1-435-222-1403
| | - Adam Closmore
- Department of Pharmacy, North Dakota State University, Fargo, ND 58102, USA;
| | - Juechen Yang
- Department of Biomedical Engineering, North Dakota State University, Fargo, ND 58102, USA; (J.Y.); (M.H.)
| | - Michael Holland
- Department of Biomedical Engineering, North Dakota State University, Fargo, ND 58102, USA; (J.Y.); (M.H.)
| | - Tina Cairns
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
| | - Gary H. Cohen
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
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45
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Uddin MB, Hasan M, Harun-Al-Rashid A, Ahsan MI, Imran MAS, Ahmed SSU. Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective. Infect Genet Evol 2020; 84:104440. [PMID: 32622082 PMCID: PMC7327474 DOI: 10.1016/j.meegid.2020.104440] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 12/22/2022]
Abstract
SARS-CoV-2, a new coronavirus strain responsible for COVID-19, has emerged in Wuhan City, China, and continuing its global pandemic nature. The availability of the complete gene sequences of the virus helps to know about the origin and molecular characteristics of this virus. In the present study, we performed bioinformatic analysis of the available gene sequence data of SARS-CoV-2 for the understanding of evolution and molecular characteristics and immunogenic resemblance of the circulating viruses. Phylogenetic analysis was performed for four types of representative viral proteins (spike, membrane, envelope and nucleoprotein) of SARS-CoV-2, HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1, MERS-CoV, HKU4, HKU5 and BufCoV-HKU26. The findings demonstrated that SARS-CoV-2 exhibited convergent evolutionary relation with previously reported SARS-CoV. It was also depicted that SARS-CoV-2 proteins were highly similar and identical to SARS-CoV proteins, though proteins from other coronaviruses showed a lower level of resemblance. The cross-checked conservancy analysis of SARS-CoV-2 antigenic epitopes showed significant conservancy with antigenic epitopes derived from SARS-CoV. Descriptive epidemiological analysis on several epidemiological indices was performed on available epidemiological outbreak information from several open databases on COVID-19 (SARS-CoV-2). Satellite-derived imaging data have been employed to understand the role of temperature in the environmental persistence of the virus. Findings of the descriptive analysis were used to describe the global impact of newly emerged SARS-CoV-2, and the risk of an epidemic in Bangladesh.
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MESH Headings
- Alphacoronavirus/classification
- Alphacoronavirus/genetics
- Alphacoronavirus/metabolism
- Amino Acid Sequence
- Animals
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/metabolism
- Bangladesh/epidemiology
- Base Sequence
- Betacoronavirus/classification
- Betacoronavirus/genetics
- Betacoronavirus/metabolism
- Binding Sites
- COVID-19
- Chiroptera/virology
- Computational Biology
- Coronavirus 229E, Human/classification
- Coronavirus 229E, Human/genetics
- Coronavirus 229E, Human/metabolism
- Coronavirus Infections/epidemiology
- Coronavirus Infections/virology
- Coronavirus NL63, Human/classification
- Coronavirus NL63, Human/genetics
- Coronavirus NL63, Human/metabolism
- Coronavirus OC43, Human/classification
- Coronavirus OC43, Human/genetics
- Coronavirus OC43, Human/metabolism
- Genome, Viral
- Humans
- Middle East Respiratory Syndrome Coronavirus/classification
- Middle East Respiratory Syndrome Coronavirus/genetics
- Middle East Respiratory Syndrome Coronavirus/metabolism
- Models, Molecular
- Mutation
- Nucleoproteins/chemistry
- Nucleoproteins/genetics
- Nucleoproteins/metabolism
- Pandemics
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/virology
- Protein Binding
- Protein Interaction Domains and Motifs
- Severe acute respiratory syndrome-related coronavirus/classification
- Severe acute respiratory syndrome-related coronavirus/genetics
- Severe acute respiratory syndrome-related coronavirus/metabolism
- SARS-CoV-2
- Sequence Alignment
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Viral Envelope Proteins/chemistry
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/metabolism
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Affiliation(s)
- Md Bashir Uddin
- Department of Medicine, Sylhet Agricultural University, Sylhet-3100, Bangladesh.
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Ahmed Harun-Al-Rashid
- Department of Aquatic Resource Management, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Md Irtija Ahsan
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Md Abdus Shukur Imran
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Syed Sayeem Uddin Ahmed
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet-3100, Bangladesh.
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46
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Sia SF, Yan LM, Chin AWH, Fung K, Choy KT, Wong AYL, Kaewpreedee P, Perera RAPM, Poon LLM, Nicholls JM, Peiris M, Yen HL. Pathogenesis and transmission of SARS-CoV-2 in golden hamsters. Nature 2020; 583:834-838. [PMID: 32408338 DOI: 10.21203/rs.3.rs-20774/v1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/07/2020] [Indexed: 05/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus with high nucleotide identity to SARS-CoV and to SARS-related coronaviruses that have been detected in horseshoe bats, has spread across the world and had a global effect on healthcare systems and economies1,2. A suitable small animal model is needed to support the development of vaccines and therapies. Here we report the pathogenesis and transmissibility of SARS-CoV-2 in golden (Syrian) hamsters (Mesocricetus auratus). Immunohistochemistry assay demonstrated the presence of viral antigens in nasal mucosa, bronchial epithelial cells and areas of lung consolidation on days 2 and 5 after inoculation with SARS-CoV-2, followed by rapid viral clearance and pneumocyte hyperplasia at 7 days after inoculation. We also found viral antigens in epithelial cells of the duodenum, and detected viral RNA in faeces. Notably, SARS-CoV-2 was transmitted efficiently from inoculated hamsters to naive hamsters by direct contact and via aerosols. Transmission via fomites in soiled cages was not as efficient. Although viral RNA was continuously detected in the nasal washes of inoculated hamsters for 14 days, the communicable period was short and correlated with the detection of infectious virus but not viral RNA. Inoculated and naturally infected hamsters showed apparent weight loss on days 6-7 post-inoculation or post-contact; all hamsters returned to their original weight within 14 days and developed neutralizing antibodies. Our results suggest that features associated with SARS-CoV-2 infection in golden hamsters resemble those found in humans with mild SARS-CoV-2 infections.
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MESH Headings
- Aerosols
- Alveolar Epithelial Cells/pathology
- Alveolar Epithelial Cells/virology
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Antigens, Viral/immunology
- Antigens, Viral/isolation & purification
- Antigens, Viral/metabolism
- Betacoronavirus/immunology
- Betacoronavirus/isolation & purification
- Betacoronavirus/metabolism
- Betacoronavirus/pathogenicity
- Bronchi/pathology
- Bronchi/virology
- COVID-19
- Coronavirus Infections/immunology
- Coronavirus Infections/transmission
- Coronavirus Infections/virology
- Disease Models, Animal
- Duodenum/virology
- Fomites/virology
- Housing, Animal
- Kidney/virology
- Lung/pathology
- Lung/virology
- Male
- Mesocricetus/immunology
- Mesocricetus/virology
- Nasal Mucosa/virology
- Pandemics
- Pneumonia, Viral/immunology
- Pneumonia, Viral/transmission
- Pneumonia, Viral/virology
- RNA, Viral/analysis
- SARS-CoV-2
- Viral Load
- Weight Loss
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Affiliation(s)
- Sin Fun Sia
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Li-Meng Yan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Alex W H Chin
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kevin Fung
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ka-Tim Choy
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Alvina Y L Wong
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Prathanporn Kaewpreedee
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ranawaka A P M Perera
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - John M Nicholls
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hui-Ling Yen
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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47
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Lindesmith LC, Brewer-Jensen PD, Mallory ML, Jensen K, Yount BL, Costantini V, Collins MH, Edwards CE, Sheahan TP, Vinjé J, Baric RS. Virus-Host Interactions Between Nonsecretors and Human Norovirus. Cell Mol Gastroenterol Hepatol 2020; 10:245-267. [PMID: 32289501 PMCID: PMC7301201 DOI: 10.1016/j.jcmgh.2020.03.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Human norovirus infection is the leading cause of acute gastroenteritis. Genetic polymorphisms, mediated by the FUT2 gene (secretor enzyme), define strain susceptibility. Secretors express a diverse set of fucosylated histoblood group antigen carbohydrates (HBGA) on mucosal cells; nonsecretors (FUT2-/-) express a limited array of HBGAs. Thus, nonsecretors have less diverse norovirus strain infections, including resistance to the epidemiologically dominant GII.4 strains. Because future human norovirus vaccines will comprise GII.4 antigen and because secretor phenotype impacts GII.4 infection and immunity, nonsecretors may mimic young children immunologically in response to GII.4 vaccination, providing a needed model to study cross-protection in the context of limited pre-exposure. METHODS By using specimens collected from the first characterized nonsecretor cohort naturally infected with GII.2 human norovirus, we evaluated the breadth of serologic immunity by surrogate neutralization assays, and cellular activation and cytokine production by flow cytometry. RESULTS GII.2 infection resulted in broad antibody and cellular immunity activation that persisted for at least 30 days for T cells, monocytes, and dendritic cells, and for 180 days for blocking antibody. Multiple cellular lineages expressing interferon-γ and tumor necrosis factor-α dominated the response. Both T-cell and B-cell responses were cross-reactive with other GII strains, but not GI strains. To promote entry mechanisms, inclusion of bile acids was essential for GII.2 binding to nonsecretor HBGAs. CONCLUSIONS These data support development of within-genogroup, cross-reactive antibody and T-cell immunity, key outcomes that may provide the foundation for eliciting broad immune responses after GII.4 vaccination in individuals with limited GII.4 immunity, including young children.
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Affiliation(s)
- Lisa C Lindesmith
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Paul D Brewer-Jensen
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Michael L Mallory
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Kara Jensen
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Veronica Costantini
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Matthew H Collins
- Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Decatur, Georgia
| | - Caitlin E Edwards
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina.
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48
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Messick TE, Tolvinski L, Zartler ER, Moberg A, Frostell Å, Smith GR, Reitz AB, Lieberman PM. Biophysical Screens Identify Fragments That Bind to the Viral DNA-Binding Proteins EBNA1 and LANA. Molecules 2020; 25:molecules25071760. [PMID: 32290261 PMCID: PMC7180839 DOI: 10.3390/molecules25071760] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 12/17/2022] Open
Abstract
The human gamma-herpesviruses Epstein-Barr virus (EBV) (HHV-4) and Kaposi's sarcoma-associated herpesvirus (KSHV) (HHV-8) are responsible for a number of diseases, including various types of cancer. Epstein-Barr nuclear antigen 1 (EBNA1) from EBV and latency-associated nuclear antigen (LANA) from KSHV are viral-encoded DNA-binding proteins that are essential for the replication and maintenance of their respective viral genomes during latent, oncogenic infection. As such, EBNA1 and LANA are attractive targets for the development of small-molecule inhibitors. To this end, we performed a biophysical screen of EBNA1 and LANA using a fragment library by saturation transfer difference (STD)-NMR spectroscopy and surface plasmon resonance (SPR). We identified and validated a number of unique fragment hits that bind to EBNA1 or LANA. We also determined the high-resolution crystal structure of one fragment bound to EBNA1. Results from this screening cascade provide new chemical starting points for the further development of potent inhibitors for this class of viral proteins.
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Affiliation(s)
- Troy E. Messick
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA;
- Correspondence: (T.E.M.); (P.M.L.); Tel.: +215-898-3896 (T.E.M.); +215-898-9523 (P.M.L.)
| | - Lois Tolvinski
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA;
| | | | - Anna Moberg
- GE Healthcare Bio-Sciences AB, Björkgatan 30, SE-751 84 Uppsala, Sweden; (A.M.); (Å.F.)
| | - Åsa Frostell
- GE Healthcare Bio-Sciences AB, Björkgatan 30, SE-751 84 Uppsala, Sweden; (A.M.); (Å.F.)
| | - Garry R. Smith
- Fox Chase Chemical Diversity Center, Inc., 3805 Old Easton Road, Doylestown, PA 18902, USA; (G.R.S.); (A.B.R.)
| | - Allen B. Reitz
- Fox Chase Chemical Diversity Center, Inc., 3805 Old Easton Road, Doylestown, PA 18902, USA; (G.R.S.); (A.B.R.)
| | - Paul M. Lieberman
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA;
- Correspondence: (T.E.M.); (P.M.L.); Tel.: +215-898-3896 (T.E.M.); +215-898-9523 (P.M.L.)
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49
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Jacob JJ, Vasudevan K, Veeraraghavan B, Iyadurai R, Gunasekaran K. Genomic evolution of severe acute respiratory syndrome Coronavirus 2 in India and vaccine impact. Indian J Med Microbiol 2020; 38:210-212. [PMID: 32883935 PMCID: PMC7709607 DOI: 10.4103/ijmm.ijmm_20_303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/04/2020] [Accepted: 07/27/2020] [Indexed: 12/28/2022]
Abstract
Recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and subsequent containment procedures have impacted the world as never seen before. Therefore, there is considerable curiosity about the genome evolution related to the origin, transmission and vaccine impact of this virus. We have analysed genome sequences of SARS-CoV-2 isolated from Indian patients to gain an in-depth understanding of genomic evolution and transmission in India. Phylogenetic analysis and mutation profiling revealed major lineages being evolved by characteristic mutations. As the mutation frequency in spike protein is comparatively lesser, the candidate vaccines expected to have wide coverage worldwide including India.
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MESH Headings
- Animals
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Antigens, Viral/metabolism
- Betacoronavirus/classification
- Betacoronavirus/genetics
- Betacoronavirus/immunology
- Betacoronavirus/pathogenicity
- COVID-19
- COVID-19 Vaccines
- Chiroptera/virology
- Coronavirus Infections/epidemiology
- Coronavirus Infections/genetics
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/transmission
- Disease Reservoirs/virology
- Eutheria/virology
- Evolution, Molecular
- Genome, Viral
- Humans
- India/epidemiology
- Mutation
- Pandemics/prevention & control
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/transmission
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Viral Vaccines/biosynthesis
- Viral Vaccines/genetics
- Viral Vaccines/immunology
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Affiliation(s)
- Jobin John Jacob
- Division of Molecular Biology and Translational Bioinformatics, Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Karthick Vasudevan
- Division of Molecular Biology and Translational Bioinformatics, Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Hilda Lazarus Core Research Chair, Christian Medical College, Vellore, Tamil Nadu, India
| | - Ramya Iyadurai
- Department of General Medicine, Unit V, Christian Medical College, Vellore, Tamil Nadu, India
| | - Karthik Gunasekaran
- Department of General Medicine, Unit V, Christian Medical College, Vellore, Tamil Nadu, India
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50
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Wu NC, Otwinowski J, Thompson AJ, Nycholat CM, Nourmohammad A, Wilson IA. Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape. Nat Commun 2020; 11:1233. [PMID: 32144244 PMCID: PMC7060233 DOI: 10.1038/s41467-020-15102-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 02/15/2020] [Indexed: 01/07/2023] Open
Abstract
Antigenic drift of influenza virus hemagglutinin (HA) is enabled by facile evolvability. However, HA antigenic site B, which has become immunodominant in recent human H3N2 influenza viruses, is also evolutionarily constrained by its involvement in receptor binding. Here, we employ deep mutational scanning to probe the local fitness landscape of HA antigenic site B in six different human H3N2 strains spanning from 1968 to 2016. We observe that the fitness landscape of HA antigenic site B can be very different between strains. Sequence variants that exhibit high fitness in one strain can be deleterious in another, indicating that the evolutionary constraints of antigenic site B have changed over time. Structural analysis suggests that the local fitness landscape of antigenic site B can be reshaped by natural mutations via modulation of the receptor-binding mode. Overall, these findings elucidate how influenza virus continues to explore new antigenic space despite strong functional constraints.
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MESH Headings
- Animals
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Antigens, Viral/metabolism
- Binding Sites/genetics
- Crystallography, X-Ray
- DNA Mutational Analysis
- Dogs
- Evolution, Molecular
- HEK293 Cells
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Humans
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza A Virus, H3N2 Subtype/metabolism
- Madin Darby Canine Kidney Cells
- Mutation
- Protein Domains/genetics
- Protein Domains/immunology
- RNA, Viral/genetics
- RNA, Viral/isolation & purification
- Receptors, Cell Surface/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
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Affiliation(s)
- Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jakub Otwinowski
- Max Planck Institute for Dynamics and Self-Organization, 37077, Göttingen, Germany
| | - Andrew J Thompson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Corwin M Nycholat
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Armita Nourmohammad
- Max Planck Institute for Dynamics and Self-Organization, 37077, Göttingen, Germany
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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