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Begum MSTM, Bokani A, Rajib SA, Soleimanpour M, Maeda Y, Yoshimura K, Satou Y, Ebrahimi D, Ikeda T. Potential Role of APOBEC3 Family Proteins in SARS-CoV-2 Replication. Viruses 2024; 16:1141. [PMID: 39066304 PMCID: PMC11281575 DOI: 10.3390/v16071141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has acquired multiple mutations since its emergence. Analyses of the SARS-CoV-2 genomes from infected patients exhibit a bias toward C-to-U mutations, which are suggested to be caused by the apolipoprotein B mRNA editing enzyme polypeptide-like 3 (APOBEC3, A3) cytosine deaminase proteins. However, the role of A3 enzymes in SARS-CoV-2 replication remains unclear. To address this question, we investigated the effect of A3 family proteins on SARS-CoV-2 replication in the myeloid leukemia cell line THP-1 lacking A3A to A3G genes. The Wuhan, BA.1, and BA.5 variants had comparable viral replication in parent and A3A-to-A3G-null THP-1 cells stably expressing angiotensin-converting enzyme 2 (ACE2) protein. On the other hand, the replication and infectivity of these variants were abolished in A3A-to-A3G-null THP-1-ACE2 cells in a series of passage experiments over 20 days. In contrast to previous reports, we observed no evidence of A3-induced SARS-CoV-2 mutagenesis in the passage experiments. Furthermore, our analysis of a large number of publicly available SARS-CoV-2 genomes did not reveal conclusive evidence for A3-induced mutagenesis. Our studies suggest that A3 family proteins can positively contribute to SARS-CoV-2 replication; however, this effect is deaminase-independent.
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Affiliation(s)
- MST Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Ayub Bokani
- School of Engineering and Technology, CQ University, Sydney, NSW 2000, Australia
| | - Samiul Alam Rajib
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| | | | - Yosuke Maeda
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Department of Nursing, Kibi International University, Takahashi 716-8508, Japan
| | | | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Diako Ebrahimi
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
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2
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Shichijo T, Yasunaga JI, Sato K, Nosaka K, Toyoda K, Watanabe M, Zhang W, Koyanagi Y, Murphy EL, Bruhn RL, Koh KR, Akari H, Ikeda T, Harris RS, Green PL, Matsuoka M. Vulnerability to APOBEC3G linked to the pathogenicity of deltaretroviruses. Proc Natl Acad Sci U S A 2024; 121:e2309925121. [PMID: 38502701 PMCID: PMC10990082 DOI: 10.1073/pnas.2309925121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/29/2024] [Indexed: 03/21/2024] Open
Abstract
Human retroviruses are derived from simian ones through cross-species transmission. These retroviruses are associated with little pathogenicity in their natural hosts, but in humans, HIV causes AIDS, and human T-cell leukemia virus type 1 (HTLV-1) induces adult T-cell leukemia-lymphoma (ATL). We analyzed the proviral sequences of HTLV-1, HTLV-2, and simian T-cell leukemia virus type 1 (STLV-1) from Japanese macaques (Macaca fuscata) and found that APOBEC3G (A3G) frequently generates G-to-A mutations in the HTLV-1 provirus, whereas such mutations are rare in the HTLV-2 and STLV-1 proviruses. Therefore, we investigated the mechanism of how HTLV-2 is resistant to human A3G (hA3G). HTLV-1, HTLV-2, and STLV-1 encode the so-called antisense proteins, HTLV-1 bZIP factor (HBZ), Antisense protein of HTLV-2 (APH-2), and STLV-1 bZIP factor (SBZ), respectively. APH-2 efficiently inhibits the deaminase activity of both hA3G and simian A3G (sA3G). HBZ and SBZ strongly suppress sA3G activity but only weakly inhibit hA3G, suggesting that HTLV-1 is incompletely adapted to humans. Unexpectedly, hA3G augments the activation of the transforming growth factor (TGF)-β/Smad pathway by HBZ, and this activation is associated with ATL cell proliferation by up-regulating BATF3/IRF4 and MYC. In contrast, the combination of APH-2 and hA3G, or the combination of SBZ and sA3G, does not enhance the TGF-β/Smad pathway. Thus, HTLV-1 is vulnerable to hA3G but utilizes it to promote the proliferation of infected cells via the activation of the TGF-β/Smad pathway. Antisense factors in each virus, differently adapted to control host cellular functions through A3G, seem to dictate the pathogenesis.
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Affiliation(s)
- Takafumi Shichijo
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto860-8556, Japan
- Laboratory of Virus Control, Institute for Life and Medical Sciences, Kyoto University, Kyoto606-8507, Japan
| | - Jun-ichirou Yasunaga
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto860-8556, Japan
- Laboratory of Virus Control, Institute for Life and Medical Sciences, Kyoto University, Kyoto606-8507, Japan
| | - Kei Sato
- Division of Systems Virology, Institute of Medical Science, The University of Tokyo, Tokyo108-8639, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama332-0012, Japan
| | - Kisato Nosaka
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto860-8556, Japan
| | - Kosuke Toyoda
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto860-8556, Japan
- Laboratory of Virus Control, Institute for Life and Medical Sciences, Kyoto University, Kyoto606-8507, Japan
| | - Miho Watanabe
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto860-8556, Japan
| | - Wenyi Zhang
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto860-8556, Japan
| | - Yoshio Koyanagi
- Laboratory of Systems Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto606-8507, Japan
| | - Edward L. Murphy
- Department of Laboratory Medicine, University of California, San Francisco94158
- Department of Epidemiology/Biostatistics, University of California, San Francisco
- Vitalant Research Institute, San Francisco94105
| | | | - Ki-Ryang Koh
- Department of Hematology, Osaka General Hospital of West Japan Railway Company, Osaka545-0053, Japan
| | - Hirofumi Akari
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi484-8506, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto860-0811, Japan
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX78229
- HHMI, University of Texas Health San Antonio, San Antonio, TX78229
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX78229
- HHMI, University of Texas Health San Antonio, San Antonio, TX78229
| | - Patrick L. Green
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, OH43210
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH
| | - Masao Matsuoka
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto860-8556, Japan
- Laboratory of Virus Control, Institute for Life and Medical Sciences, Kyoto University, Kyoto606-8507, Japan
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3
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Timmerman AL, Schönert ALM, van der Hoek L. Anelloviruses versus human immunity: how do we control these viruses? FEMS Microbiol Rev 2024; 48:fuae005. [PMID: 38337179 PMCID: PMC10883694 DOI: 10.1093/femsre/fuae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/22/2023] [Accepted: 02/08/2024] [Indexed: 02/12/2024] Open
Abstract
One continuous companion and one of the major players in the human blood virome are members of the Anelloviridae family. Anelloviruses are probably found in all humans, infection occurs early in life and the composition (anellome) is thought to remain stable and personal during adulthood. The stable anellome implies a great balance between the host immune system and the virus. However, the lack of a robust culturing system hampers direct investigation of interactions between virus and host cells. Other techniques, however, including next generation sequencing, AnelloScan-antibody tests, evolution selection pressure analysis, and virus protein structures, do provide new insights into the interactions between anelloviruses and the host immune system. This review aims at providing an overview of the current knowledge on the immune mechanisms acting on anelloviruses and the countering viral mechanisms allowing immune evasion.
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Affiliation(s)
- Anne L Timmerman
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
| | - Antonia L M Schönert
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
| | - Lia van der Hoek
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
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4
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Timmerman AL, Commandeur L, Deijs M, Burggraaff MGJM, Lavell AHA, van der Straten K, Tejjani K, van Rijswijk J, van Gils MJ, Sikkens JJ, Bomers MK, van der Hoek L. The Impact of First-Time SARS-CoV-2 Infection on Human Anelloviruses. Viruses 2024; 16:99. [PMID: 38257799 PMCID: PMC10818381 DOI: 10.3390/v16010099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Members of the Anelloviridae family dominate the blood virome, emerging early in life. The anellome, representing the variety of anelloviruses within an individual, stabilizes by adulthood. Despite their supposedly commensal nature, elevated anellovirus concentrations under immunosuppressive treatment indicate an equilibrium controlled by immunity. Here, we investigated whether anelloviruses are sensitive to the immune activation that accompanies a secondary infection. As a model, we investigated 19 health care workers (HCWs) with initial SARS-CoV-2 infection, with blood sampling performed pre and post infection every 4 weeks in a 3-month-follow-up during the early 2020 COVID-19 pandemic. A concurrently followed control group (n = 27) remained SARS-CoV-2-negative. Serum anellovirus loads were measured using qPCR. A significant decrease in anellovirus load was found in the first weeks after SARS-CoV-2 infection, whereas anellovirus concentrations remained stable in the uninfected control group. A restored anellovirus load was seen approximately 10 weeks after SARS-CoV-2 infection. For five subjects, an in-time anellome analysis via Illumina sequencing could be performed. In three of the five HCWs, the anellome visibly changed during SARS-CoV-2 infection and returned to baseline in two of these cases. In conclusion, anellovirus loads in blood can temporarily decrease upon an acute secondary infection.
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Affiliation(s)
- Anne L. Timmerman
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Lisanne Commandeur
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Maarten G. J. M. Burggraaff
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - A. H. Ayesha Lavell
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
- Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Karlijn van der Straten
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Khadija Tejjani
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Jacqueline van Rijswijk
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Marit J. van Gils
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Jonne J. Sikkens
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
- Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Marije K. Bomers
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
- Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
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5
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Butic AB, Spencer SA, Shaheen SK, Lukacher AE. Polyomavirus Wakes Up and Chooses Neurovirulence. Viruses 2023; 15:2112. [PMID: 37896889 PMCID: PMC10612099 DOI: 10.3390/v15102112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
JC polyomavirus (JCPyV) is a human-specific polyomavirus that establishes a silent lifelong infection in multiple peripheral organs, predominantly those of the urinary tract, of immunocompetent individuals. In immunocompromised settings, however, JCPyV can infiltrate the central nervous system (CNS), where it causes several encephalopathies of high morbidity and mortality. JCPyV-induced progressive multifocal leukoencephalopathy (PML), a devastating demyelinating brain disease, was an AIDS-defining illness before antiretroviral therapy that has "reemerged" as a complication of immunomodulating and chemotherapeutic agents. No effective anti-polyomavirus therapeutics are currently available. How depressed immune status sets the stage for JCPyV resurgence in the urinary tract, how the virus evades pre-existing antiviral antibodies to become viremic, and where/how it enters the CNS are incompletely understood. Addressing these questions requires a tractable animal model of JCPyV CNS infection. Although no animal model can replicate all aspects of any human disease, mouse polyomavirus (MuPyV) in mice and JCPyV in humans share key features of peripheral and CNS infection and antiviral immunity. In this review, we discuss the evidence suggesting how JCPyV migrates from the periphery to the CNS, innate and adaptive immune responses to polyomavirus infection, and how the MuPyV-mouse model provides insights into the pathogenesis of JCPyV CNS disease.
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Affiliation(s)
| | | | | | - Aron E. Lukacher
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (A.B.B.); (S.A.S.); (S.K.S.)
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6
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Fanunza E, Cheng AZ, Auerbach AA, Stefanovska B, Moraes SN, Lokensgard JR, Biolatti M, Dell'Oste V, Bierle CJ, Bresnahan WA, Harris RS. Human cytomegalovirus mediates APOBEC3B relocalization early during infection through a ribonucleotide reductase-independent mechanism. J Virol 2023; 97:e0078123. [PMID: 37565748 PMCID: PMC10506462 DOI: 10.1128/jvi.00781-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/21/2023] [Indexed: 08/12/2023] Open
Abstract
The APOBEC3 family of DNA cytosine deaminases comprises an important arm of the innate antiviral defense system. The gamma-herpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus and the alpha-herpesviruses herpes simplex virus (HSV)-1 and HSV-2 have evolved an efficient mechanism to avoid APOBEC3 restriction by directly binding to APOBEC3B and facilitating its exclusion from the nuclear compartment. The only viral protein required for APOBEC3B relocalization is the large subunit of the ribonucleotide reductase (RNR). Here, we ask whether this APOBEC3B relocalization mechanism is conserved with the beta-herpesvirus human cytomegalovirus (HCMV). Although HCMV infection causes APOBEC3B relocalization from the nucleus to the cytoplasm in multiple cell types, the viral RNR (UL45) is not required. APOBEC3B relocalization occurs rapidly following infection suggesting the involvement of an immediate early or early (IE/E) viral protein. In support of this possibility, genetic (IE1 mutant) and pharmacologic (cycloheximide) strategies that prevent the expression of IE/E viral proteins also block APOBEC3B relocalization. In comparison, the treatment of infected cells with phosphonoacetic acid, which interferes with viral late protein expression, still permits A3B relocalization. These results combine to indicate that the beta-herpesvirus HCMV uses an RNR-independent, yet phenotypically similar, molecular mechanism to antagonize APOBEC3B. IMPORTANCE Human cytomegalovirus (HCMV) infections can range from asymptomatic to severe, particularly in neonates and immunocompromised patients. HCMV has evolved strategies to overcome host-encoded antiviral defenses to achieve lytic viral DNA replication and dissemination and, under some conditions, latency and long-term persistence. Here, we show that HCMV infection causes the antiviral factor, APOBEC3B, to relocalize from the nuclear compartment to the cytoplasm. This overall strategy resembles that used by related herpesviruses. However, the HCMV relocalization mechanism utilizes a different viral factor(s) and available evidence suggests the involvement of at least one protein expressed at the early stages of infection. This knowledge is important because a greater understanding of this mechanism could lead to novel antiviral strategies that enable APOBEC3B to naturally restrict HCMV infection.
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Affiliation(s)
- Elisa Fanunza
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Cagilari, Italy
| | - Adam Z. Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ashley A. Auerbach
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Bojana Stefanovska
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - James R. Lokensgard
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Valentina Dell'Oste
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Craig J. Bierle
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wade A. Bresnahan
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
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7
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Delamonica B, Davalos L, Larijani M, Anthony SJ, Liu J, MacCarthy T. Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes. Virus Evol 2023; 9:vead047. [PMID: 37577211 PMCID: PMC10422979 DOI: 10.1093/ve/vead047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/27/2023] [Accepted: 07/26/2023] [Indexed: 08/15/2023] Open
Abstract
APOBEC3, an enzyme subfamily that plays a role in virus restriction by generating mutations at particular DNA motifs or mutational 'hotspots', can drive viral mutagenesis with host-specific preferential hotspot mutations contributing to pathogen variation. While previous analysis of viral genomes from the 2022 Mpox (formerly Monkeypox) disease outbreak has shown a high frequency of C>T mutations at TC motifs, suggesting recent mutations are human APOBEC3-mediated, how emerging monkeypox virus (MPXV) strains will evolve as a consequence of APOBEC3-mediated mutations remains unknown. By measuring hotspot under-representation, depletion at synonymous sites, and a combination of the two, we analyzed APOBEC3-driven evolution in human poxvirus genomes, finding varying hotspot under-representation patterns. While the native poxvirus molluscum contagiosum exhibits a signature consistent with extensive coevolution with human APOBEC3, including depletion of TC hotspots, variola virus shows an intermediate effect consistent with ongoing evolution at the time of eradication. MPXV, likely the result of recent zoonosis, showed many genes with more TC hotspots than expected by chance (over-representation) and fewer GC hotspots than expected (under-representation). These results suggest the MPXV genome: (1) may have evolved in a host with a particular APOBEC GC hotspot preference, (2) has inverted terminal repeat (ITR) regions-which may be exposed to APOBEC3 for longer during viral replication-and longer genes likely to evolve faster, and therefore (3) has a heightened potential for future human APOBEC3-meditated evolution as the virus spreads in the human population. Our predictions of MPXV mutational potential can both help guide future vaccine development and identification of putative drug targets and add urgency to the task of containing human Mpox disease transmission and uncovering the ecology of the virus in its reservoir host.
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Affiliation(s)
- Brenda Delamonica
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Liliana Davalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mani Larijani
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Department of Pathology, Microbiology, and Immunology, University of California-Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California-Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Jia Liu
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR 72205, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
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8
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Burk RD, Mirabello L, DeSalle R. Distinguishing Genetic Drift from Selection in Papillomavirus Evolution. Viruses 2023; 15:1631. [PMID: 37631973 PMCID: PMC10458755 DOI: 10.3390/v15081631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history, but the role of selection on and the drift of non-coding DNA motifs on HPV diversification is poorly understood. In this study, more than a thousand complete genomes representing Alphapapillomavirus types, lineages, and SNP variants were examined phylogenetically and interrogated for the number and position of non-coding DNA sequence motifs using Principal Components Analyses, Ancestral State Reconstructions, and Phylogenetic Independent Contrasts. For anciently diverged Alphapapillomavirus types, composition of the four nucleotides (A, C, G, T), codon usage, trimer usage, and 13 established non-coding DNA sequence motifs revealed phylogenetic clusters consistent with genetic drift. Ancestral state reconstruction and Phylogenetic Independent Contrasts revealed ancient genome alterations, particularly for the CpG and APOBEC3 motifs. Each evolutionary analytical method we performed supports the unanticipated conclusion that genetic drift and different evolutionary drivers have structured Alphapapillomavirus genomes in distinct ways during successive epochs, even extending to differences in more recently formed variant lineages.
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Affiliation(s)
- Robert D. Burk
- Departments of Pediatrics, Microbiology & Immunology, Epidemiology & Population Health, Obstetrics, Gynecology and Woman’s Health, and Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Robert DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
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9
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Delamonica B, Davalos L, Larijani M, Anthony SJ, Liu J, MacCarthy T. Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546779. [PMID: 37425914 PMCID: PMC10326987 DOI: 10.1101/2023.06.27.546779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
APOBEC3, an enzyme subfamily that plays a role in virus restriction by generating mutations at particular DNA motifs or mutational "hotspots," can drive viral mutagenesis with host-specific preferential hotspot mutations contributing to pathogen variation. While previous analysis of viral genomes from the 2022 Mpox (formerly Monkeypox) disease outbreak has shown a high frequency of C>T mutations at T C motifs, suggesting recent mutations are human APOBEC3-mediated, how emerging monkeypox virus (MPXV) strains will evolve as a consequence of APOBEC3-mediated mutations remains unknown. By measuring hotspot under-representation, depletion at synonymous sites, and a combination of the two, we analyzed APOBEC3-driven evolution in human poxvirus genomes, finding varying hotspot under-representation patterns. While the native poxvirus molluscum contagiosum exhibits a signature consistent with extensive coevolution with human APOBEC3, including depletion of T C hotspots, variola virus shows an intermediate effect consistent with ongoing evolution at the time of eradication. MPXV, likely the result of recent zoonosis, showed many genes with more T C hotspots than expected by chance (over-representation) and fewer G C hotspots than expected (under-representation). These results suggest the MPXV genome: 1) may have evolved in a host with a particular APOBEC G C hotspot preference, 2) has inverted terminal repeat (ITR) regions -which may be exposed to APOBEC3 for longer during viral replication- and longer genes likely to evolve faster, and therefore 3) has a heightened potential for future human APOBEC3-meditated evolution as the virus spreads in the human population. Our predictions of MPXV mutational potential can both help guide future vaccine development and identification of putative drug targets and add urgency to the task of containing human Mpox disease transmission and uncovering the ecology of the virus in its reservoir host.
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Affiliation(s)
- Brenda Delamonica
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Liliana Davalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA; Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Mani Larijani
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada; Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California-Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Jia Liu
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
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10
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Starrett GJ, Yu K, Golubeva Y, Lenz P, Piaskowski ML, Petersen D, Dean M, Israni A, Hernandez BY, Tucker TC, Cheng I, Gonsalves L, Morris CR, Hussain SK, Lynch CF, Harris RS, Prokunina-Olsson L, Meltzer PS, Buck CB, Engels EA. Evidence for virus-mediated oncogenesis in bladder cancers arising in solid organ transplant recipients. eLife 2023; 12:e82690. [PMID: 36961501 PMCID: PMC10446826 DOI: 10.7554/elife.82690] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 03/22/2023] [Indexed: 03/25/2023] Open
Abstract
A small percentage of bladder cancers in the general population have been found to harbor DNA viruses. In contrast, up to 25% of tumors of solid organ transplant recipients, who are at an increased risk of developing bladder cancer and have an overall poorer outcomes, harbor BK polyomavirus (BKPyV). To better understand the biology of the tumors and the mechanisms of carcinogenesis from potential oncoviruses, we performed whole genome and transcriptome sequencing on bladder cancer specimens from 43 transplant patients. Nearly half of the tumors from this patient population contained viral sequences. The most common were from BKPyV (N=9, 21%), JC polyomavirus (N=7, 16%), carcinogenic human papillomaviruses (N=3, 7%), and torque teno viruses (N=5, 12%). Immunohistochemistry revealed variable Large T antigen expression in BKPyV-positive tumors ranging from 100% positive staining of tumor tissue to less than 1%. In most cases of BKPyV-positive tumors, the viral genome appeared to be clonally integrated into the host chromosome consistent with microhomology-mediated end joining and coincided with focal amplifications of the tumor genome similar to other virus-mediated cancers. Significant changes in host gene expression consistent with the functions of BKPyV Large T antigen were also observed in these tumors. Lastly, we identified four mutation signatures in our cases, with those attributable to APOBEC3 and SBS5 being the most abundant. Mutation signatures associated with an antiviral drug, ganciclovir, and aristolochic acid, a nephrotoxic compound found in some herbal medicines, were also observed. The results suggest multiple pathways to carcinogenesis in solid organ transplant recipients with a large fraction being virus-associated.
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Affiliation(s)
| | - Kelly Yu
- DCEG, NCI, NIHRockvilleUnited States
| | | | - Petra Lenz
- Leidos Biomedical Research IncFrederickUnited States
| | | | | | | | - Ajay Israni
- Department of Medicine, Nephrology Division, Hennepin Healthcare System, University of MinnesotaMinneapolisUnited States
| | | | - Thomas C Tucker
- The Kentucky Cancer Registry, University of KentuckyLexingtonUnited States
| | - Iona Cheng
- Department of Epidemiology and Biostatistics,and Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoFremontUnited States
| | - Lou Gonsalves
- Connecticut Tumor Registry, Connecticut Department of Public HealthHartfordUnited States
| | - Cyllene R Morris
- California Cancer Reporting and Epidemiologic Surveillance Program, University of California, DavisDavisUnited States
| | - Shehnaz K Hussain
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Charles F Lynch
- The Iowa Cancer Registry, University of IowaIowa CityUnited States
| | - Reuben S Harris
- Howard Hughes Medical Institute, University of MinnesotaMinneapolisUnited States
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11
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An APOBEC3 Mutational Signature in the Genomes of Human-Infecting Orthopoxviruses. mSphere 2023; 8:e0006223. [PMID: 36920219 PMCID: PMC10117092 DOI: 10.1128/msphere.00062-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
The ongoing worldwide monkeypox outbreak is caused by viral lineages (globally referred to as hMPXV1) that are related to but distinct from clade IIb MPXV viruses transmitted within Nigeria. Analysis of the genetic differences has indicated that APOBEC-mediated editing might be responsible for the unexpectedly high number of mutations observed in hMPXV1 genomes. Here, using 1,624 publicly available hMPXV1 sequences, we analyzed the mutations that accrued between 2017 and the emergence of the current predominant variant (B.1), as well as those that that have been accumulating during the 2022 outbreak. We confirmed an overwhelming prevalence of C-to-T and G-to-A mutations, with a sequence context (5'-TC-3') consistent with the preferences of several human APOBEC3 enzymes. We also found that mutations preferentially occur in highly expressed viral genes, although no transcriptional asymmetry was observed. A comparison of the mutation spectrum and context was also performed against the human-specific variola virus (VARV) and the zoonotic cowpox virus (CPXV), as well as fowlpox virus (FWPV). The results indicated that in VARV genomes, C-to-T and G-to-A changes were more common than the opposite substitutions, although the effect was less marked than for hMPXV1. Conversely, no preference toward C-to-T and G-to-A changes was observed in CPXV and FWPV. Consistently, the sequence context of C-to-T changes confirmed a preference for a T in the -1 position for VARV, but not for CPXV or FWPV. Overall, our results strongly support the view that, irrespective of the transmission route, orthopoxviruses infecting humans are edited by the host APOBEC3 enzymes. IMPORTANCE Analysis of the viral lineages responsible for the 2022 monkeypox outbreak suggested that APOBEC enzymes are driving hMPXV1 evolution. Using 1,624 public sequences, we analyzed the mutations that accumulated between 2017 and the emergence of the predominant variant and those that characterize the last outbreak. We found that the mutation spectrum of hMPXV1 has been dominated by TC-to-TT and GA-to-AA changes, consistent with the editing activity of human APOBEC3 proteins. We also found that mutations preferentially affect highly expressed viral genes, possibly because transcription exposes single-stranded DNA (ssDNA), a target of APOBEC3 editing. Notably, analysis of the human-specific variola virus (VARV) and the zoonotic cowpox virus (CPXV) indicated that in VARV genomes, TC-to-TT and GA-to-AA changes are likewise extremely frequent. Conversely, no preference toward TC-to-TT and GA-to-AA changes is observed in CPXV. These results suggest that APOBEC3 proteins have an impact on the evolution of different human-infecting orthopoxviruses.
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12
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Karakasiliotis I, Lagopati N, Evangelou K, Gorgoulis VG. Cellular senescence as a source of SARS-CoV-2 quasispecies. FEBS J 2023; 290:1384-1392. [PMID: 34653312 DOI: 10.1111/febs.16230] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/09/2021] [Accepted: 10/14/2021] [Indexed: 02/01/2023]
Abstract
In-depth analysis of SARS-CoV-2 biology and pathogenesis is rapidly unraveling the mechanisms through which the virus induces all aspects of COVID-19 pathology. Emergence of hundreds of variants and several important variants of concern has focused research on the mechanistic elucidation of virus mutagenesis. RNA viruses evolve quickly either through the error-prone polymerase or the RNA-editing machinery of the cell. In this review, we are discussing the links between cellular senescence, a natural aging process that has been recently linked to SARS-CoV-2 infection, and virus mutagenesis through the RNA-editing enzymes APOBEC. The action of APOBEC, enhanced by cellular senescence, is hypothesized to assist the emergence of novel variants, called quasispecies, within a cell or organism. These variants when introduced to the community may lead to the generation of a variant of concern, depending on fitness and transmissibility of the new genome. Such a mechanism of virus evolution may highlight the importance of inhibitors of cellular senescence during SARS-CoV-2 clinical treatment.
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Affiliation(s)
- Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Nefeli Lagopati
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, Greece.,Biomedical Research Foundation, Academy of Athens, Greece
| | - Konstantinos Evangelou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, Greece
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, Greece.,Biomedical Research Foundation, Academy of Athens, Greece.,Faculty Institute for Cancer Sciences, Manchester Academic Health Sciences Centre, University of Manchester, UK.,Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, Greece.,Faculty of Health and Medical Sciences, University of Surrey, UK
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13
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The APOBEC3B cytidine deaminase is an adenovirus restriction factor. PLoS Pathog 2023; 19:e1011156. [PMID: 36745676 PMCID: PMC9934312 DOI: 10.1371/journal.ppat.1011156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/16/2023] [Accepted: 01/26/2023] [Indexed: 02/07/2023] Open
Abstract
Human adenoviruses (HAdVs) are a large family of DNA viruses counting more than a hundred strains divided into seven species (A to G). HAdVs induce respiratory tract infections, gastroenteritis and conjunctivitis. APOBEC3B is a cytidine deaminase that restricts several DNA viruses. APOBEC3B is also implicated in numerous cancers where it is responsible for the introduction of clustered mutations into the cellular genome. In this study, we demonstrate that APOBEC3B is an adenovirus restriction factor acting through a deaminase-dependent mechanism. APOBEC3B introduces C-to-T clustered mutations into the adenovirus genome. APOBEC3B reduces the propagation of adenoviruses by limiting viral genome replication, progression to late phase, and production of infectious virions. APOBEC3B restriction efficiency varies between adenoviral strains, the A12 strain being more sensitive to APOBEC3B than the B3 or C2 strains. In A12-infected cells, APOBEC3B clusters in the viral replication centers. Importantly, we show that adenovirus infection leads to a reduction of the quantity and/or enzymatic activity of the APOBEC3B protein depending on the strains. The A12 strain seems less able to resist APOBEC3B than the B3 or C2 strains, a characteristic which could explain the strong depletion of the APOBEC3-targeted motifs in the A12 genome. These findings suggest that adenoviruses evolved different mechanisms to antagonize APOBEC3B. Elucidating these mechanisms could benefit the design of cancer treatments. This study also identifies adenoviruses as triggers of the APOBEC3B-mediated innate response. The involvement of certain adenoviral strains in the genesis of the APOBEC3 mutational signature observed in tumors deserves further study.
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14
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A Long-Running Arms Race between APOBEC1 Genes and Retroviruses in Tetrapods. J Virol 2023; 97:e0179522. [PMID: 36598198 PMCID: PMC9888297 DOI: 10.1128/jvi.01795-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Activation-induced cytidine deaminase/apolipoprotein B mRNA editing catalytic polypeptide-like (AID/APOBEC) proteins are cytosine deaminases implicated in diverse biological functions. APOBEC1 (A1) proteins have long been thought to regulate lipid metabolism, whereas the evolutionary significance of A1 proteins in antiviral defense remains largely obscure. Endogenous retroviruses (ERVs) document past retroviral infections and are ubiquitous within the vertebrate genomes. Here, we identify the A1 gene repertoire, characterize the A1-mediated mutation footprints in ERVs, and interrogate the evolutionary arms race between A1 genes and ERVs across vertebrate species. We find that A1 genes are widely present in tetrapods, recurrently amplified and lost in certain lineages, suggesting that A1 genes might have originated during the early evolution of tetrapods. A1-mediated mutation footprints can be detected in ERVs across tetrapods. Moreover, A1 genes appear to have experienced episodic positive selection in many tetrapod lineages. Taken together, we propose that a long-running arms race between A1 genes and retroviruses might have persisted throughout the evolutionary course of tetrapods. IMPORTANCE APOBEC3 (A3) genes have been thought to function in defense against retroviruses, whereas the evolutionary significance of A1 proteins in antiviral defense remains largely obscure. In this study, we identify the A1 gene repertoire, characterize the A1-mediated mutation footprints in endogenous retroviruses (ERVs), and explore the evolutionary arms race between A1 genes and ERVs across vertebrate species. We found A1 proteins originated during the early evolution of tetrapods, and detected the footprints of A1-induced hypermutations in retroviral fossils. A1 genes appear to have experienced pervasive positive selection in tetrapods. Our study indicates a long-running arms race between A1 genes and retroviruses taking place throughout the evolutionary course of tetrapods.
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15
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Fanunza E, Cheng AZ, Auerbach AA, Stefanovska B, Moraes SN, Lokensgard JR, Biolatti M, Dell’Oste V, Bierle CJ, Bresnahan WA, Harris RS. Human cytomegalovirus mediates APOBEC3B relocalization early during infection through a ribonucleotide reductase-independent mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526383. [PMID: 36778493 PMCID: PMC9915650 DOI: 10.1101/2023.01.30.526383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The APOBEC3 family of DNA cytosine deaminases comprises an important arm of the innate antiviral defense system. The gamma-herpesviruses EBV and KSHV and the alpha-herpesviruses HSV-1 and HSV-2 have evolved an efficient mechanism to avoid APOBEC3 restriction by directly binding to APOBEC3B and facilitating its exclusion from the nuclear compartment. The only viral protein required for APOBEC3B relocalization is the large subunit of the ribonucleotide reductase (RNR). Here, we ask whether this APOBEC3B relocalization mechanism is conserved with the beta-herpesvirus human cytomegalovirus (HCMV). Although HCMV infection causes APOBEC3B relocalization from the nucleus to the cytoplasm in multiple cell types, the viral RNR (UL45) is not required. APOBEC3B relocalization occurs rapidly following infection suggesting involvement of an immediate early or early (IE-E) viral protein. In support of this mechanism, cycloheximide treatment of HCMV-infected cells prevents the expression of viral proteins and simultaneously blocks APOBEC3B relocalization. In comparison, the treatment of infected cells with phosphonoacetic acid, which is a viral DNA synthesis inhibitor affecting late protein expression, still permits A3B relocalization. These results combine to show that the beta-herpesvirus HCMV uses a fundamentally different, RNR-independent molecular mechanism to antagonize APOBEC3B. Importance Human cytomegalovirus (HCMV) infections can range from asymptomatic to severe, particularly in neonates and immunocompromised patients. HCMV has evolved strategies to overcome host-encoded antiviral defenses in order to achieve lytic viral DNA replication and dissemination and, under some conditions, latency and long-term persistence. Here, we show that HCMV infection causes the antiviral factor, APOBEC3B, to relocalize from the nuclear compartment to the cytoplasm. This overall strategy resembles that used by related herpesviruses. However, the HCMV relocalization mechanism utilizes a different viral factor(s) and available evidence suggests the involvement of at least one protein expressed at the early stages of infection. This knowledge is important because a greater understanding of this mechanism could lead to novel antiviral strategies that enable APOBEC3B to naturally restrict HCMV infection.
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Affiliation(s)
- Elisa Fanunza
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Adam Z. Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ashley A. Auerbach
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Bojana Stefanovska
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - James R. Lokensgard
- Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, 10126, Italy
| | - Valentina Dell’Oste
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, 10126, Italy
| | - Craig J. Bierle
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wade A. Bresnahan
- Department of Microbiology and Immunology, University of Minnesota, MN 55455, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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16
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Gessain A, Ramassamy JL, Afonso PV, Cassar O. Geographic distribution, clinical epidemiology and genetic diversity of the human oncogenic retrovirus HTLV-1 in Africa, the world's largest endemic area. Front Immunol 2023; 14:1043600. [PMID: 36817417 PMCID: PMC9935834 DOI: 10.3389/fimmu.2023.1043600] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/04/2023] [Indexed: 02/05/2023] Open
Abstract
The African continent is considered the largest high endemic area for the oncogenic retrovirus HTLV-1 with an estimated two to five million infected individuals. However, data on epidemiological aspects, in particular prevalence, risk factors and geographical distribution, are still very limited for many regions: on the one hand, few large-scale and representative studies have been performed and, on the other hand, many studies do not include confirmatory tests, resulting in indeterminate serological results, and a likely overestimation of HTLV-1 seroprevalence. For this review, we included the most robust studies published since 1984 on the prevalence of HTLV-1 and the two major diseases associated with this infection in people living in Africa and the Indian Ocean islands: adult T-cell leukemia (ATL) and tropical spastic paraparesis or HTLV-1-associated myelopathy (HAM/TSP). We also considered most of the book chapters and abstracts published at the 20 international conferences on HTLV and related viruses held since 1985, as well as the results of recent meta-analyses regarding the status of HTLV-1 in West and sub-Saharan Africa. Based on this bibliography, it appears that HTLV-1 distribution is very heterogeneous in Africa: The highest prevalences of HTLV-1 are reported in western, central and southern Africa, while eastern and northern Africa show lower prevalences. In highly endemic areas, the HTLV-1 prevalence in the adult population ranges from 0.3 to 3%, increases with age, and is highest among women. In rural areas of Gabon and the Democratic Republic of the Congo (DRC), HTLV-1 prevalence can reach up to 10-25% in elder women. HTLV-1-associated diseases in African patients have rarely been reported in situ on hospital wards, by local physicians. With the exception of the Republic of South Africa, DRC and Senegal, most reports on ATL and HAM/TSP in African patients have been published by European and American clinicians and involve immigrants or medical returnees to Europe (France and the UK) and the United States. There is clearly a huge underreporting of these diseases on the African continent. The genetic diversity of HTLV-1 is greatest in Africa, where six distinct genotypes (a, b, d, e, f, g) have been identified. The most frequent genotype in central Africa is genotype b. The other genotypes found in central Africa (d, e, f and g) are very rare. The vast majority of HTLV-1 strains from West and North Africa belong to genotype a, the so-called 'Cosmopolitan' genotype. These strains form five clades roughly reflecting the geographic origin of the infected individuals. We have recently shown that some of these clades are the result of recombination between a-WA and a-NA strains. Almost all sequences from southern Africa belong to Transcontinental a-genotype subgroup.
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Affiliation(s)
- Antoine Gessain
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Jill-Léa Ramassamy
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Philippe V Afonso
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Olivier Cassar
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
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17
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Auerbach AA, Becker JT, Moraes SN, Moghadasi SA, Duda JM, Salamango DJ, Harris RS. Ancestral APOBEC3B Nuclear Localization Is Maintained in Humans and Apes and Altered in Most Other Old World Primate Species. mSphere 2022; 7:e0045122. [PMID: 36374108 PMCID: PMC9769932 DOI: 10.1128/msphere.00451-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
APOBEC3B is an innate immune effector enzyme capable of introducing mutations in viral genomes through DNA cytosine-to-uracil editing. Recent studies have shown that gamma-herpesviruses, such as Epstein-Barr virus (EBV), have evolved a potent APOBEC3B neutralization mechanism to protect lytic viral DNA replication intermediates in the nuclear compartment. APOBEC3B is additionally unique as the only human DNA deaminase family member that is constitutively nuclear. Nuclear localization has therefore been inferred to be essential for innate antiviral function. Here, we combine evolutionary, molecular, and cell biology approaches to address whether nuclear localization is a conserved feature of APOBEC3B in primates. Despite the relatively recent emergence of APOBEC3B approximately 30 to 40 million years ago (MYA) in Old World primates by genetic recombination (after the split from the New World monkey lineage 40 to 50 MYA), we find that the hallmark nuclear localization of APOBEC3B shows variability. For instance, although human and several nonhuman primate APOBEC3B enzymes are predominantly nuclear, rhesus macaque and other Old World primate APOBEC3B proteins are clearly cytoplasmic or cell wide. A series of human/rhesus macaque chimeras and mutants combined to map localization determinants to the N-terminal half of the protein with residues 15, 19, and 24 proving critical. Ancestral APOBEC3B reconstructed from present-day primate species also shows strong nuclear localization. Together, these results indicate that the ancestral nuclear localization of APOBEC3B is maintained in present-day human and ape proteins, but nuclear localization is not conserved in all Old World monkey species despite a need for antiviral functions in the nuclear compartment. IMPORTANCE APOBEC3 enzymes are single-stranded DNA cytosine-to-uracil deaminases with beneficial roles in antiviral immunity and detrimental roles in cancer mutagenesis. Regarding viral infection, all seven human APOBEC3 enzymes have overlapping roles in restricting virus types that require DNA for replication, including EBV, HIV, human papillomavirus (HPV), and human T-cell leukemia virus (HTLV). Regarding cancer, at least two APOBEC3 enzymes, APOBEC3B and APOBEC3A, are prominent sources of mutation capable of influencing clinical outcomes. Here, we combine evolutionary, molecular, and cell biology approaches to characterize primate APOBEC3B enzymes. We show that nuclear localization is an ancestral property of APOBEC3B that is maintained in present-day human and ape enzymes, but not conserved in other nonhuman primates. This partial mechanistic conservation indicates that APOBEC3B is important for limiting the replication of DNA-based viruses in the nuclear compartment. Understanding these pathogen-host interactions may contribute to the development of future antiviral and antitumor therapies.
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Affiliation(s)
- Ashley A Auerbach
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Jordan T Becker
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Microbiology and Immunology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Sofia N Moraes
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Seyed Arad Moghadasi
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Jolene M Duda
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Daniel J Salamango
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
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18
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Abstract
Anelloviruses are the most common viruses infecting humans. Every human carries a nonpathogenic personal anellovirus virome (anellome), yet it is unknown which mechanisms contribute to its stability. Here, we assessed the dynamics and impact of a host antiviral defense mechanism-cytidine deaminase activity leading to C to U editing in anelloviruses-on the stability of the anellome. We investigated anellome sequence data obtained from serum samples collected every 6 months from two healthy subjects followed for more than 30 years. The subjects were infected by a total of 64 anellovirus lineages. Minus-stranded C to U editing was observed in lineages belonging to the Alpha-, Beta-, and Gammatorquevirus genera. The edited genomes were present within virus particles, therefore editing must have occurred at the late stages of the virus life cycle. Editing was favored by 5'-TC contexts in the virus genome, indicating that apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like, catalytic subunit 3 or A3 (APOBEC3) proteins are involved. Within a lineage, mutational dynamics varied over time and few fixations of mutations were detected, indicating that C to U editing is a dead end for a virus genome. We detected an editing coldspot in the GC-rich regions, suggesting that the GC-rich region is crucial for genome packaging, since only packaged virus particles were included in the analysis. Finally, we noticed a lineage-specific reduced concentration after an editing event, yet no clearance. In conclusion, cytidine deaminase activity does not clear anelloviruses, nor does it play a major role in virus evolution, but it does contribute to the stability of the anellome. IMPORTANCE Despite significant attention on anellovirus research, the interaction between the anellovirus virome and the human host remains unknown. We show the dynamics of APOBEC3-mediated cytidine deaminase activity on anelloviruses during a 30-year period of chronic infection and postulate that this antiviral mechanism controls anelloviruses. These results expand our knowledge of anellovirus-host interactions, which may be important for the design of gene therapies.
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19
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Hu J, Wang H, Yang L, Wu S, Li Y, Li Y, Li Z. Compound IMB-Z inhibits hepatitis B virus replication through increasing APOBEC3G expression and incorporation into viral nucleocapsids. J Glob Antimicrob Resist 2022; 31:371-378. [PMID: 36396043 DOI: 10.1016/j.jgar.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/01/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES As a host restriction factor, apolipoprotein B messenger RNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G or A3G) has been shown to suppress the replication of several viruses including hepatitis B virus (HBV). Recently, we reported that IMB-Z, a N-phenylbenzamide derivative, could inhibit Enterovirus 71 replication, and A3G mediated its antiviral activity. Whether IMB-Z exhibits an inhibitory effect on HBV replication has not been investigated. MATERIAL AND METHODS HBV DNA, pregenomic RNA (pgRNA), core protein, and capsid levels were determined by a qPCR assay or Southern blot, Northern blot, Western blot, and particle gel assay, respectively. Mutation analysis of HBV DNAs was conducted by a differential DNA denaturation PCR assay. A3G encapsidation into HBV nucleocapsids was examined by Western blot analysis after ultracentrifugation and a co-immunoprecipitation (IP) assay between HBV core and A3G proteins. RESULTS In the present study, we found that IMB-Z could considerably inhibit HBV replication in HepAD38 cells. Interestingly, IMB-Z did not alter the HBV pgRNA production but could reduce the level of core protein, viral nucleocapsids, and core-associated DNA, as well as cccDNA intracellular amplification. Similar to the action of IMB-Z's inhibition of Enterovirus 71 replication, we found that IMB-Z's inhibition of HBV replication was associated with increased level of A3G. Mechanistically, we demonstrated that the inhibitory effect of IMB-Z is independent of the cytidine deaminase activity of A3G and is exerted by increasing its incorporation into viral nucleocapsids. CONCLUSIONS Our results indicate that IMB-Z inhibits HBV through pharmacological induction A3G expression and incorporation into HBV nucleocapsids.
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Affiliation(s)
- Jin Hu
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huiqiang Wang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lu Yang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuo Wu
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yanping Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yuhuan Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Zhuorong Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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20
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Zhao L, Hall M, de Cesare M, MacIntyre-Cockett G, Lythgoe K, Fraser C, Bonsall D, Golubchik T, Ferretti L. The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA. Proc Biol Sci 2022; 289:20221747. [PMID: 36382519 PMCID: PMC9667359 DOI: 10.1098/rspb.2022.1747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The raw material for viral evolution is provided by intra-host mutations occurring during replication, transcription or post-transcription. Replication and transcription of Coronaviridae proceed through the synthesis of negative-sense 'antigenomes' acting as templates for positive-sense genomic and subgenomic RNA. Hence, mutations in the genomes of SARS-CoV-2 and other coronaviruses can occur during (and after) the synthesis of either negative-sense or positive-sense RNA, with potentially distinct patterns and consequences. We explored for the first time the mutational spectrum of SARS-CoV-2 (sub)genomic and anti(sub)genomic RNA. We use a high-quality deep sequencing dataset produced using a quantitative strand-aware sequencing method, controlled for artefacts and sequencing errors, and scrutinized for accurate detection of within-host diversity. The nucleotide differences between negative- and positive-sense strand consensus vary between patients and do not show dependence on age or sex. Similarities and differences in mutational patterns between within-host minor variants on the two RNA strands suggested strand-specific mutations or editing by host deaminases and oxidative damage. We observe generally neutral and slight negative selection on the negative strand, contrasting with purifying selection in ORF1a, ORF1b and S genes of the positive strand of the genome.
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Affiliation(s)
- Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | | | | | - Katrina Lythgoe
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK,Sydney Infectious Diseases Institute (Sydney ID), Faculty of Medicine and Health, University of Sydney, Sydney NSW 2006, Australia
| | | | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
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21
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Dananberg A, Maciejowski J. Monitoring APOBEC3A protein levels in human cancer cells. Methods Cell Biol 2022; 182:313-327. [PMID: 38359985 PMCID: PMC10869936 DOI: 10.1016/bs.mcb.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The APOBEC3 family of cytosine deaminases, which target single-stranded DNA and RNA of viruses and retroelements as part of the innate immune defense, generate mutations in many human cancers. Although the APOBEC3A paralog is a major endogenous source of these mutations, low APOBEC3A mRNA levels and protein abundance have hampered functional characterization. Extensive homology across APOBEC3 paralogs have further challenged the development of specific detection reagents. Here, we describe the isolation and use of monoclonal antibodies with specificity for APOBEC3A and the APOBEC3A/APOBEC3B/APOBEC3G proteins. We provide protocols and technical advice for detection and measurement of APOBEC3A protein across human cancer cell lines using standard immunoblotting and immunofluorescence protocols.
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Affiliation(s)
- Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
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22
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Soikkeli AI, Kyläniemi MK, Sihto H, Alinikula J. Oncogenic Merkel Cell Polyomavirus T Antigen Truncating Mutations are Mediated by APOBEC3 Activity in Merkel Cell Carcinoma. CANCER RESEARCH COMMUNICATIONS 2022; 2:1344-1354. [PMID: 36970060 PMCID: PMC10035372 DOI: 10.1158/2767-9764.crc-22-0211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/17/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
Merkel cell carcinoma (MCC) is an aggressive skin cancer, which is frequently caused by Merkel cell polyomavirus (MCPyV). Mutations of MCPyV tumor (T) antigens are major pathologic events of virus-positive (MCPyV+) MCCs, but their source is unclear. Activation-induced cytidine deaminase (AID)/APOBEC family cytidine deaminases contribute to antiviral immunity by mutating viral genomes and are potential carcinogenic mutators. We studied the contribution of AID/APOBEC cytidine deaminases to MCPyV large T (LT) truncation events. The MCPyV LT area in MCCs was enriched with cytosine-targeting mutations, and a strong APOBEC3 mutation signature was observed in MCC sequences. AICDA and APOBEC3 expression were detected in the Finnish MCC sample cohort, and LT expression correlated with APOBEC3H and APOBEC3G. Marginal but statistically significant somatic hypermutation targeting activity was detected in the MCPyV regulatory region. Our results suggest that APOBEC3 cytidine deaminases are a plausible cause of the LT truncating mutations in MCPyV+ MCC, while the role of AID in MCC carcinogenesis is unlikely.
Significance:
We uncover APOBEC3 mutation signature in MCPyV LT that reveals the likely cause of mutations underlying MCPyV+ MCC. We further reveal an expression pattern of APOBECs in a large Finnish MCC sample cohort. Thus, the findings presented here suggest a molecular mechanism underlying an aggressive carcinoma with poor prognosis.
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Affiliation(s)
- Anni I. Soikkeli
- 1Unit of Infection and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
- 2Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Minna K. Kyläniemi
- 3Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Harri Sihto
- 4Department of Pathology, University of Helsinki, Helsinki, Finland
| | - Jukka Alinikula
- 1Unit of Infection and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
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23
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Warren CJ, Santiago ML, Pyeon D. APOBEC3: Friend or Foe in Human Papillomavirus Infection and Oncogenesis? Annu Rev Virol 2022; 9:375-395. [PMID: 35671565 PMCID: PMC9637027 DOI: 10.1146/annurev-virology-092920-030354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human papillomavirus (HPV) infection is a causative agent of multiple human cancers, including cervical and head and neck cancers. In these HPV-positive tumors, somatic mutations are caused by aberrant activation of DNA mutators such as members of the apolipoprotein B messenger RNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of cytidine deaminases. APOBEC3 proteins are most notable for their restriction of various viruses, including anti-HPV activity. However, the potential role of APOBEC3 proteins in HPV-induced cancer progression has recently garnered significant attention. Ongoing research stems from the observations that elevated APOBEC3 expression is driven by HPV oncogene expression and that APOBEC3 activity is likely a significant contributor to somatic mutagenesis in HPV-positive cancers. This review focuses on recent advances in the study of APOBEC3 proteins and their roles in HPV infection and HPV-driven oncogenesis. Further, we discuss critical gaps and unanswered questions in our understanding of APOBEC3 in virus-associated cancers.
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Affiliation(s)
- Cody J Warren
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Mario L Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA;
| | - Dohun Pyeon
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA;
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24
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Løvestad AH, Repesa A, Costanzi JM, Lagström S, Christiansen IK, Rounge TB, Ambur OH. Differences in integration frequencies and APOBEC3 profiles of five high-risk HPV types adheres to phylogeny. Tumour Virus Res 2022; 14:200247. [PMID: 36100161 PMCID: PMC9485212 DOI: 10.1016/j.tvr.2022.200247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 02/06/2023] Open
Abstract
Persistent infection with Human Papillomavirus (HPV) is responsible for almost all cases of cervical cancers, and HPV16 and HPV18 associated with the majority of these. These types differ in the proportion of viral minor nucleotide variants (MNVs) caused by APOBEC3 mutagenesis as well as integration frequencies. Whether these traits extend to other types remains uncertain. This study aimed to investigate and compare genomic variability and chromosomal integration in the two phylogenetically distinct Alpha-7 and Alpha-9 clades of carcinogenic HPV types. The TaME-seq protocol was employed to sequence cervical cell samples positive for HPV31, HPV33 or HPV45 and combine these with data from a previous study on HPV16 and HPV18. APOBEC3 mutation signatures were found in Alpha-9 (HPV16/31/33) but not in Alpha-7 (HPV18/45). HPV45 had significantly more MNVs compared to the other types. Alpha-7 had higher integration frequency compared to Alpha-9. An increase in integration frequency with increased diagnostic severity was found for Alpha-7. The results highlight important differences and broaden our understanding of the molecular mechanisms behind cervical cancer induced by high-risk HPV types from the Alpha-7 and Alpha-9 clades.
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Affiliation(s)
- Alexander Hesselberg Løvestad
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Adina Repesa
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Jean-Marc Costanzi
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Sonja Lagström
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway,Department of Research, Cancer Registry of Norway, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway,Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, Lørenskog, Norway
| | - Trine B. Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway,Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway,Corresponding author. Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Ole Herman Ambur
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway,Corresponding authors.
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25
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Carcone A, Journo C, Dutartre H. Is the HTLV-1 Retrovirus Targeted by Host Restriction Factors? Viruses 2022; 14:v14081611. [PMID: 35893677 PMCID: PMC9332716 DOI: 10.3390/v14081611] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
Human T cell leukemia virus type 1 (HTLV-1), the etiological agent of adult T cell leukemia/lymphoma (ATLL) and of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), was identified a few years before Human Immunodeficiency Virus (HIV). However, forty years later, our comprehension of HTLV-1 immune detection and the host immune responses to HTLV-1 is far more limited than for HIV. In addition to innate and adaptive immune responses that rely on specialized cells of the immune system, host cells may also express a range of antiviral factors that inhibit viral replication at different stages of the cycle, in a cell-autonomous manner. Multiple antiviral factors allowing such an intrinsic immunity have been primarily and extensively described in the context HIV infection. Here, we provide an overview of whether known HIV restriction factors might act on HTLV-1 replication. Interestingly, many of them do not exert any antiviral activity against HTLV-1, and we discuss viral replication cycle specificities that could account for these differences. Finally, we highlight future research directions that could help to identify antiviral factors specific to HTLV-1.
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26
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Fé LXSGM, Cipolatti EP, Pinto MCC, Branco S, Nogueira FCS, Ortiz GMD, Pinheiro ADS, Manoel EA. Enzymes in the time of COVID-19: An overview about the effects in the human body, enzyme market, and perspectives for new drugs. Med Res Rev 2022; 42:2126-2167. [PMID: 35762498 PMCID: PMC9350392 DOI: 10.1002/med.21919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 01/27/2022] [Accepted: 06/08/2022] [Indexed: 12/11/2022]
Abstract
The rising pandemic caused by a coronavirus, resulted in a scientific quest to discover some effective treatments against its etiologic agent, the severe acute respiratory syndrome‐coronavirus 2 (SARS‐CoV‐2). This research represented a significant scientific landmark and resulted in many medical advances. However, efforts to understand the viral mechanism of action and how the human body machinery is subverted during the infection are still ongoing. Herein, we contributed to this field with this compilation of the roles of both viral and human enzymes in the context of SARS‐CoV‐2 infection. In this sense, this overview reports that proteases are vital for the infection to take place: from SARS‐CoV‐2 perspective, the main protease (Mpro) and papain‐like protease (PLpro) are highlighted; from the human body, angiotensin‐converting enzyme‐2, transmembrane serine protease‐2, and cathepsins (CatB/L) are pointed out. In addition, the influence of the virus on other enzymes is reported as the JAK/STAT pathway and the levels of lipase, enzymes from the cholesterol metabolism pathway, amylase, aspartate aminotransferase, alanine aminotransferase, lactate dehydrogenase, and glyceraldehyde 3‐phosphate dehydrogenase are also be disturbed in SARS‐CoV‐2 infection. Finally, this paper discusses the importance of detailed enzymatic studies for future treatments against SARS‐CoV‐2, and how some issues related to the syndrome treatment can create opportunities in the biotechnological market of enzymes and the development of new drugs.
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Affiliation(s)
- Luana Xavier Soares Gomes Moura Fé
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Centro de Ciências da Saúde (CCS), Universidade Federal do Rio de Janeiro (UFRJ)-Cidade Universitária, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eliane Pereira Cipolatti
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Centro de Ciências da Saúde (CCS), Universidade Federal do Rio de Janeiro (UFRJ)-Cidade Universitária, Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Engenharia Química, Instituto de Tecnologia, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropédica, Rio de Janeiro, Brazil
| | - Martina Costa Cerqueira Pinto
- Departamento de Bioquímica, Instituto de Química, Centro de Tecnologia (CT), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Rio de Janeiro, Brazil.,Chemical Engineering Program, Instituto Alberto Luiz Coimbra de Pós-graduação e Pesquisa de Engenharia (COPPE), Centro de Tecnologia (CT), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Suema Branco
- Biofísica Ambiental, Instituto de Biofísica Carlos Chagas Filho, Centro de Ciências da Saúde (CCS), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fábio César Sousa Nogueira
- Departamento de Bioquímica, Instituto de Química, Centro de Tecnologia (CT), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gisela Maria Dellamora Ortiz
- Departamento de Fármacos e Medicamentos, Faculdade de Farmácia, Centro de Ciências da Saúde (CCS), Universidade Federal do Rio de Janeiro (UFRJ)-Cidade Universitária, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anderson de Sá Pinheiro
- Departamento de Bioquímica, Instituto de Química, Centro de Tecnologia (CT), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Evelin Andrade Manoel
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Centro de Ciências da Saúde (CCS), Universidade Federal do Rio de Janeiro (UFRJ)-Cidade Universitária, Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Bioquímica, Instituto de Química, Centro de Tecnologia (CT), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Rio de Janeiro, Brazil
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27
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Meissner ME, Talledge N, Mansky LM. Molecular Biology and Diversification of Human Retroviruses. FRONTIERS IN VIROLOGY 2022; 2:872599. [PMID: 35783361 PMCID: PMC9242851 DOI: 10.3389/fviro.2022.872599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Studies of retroviruses have led to many extraordinary discoveries that have advanced our understanding of not only human diseases, but also molecular biology as a whole. The most recognizable human retrovirus, human immunodeficiency virus type 1 (HIV-1), is the causative agent of the global AIDS epidemic and has been extensively studied. Other human retroviruses, such as human immunodeficiency virus type 2 (HIV-2) and human T-cell leukemia virus type 1 (HTLV-1), have received less attention, and many of the assumptions about the replication and biology of these viruses are based on knowledge of HIV-1. Existing comparative studies on human retroviruses, however, have revealed that key differences between these viruses exist that affect evolution, diversification, and potentially pathogenicity. In this review, we examine current insights on disparities in the replication of pathogenic human retroviruses, with a particular focus on the determinants of structural and genetic diversity amongst HIVs and HTLV.
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Affiliation(s)
- Morgan E. Meissner
- Institute for Molecular Virology, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Molecular, Cellular, Developmental Biology and Genetics Graduate Program, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
| | - Nathaniel Talledge
- Institute for Molecular Virology, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Masonic Cancer Center, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
| | - Louis M. Mansky
- Institute for Molecular Virology, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Molecular, Cellular, Developmental Biology and Genetics Graduate Program, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Masonic Cancer Center, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
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28
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Bergstrom EN, Luebeck J, Petljak M, Khandekar A, Barnes M, Zhang T, Steele CD, Pillay N, Landi MT, Bafna V, Mischel PS, Harris RS, Alexandrov LB. Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA. Nature 2022; 602:510-517. [PMID: 35140399 PMCID: PMC8850194 DOI: 10.1038/s41586-022-04398-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 01/04/2022] [Indexed: 12/28/2022]
Abstract
Clustered somatic mutations are common in cancer genomes and previous analyses reveal several types of clustered single-base substitutions, which include doublet- and multi-base substitutions1-5, diffuse hypermutation termed omikli6, and longer strand-coordinated events termed kataegis3,7-9. Here we provide a comprehensive characterization of clustered substitutions and clustered small insertions and deletions (indels) across 2,583 whole-genome-sequenced cancers from 30 types of cancer10. Clustered mutations were highly enriched in driver genes and associated with differential gene expression and changes in overall survival. Several distinct mutational processes gave rise to clustered indels, including signatures that were enriched in tobacco smokers and homologous-recombination-deficient cancers. Doublet-base substitutions were caused by at least 12 mutational processes, whereas most multi-base substitutions were generated by either tobacco smoking or exposure to ultraviolet light. Omikli events, which have previously been attributed to APOBEC3 activity6, accounted for a large proportion of clustered substitutions; however, only 16.2% of omikli matched APOBEC3 patterns. Kataegis was generated by multiple mutational processes, and 76.1% of all kataegic events exhibited mutational patterns that are associated with the activation-induced deaminase (AID) and APOBEC3 family of deaminases. Co-occurrence of APOBEC3 kataegis and extrachromosomal DNA (ecDNA), termed kyklonas (Greek for cyclone), was found in 31% of samples with ecDNA. Multiple distinct kyklonic events were observed on most mutated ecDNA. ecDNA containing known cancer genes exhibited both positive selection and kyklonic hypermutation. Our results reveal the diversity of clustered mutational processes in human cancer and the role of APOBEC3 in recurrently mutating and fuelling the evolution of ecDNA.
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Affiliation(s)
- Erik N Bergstrom
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Mia Petljak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher D Steele
- Research Department of Pathology, Cancer Institute, University College London, London, UK
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
| | - Reuben S Harris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
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Zhang Y, Chen X, Cao Y, Yang Z. Roles of APOBEC3 in hepatitis B virus (HBV) infection and hepatocarcinogenesis. Bioengineered 2021; 12:2074-2086. [PMID: 34043485 PMCID: PMC8806738 DOI: 10.1080/21655979.2021.1931640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 02/08/2023] Open
Abstract
APOBEC3 (A3) cytidine deaminases inhibit hepatitis B virus (HBV) infection and play vital roles in maintaining a variety of biochemical processes, including the regulation of protein expression and innate immunity. Emerging evidence indicates that the deaminated deoxycytidine biochemical activity of A3 proteins in single-stranded DNA makes them a double-edged sword. These enzymes can cause cellular genetic mutations at replication forks or within transcription bubbles, depending on the physiological state of the cell and the phase of the cell cycle. Under pathological conditions, aberrant expression of A3 genes with improper deaminase activity regulation may threaten genomic stability and eventually lead to cancer development. This review attempted to summarize the antiviral activities and underlying mechanisms of A3 editing enzymes in HBV infections. Moreover, the correlations between A3 genes and hepatocarcinogenesis were also elucidated.
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Affiliation(s)
- Yuan Zhang
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xiaorong Chen
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yajuan Cao
- Central Laboratory, Shanghai Pulmonary HospitalSchool of Medicine, Tongji University School of Medicine, Shanghai, China
- Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zongguo Yang
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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Que L, Li Y, Dainichi T, Kukimoto I, Nishiyama T, Nakano Y, Shima K, Suzuki T, Sato Y, Horike S, Aizaki H, Watashi K, Kato T, Aly HH, Watanabe N, Kabashima K, Wakae K, Muramatsu M. Interferon-gamma induced APOBEC3B contributes to Merkel cell polyomavirus genome mutagenesis in Merkel cell carcinoma. J Invest Dermatol 2021; 142:1793-1803.e11. [DOI: 10.1016/j.jid.2021.12.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 11/29/2021] [Accepted: 12/07/2021] [Indexed: 11/29/2022]
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Scholtes GK, Sawyer AM, Vaca CC, Clerc I, Roh M, Song C, D'Aquila RT. The von Hippel-Lindau Cullin-RING E3 ubiquitin ligase regulates APOBEC3 cytidine deaminases. Transl Res 2021; 237:1-15. [PMID: 34004371 PMCID: PMC8440357 DOI: 10.1016/j.trsl.2021.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
The 7 members of the A3 family of cytidine deaminases (A3A to A3H) share a conserved catalytic activity that converts cytidines in single-stranded (ss) DNA into uridines, thereby inducing mutations. After their initial identification as cell-intrinsic defenses against HIV and other retroviruses, A3s were also found to impair many additional viruses. Moreover, some of the A3 proteins (A3A, A3B, and A3H haplotype I) are dysregulated in cancer cells, thereby causing chromosomal mutations that can be selected to fuel progression of malignancy. Viral mechanisms that increase transcription of A3 genes or induce proteasomal degradation of A3 proteins have been characterized. However, only a few underlying biological mechanisms regulating levels of A3s in uninfected cells have been described. Here, we characterize that the von Hippel-Lindau tumor suppressor (pVHL), via its CRLpVHL, induces degradation of all 7 A3 proteins. Two independent lines of evidence supported the conclusion that the multiprotein CRLpVHL complex is necessary for A3 degradation. CRLpVHL more effectively induced degradation of nuclear, procancer A3 (A3B) than the cytoplasmic, antiretroviral A3 (A3G). These results identify specific cellular factors that regulate A3s post-translationally.
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Affiliation(s)
- Gael K Scholtes
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Aubrey M Sawyer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Cristina C Vaca
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Isabelle Clerc
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Meejeon Roh
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Chisu Song
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Richard T D'Aquila
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
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SAR-CoV-2 infection, emerging new variants and the role of activation induced cytidine deaminase (AID) in lasting immunity. Saudi Pharm J 2021; 29:1181-1184. [PMID: 34566457 PMCID: PMC8452370 DOI: 10.1016/j.jsps.2021.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/12/2021] [Indexed: 12/31/2022] Open
Abstract
As the world faces a fourth COVID-19 spike, scientists are learning a lot more about the new SARS-CoV-2 strains that were previously unknown. Currently, the Delta versions of SARS-CoV-2 have become the prevalent strains in much of the world since it first appeared in India in late 2020. Researchers believe they have discovered why Delta has been so successful: those infected with it create significantly more virus than those infected with the original strain of SARS-CoV-2, making it extremely contagious. This has redirected the focus to how our immune system defends us from these various pathogens and initiates such varied responses. Hundreds of research papers have been published on the origins of long-lasting immune responses and disparities in the numbers of different immune cell types in COVID 19 survivors, but the primary architect of these discrepancies has yet to be discovered. In this essay, we will concentrate on the primary architect protein, activation induced cytidine deaminase (AID), which triggers molecular processes that allow our immune system to produce powerful antibodies and SARS-CoV-2 specific B cells, allowing us to outwit the virus. We believe that if we ever achieve permanent immunity to SARS-CoV-2 infection, AID will be the key to releasing it.
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Forlani G, Shallak M, Accolla RS, Romanelli MG. HTLV-1 Infection and Pathogenesis: New Insights from Cellular and Animal Models. Int J Mol Sci 2021; 22:ijms22158001. [PMID: 34360767 PMCID: PMC8347336 DOI: 10.3390/ijms22158001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/12/2022] Open
Abstract
Since the discovery of the human T-cell leukemia virus-1 (HTLV-1), cellular and animal models have provided invaluable contributions in the knowledge of viral infection, transmission and progression of HTLV-associated diseases. HTLV-1 is the causative agent of the aggressive adult T-cell leukemia/lymphoma and inflammatory diseases such as the HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP). Cell models contribute to defining the role of HTLV proteins, as well as the mechanisms of cell-to-cell transmission of the virus. Otherwise, selected and engineered animal models are currently applied to recapitulate in vivo the HTLV-1 associated pathogenesis and to verify the effectiveness of viral therapy and host immune response. Here we review the current cell models for studying virus–host interaction, cellular restriction factors and cell pathway deregulation mediated by HTLV products. We recapitulate the most effective animal models applied to investigate the pathogenesis of HTLV-1-associated diseases such as transgenic and humanized mice, rabbit and monkey models. Finally, we summarize the studies on STLV and BLV, two closely related HTLV-1 viruses in animals. The most recent anticancer and HAM/TSP therapies are also discussed in view of the most reliable experimental models that may accelerate the translation from the experimental findings to effective therapies in infected patients.
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Affiliation(s)
- Greta Forlani
- Laboratory of General Pathology and Immunology “Giovanna Tosi”, Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (G.F.); (M.S.); (R.S.A.)
| | - Mariam Shallak
- Laboratory of General Pathology and Immunology “Giovanna Tosi”, Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (G.F.); (M.S.); (R.S.A.)
| | - Roberto Sergio Accolla
- Laboratory of General Pathology and Immunology “Giovanna Tosi”, Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (G.F.); (M.S.); (R.S.A.)
| | - Maria Grazia Romanelli
- Department of Biosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
- Correspondence:
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Tasakis RN, Samaras G, Jamison A, Lee M, Paulus A, Whitehouse G, Verkoczy L, Papavasiliou FN, Diaz M. SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts. PLoS One 2021; 16:e0255169. [PMID: 34297786 PMCID: PMC8301627 DOI: 10.1371/journal.pone.0255169] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/11/2021] [Indexed: 12/13/2022] Open
Abstract
Since the first case of COVID-19 in December 2019 in Wuhan, China, SARS-CoV-2 has spread worldwide and within a year and a half has caused 3.56 million deaths globally. With dramatically increasing infection numbers, and the arrival of new variants with increased infectivity, tracking the evolution of its genome is crucial for effectively controlling the pandemic and informing vaccine platform development. Our study explores evolution of SARS-CoV-2 in a representative cohort of sequences covering the entire genome in the United States, through all of 2020 and early 2021. Strikingly, we detected many accumulating Single Nucleotide Variations (SNVs) encoding amino acid changes in the SARS-CoV-2 genome, with a pattern indicative of RNA editing enzymes as major mutators of SARS-CoV-2 genomes. We report three major variants through October of 2020. These revealed 14 key mutations that were found in various combinations among 14 distinct predominant signatures. These signatures likely represent evolutionary lineages of SARS-CoV-2 in the U.S. and reveal clues to its evolution such as a mutational burst in the summer of 2020 likely leading to a homegrown new variant, and a trend towards higher mutational load among viral isolates, but with occasional mutation loss. The last quartile of 2020 revealed a concerning accumulation of mostly novel low frequency replacement mutations in the Spike protein, and a hypermutable glutamine residue near the putative furin cleavage site. Finally, end of the year data and 2021 revealed the gradual increase to prevalence of known variants of concern, particularly B.1.1.7, that have acquired additional Spike mutations. Overall, our results suggest that predominant viral genomes are dynamically evolving over time, with periods of mutational bursts and unabated mutation accumulation. This high level of existing variation, even at low frequencies and especially in the Spike-encoding region may become problematic when super-spreader events, akin to serial Founder Events in evolution, drive these rare mutations to prominence.
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Affiliation(s)
- Rafail Nikolaos Tasakis
- Division of Immune Diversity, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Georgios Samaras
- Division of Immune Diversity, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Program of Translational Medical Research, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Anna Jamison
- The Nightingale-Bamford School, New York, NY, United States of America
| | - Michelle Lee
- Cornell University, Ithaca, NY, United States of America
| | - Alexandra Paulus
- The Nightingale-Bamford School, New York, NY, United States of America
| | | | - Laurent Verkoczy
- San Diego Biomedical Research Institute (SDBRI), San Diego, CA, United States of America
| | - F. Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marilyn Diaz
- San Diego Biomedical Research Institute (SDBRI), San Diego, CA, United States of America
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Sadeghpour S, Khodaee S, Rahnama M, Rahimi H, Ebrahimi D. Human APOBEC3 Variations and Viral Infection. Viruses 2021; 13:1366. [PMID: 34372572 PMCID: PMC8310219 DOI: 10.3390/v13071366] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
Human APOBEC3 (apolipoprotein B mRNA-editing catalytic polypeptide-like 3) enzymes are capable of inhibiting a wide range of endogenous and exogenous viruses using deaminase and deaminase-independent mechanisms. These enzymes are essential components of our innate immune system, as evidenced by (a) their strong positive selection and expansion in primates, (b) the evolution of viral counter-defense mechanisms, such as proteasomal degradation mediated by HIV Vif, and (c) hypermutation and inactivation of a large number of integrated HIV-1 proviruses. Numerous APOBEC3 single nucleotide polymorphisms, haplotypes, and splice variants have been identified in humans. Several of these variants have been reported to be associated with differential antiviral immunity. This review focuses on the current knowledge in the field about these natural variations and their roles in infectious diseases.
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Affiliation(s)
- Shiva Sadeghpour
- Department of Biological Science, University of California Irvine, Irvine, CA 92697, USA;
| | - Saeideh Khodaee
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran;
| | - Mostafa Rahnama
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA;
| | - Hamzeh Rahimi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran;
| | - Diako Ebrahimi
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
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36
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Infection of Bronchial Epithelial Cells by the Human Adenoviruses A12, B3, and C2 Differently Regulates the Innate Antiviral Effector APOBEC3B. J Virol 2021; 95:e0241320. [PMID: 33853956 DOI: 10.1128/jvi.02413-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Human adenoviruses (HAdVs) are a large family of DNA viruses that include more than 100 genotypes divided into seven species (A to G) and induce respiratory tract infections, gastroenteritis, and conjunctivitis. Genetically modified adenoviruses are also used as vaccines, gene therapies, and anticancer treatments. The APOBEC3s are a family of cytidine deaminases that restrict viruses by introducing mutations in their genomes. Viruses developed different strategies to cope with the APOBEC3 selection pressure, but nothing is known on the interplay between the APOBEC3s and the HAdVs. In this study, we focused on three HAdV strains: the B3 and C2 strains, as they are very frequent, and the A12 strain, which is less common but is oncogenic in animal models. We demonstrated that the three HAdV strains induce a similar APOBEC3B upregulation at the transcriptional level. At the protein level, however, APOBEC3B is abundantly expressed during HAdV-A12 and -C2 infection and shows a nuclear distribution. On the contrary, APOBEC3B is barely detectable in HAdV-B3-infected cells. APOBEC3B deaminase activity is detected in total protein extracts upon HAdV-A12 and -C2 infection. Bioinformatic analysis demonstrates that the HAdV-A12 genome bears a stronger APOBEC3 evolutionary footprint than that of the HAdV-C2 and HAdV-B3 genomes. Our results show that HAdV infection triggers the transcriptional upregulation of the antiviral innate effector APOBEC3B. The discrepancies between the APOBEC3B mRNA and protein levels might reflect the ability of some HAdV strains to antagonize the APOBEC3B protein. These findings point toward an involvement of APOBEC3B in HAdV restriction and evolution. IMPORTANCE The APOBEC3 family of cytosine deaminases has important roles in antiviral innate immunity and cancer. Notably, APOBEC3A and APOBEC3B are actively upregulated by several DNA tumor viruses and contribute to transformation by introducing mutations in the cellular genome. Human adenoviruses (HAdVs) are a large family of DNA viruses that cause generally asymptomatic infections in immunocompetent adults. HAdVs encode several oncogenes, and some HAdV strains, like HAdV-A12, induce tumors in hamsters and mice. Here, we show that HAdV infection specifically promotes the expression of the APOBEC3B gene. We report that infection with the A12 strain induces a strong expression of an enzymatically active APOBEC3B protein in bronchial epithelial cells. We provide bioinformatic evidence that HAdVs' genomes and notably the A12 genome are under APOBEC3 selection pressure. Thus, APOBEC3B might contribute to adenoviral restriction, diversification, and oncogenic potential of particular strains.
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Gaba A, Flath B, Chelico L. Examination of the APOBEC3 Barrier to Cross Species Transmission of Primate Lentiviruses. Viruses 2021; 13:1084. [PMID: 34200141 PMCID: PMC8228377 DOI: 10.3390/v13061084] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
The transmission of viruses from animal hosts into humans have led to the emergence of several diseases. Usually these cross-species transmissions are blocked by host restriction factors, which are proteins that can block virus replication at a specific step. In the natural virus host, the restriction factor activity is usually suppressed by a viral antagonist protein, but this is not the case for restriction factors from an unnatural host. However, due to ongoing viral evolution, sometimes the viral antagonist can evolve to suppress restriction factors in a new host, enabling cross-species transmission. Here we examine the classical case of this paradigm by reviewing research on APOBEC3 restriction factors and how they can suppress human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). APOBEC3 enzymes are single-stranded DNA cytidine deaminases that can induce mutagenesis of proviral DNA by catalyzing the conversion of cytidine to promutagenic uridine on single-stranded viral (-)DNA if they escape the HIV/SIV antagonist protein, Vif. APOBEC3 degradation is induced by Vif through the proteasome pathway. SIV has been transmitted between Old World Monkeys and to hominids. Here we examine the adaptations that enabled such events and the ongoing impact of the APOBEC3-Vif interface on HIV in humans.
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Affiliation(s)
| | | | - Linda Chelico
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SA S7H 0E5, Canada; (A.G.); (B.F.)
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Simmonds P, Ansari MA. Extensive C->U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral RNA. PLoS Pathog 2021; 17:e1009596. [PMID: 34061905 PMCID: PMC8195396 DOI: 10.1371/journal.ppat.1009596] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/11/2021] [Accepted: 04/29/2021] [Indexed: 11/18/2022] Open
Abstract
The rapid evolution of RNA viruses has been long considered to result from a combination of high copying error frequencies during RNA replication, short generation times and the consequent extensive fixation of neutral or adaptive changes over short periods. While both the identities and sites of mutations are typically modelled as being random, recent investigations of sequence diversity of SARS coronavirus 2 (SARS-CoV-2) have identified a preponderance of C->U transitions, proposed to be driven by an APOBEC-like RNA editing process. The current study investigated whether this phenomenon could be observed in datasets of other RNA viruses. Using a 5% divergence filter to infer directionality, 18 from 36 datasets of aligned coding region sequences from a diverse range of mammalian RNA viruses (including Picornaviridae, Flaviviridae, Matonaviridae, Caliciviridae and Coronaviridae) showed a >2-fold base composition normalised excess of C->U transitions compared to U->C (range 2.1x-7.5x), with a consistently observed favoured 5' U upstream context. The presence of genome scale RNA secondary structure (GORS) was the only other genomic or structural parameter significantly associated with C->U/U->C transition asymmetries by multivariable analysis (ANOVA), potentially reflecting RNA structure dependence of sites targeted for C->U mutations. Using the association index metric, C->U changes were specifically over-represented at phylogenetically uninformative sites, potentially paralleling extensive homoplasy of this transition reported in SARS-CoV-2. Although mechanisms remain to be functionally characterised, excess C->U substitutions accounted for 11-14% of standing sequence variability of structured viruses and may therefore represent a potent driver of their sequence diversification and longer-term evolution.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - M. Azim Ansari
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
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39
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Callens M, Pradier L, Finnegan M, Rose C, Bedhomme S. Read between the lines: Diversity of non-translational selection pressures on local codon usage. Genome Biol Evol 2021; 13:6263832. [PMID: 33944930 PMCID: PMC8410138 DOI: 10.1093/gbe/evab097] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 12/14/2022] Open
Abstract
Protein coding genes can contain specific motifs within their nucleotide sequence that function as a signal for various biological pathways. The presence of such sequence motifs within a gene can have beneficial or detrimental effects on the phenotype and fitness of an organism, and this can lead to the enrichment or avoidance of this sequence motif. The degeneracy of the genetic code allows for the existence of alternative synonymous sequences that exclude or include these motifs, while keeping the encoded amino acid sequence intact. This implies that locally, there can be a selective pressure for preferentially using a codon over its synonymous alternative in order to avoid or enrich a specific sequence motif. This selective pressure could -in addition to mutation, drift and selection for translation efficiency and accuracy- contribute to shape the codon usage bias. In this review, we discuss patterns of avoidance of (or enrichment for) the various biological signals contained in specific nucleotide sequence motifs: transcription and translation initiation and termination signals, mRNA maturation signals, and antiviral immune system targets. Experimental data on the phenotypic or fitness effects of synonymous mutations in these sequence motifs confirm that they can be targets of local selection pressures on codon usage. We also formulate the hypothesis that transposable elements could have a similar impact on codon usage through their preferred integration sequences. Overall, selection on codon usage appears to be a combination of a global selection pressure imposed by the translation machinery, and a patchwork of local selection pressures related to biological signals contained in specific sequence motifs.
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Affiliation(s)
- Martijn Callens
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Léa Pradier
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Michael Finnegan
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Caroline Rose
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Stéphanie Bedhomme
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
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Shapiro M, Krug LT, MacCarthy T. Mutational pressure by host APOBEC3s more strongly affects genes expressed early in the lytic phase of herpes simplex virus-1 (HSV-1) and human polyomavirus (HPyV) infection. PLoS Pathog 2021; 17:e1009560. [PMID: 33930088 PMCID: PMC8115780 DOI: 10.1371/journal.ppat.1009560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 05/12/2021] [Accepted: 04/14/2021] [Indexed: 01/22/2023] Open
Abstract
Herpes-Simplex Virus 1 (HSV-1) infects most humans when they are young, sometimes with fatal consequences. Gene expression occurs in a temporal order upon lytic HSV-1 infection: immediate early (IE) genes are expressed, then early (E) genes, followed by late (L) genes. During this infection cycle, the HSV-1 genome has the potential for exposure to APOBEC3 (A3) proteins, a family of cytidine deaminases that cause C>U mutations on single-stranded DNA (ssDNA), often resulting in a C>T transition. We developed a computational model for the mutational pressure of A3 on the lytic cycle of HSV-1 to determine which viral kinetic gene class is most vulnerable to A3 mutations. Using in silico stochastic methods, we simulated the infectious cycle under varying intensities of A3 mutational pressure. We found that the IE and E genes are more vulnerable to A3 than L genes. We validated this model by analyzing the A3 evolutionary footprints in 25 HSV-1 isolates. We find that IE and E genes have evolved to underrepresent A3 hotspot motifs more so than L genes, consistent with greater selection pressure on IE and E genes. We extend this model to two-step infections, such as those of polyomavirus, and find that the same pattern holds for over 25 human Polyomavirus (HPyVs) genomes. Genes expressed earlier during infection are more vulnerable to mutations than those expressed later.
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Affiliation(s)
- Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
| | - Laurie T. Krug
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, United States of America
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Cheng AZ, Moraes SN, Shaban NM, Fanunza E, Bierle CJ, Southern PJ, Bresnahan WA, Rice SA, Harris RS. APOBECs and Herpesviruses. Viruses 2021; 13:v13030390. [PMID: 33671095 PMCID: PMC7998176 DOI: 10.3390/v13030390] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 12/14/2022] Open
Abstract
The apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) family of DNA cytosine deaminases provides a broad and overlapping defense against viral infections. Successful viral pathogens, by definition, have evolved strategies to escape restriction by the APOBEC enzymes of their hosts. HIV-1 and related retroviruses are thought to be the predominant natural substrates of APOBEC enzymes due to obligate single-stranded (ss)DNA replication intermediates, abundant evidence for cDNA strand C-to-U editing (genomic strand G-to-A hypermutation), and a potent APOBEC degradation mechanism. In contrast, much lower mutation rates are observed in double-stranded DNA herpesviruses and the evidence for APOBEC mutation has been less compelling. However, recent work has revealed that Epstein-Barr virus (EBV), Kaposi’s sarcoma-associated herpesvirus (KSHV), and herpes simplex virus-1 (HSV-1) are potential substrates for cellular APOBEC enzymes. To prevent APOBEC-mediated restriction these viruses have repurposed their ribonucleotide reductase (RNR) large subunits to directly bind, inhibit, and relocalize at least two distinct APOBEC enzymes—APOBEC3B and APOBEC3A. The importance of this interaction is evidenced by genetic inactivation of the EBV RNR (BORF2), which results in lower viral infectivity and higher levels of C/G-to-T/A hypermutation. This RNR-mediated mechanism therefore likely functions to protect lytic phase viral DNA replication intermediates from APOBEC-catalyzed DNA C-to-U deamination. The RNR-APOBEC interaction defines a new pathogen-host conflict that the virus must win in real-time for transmission and pathogenesis. However, partial losses over evolutionary time may also benefit the virus by providing mutational fuel for adaptation.
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Affiliation(s)
- Adam Z. Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (S.N.M.); (N.M.S.); (E.F.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: (A.Z.C.); (R.S.H.)
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (S.N.M.); (N.M.S.); (E.F.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nadine M. Shaban
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (S.N.M.); (N.M.S.); (E.F.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Elisa Fanunza
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (S.N.M.); (N.M.S.); (E.F.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Craig J. Bierle
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Peter J. Southern
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wade A. Bresnahan
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stephen A. Rice
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (S.N.M.); (N.M.S.); (E.F.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.B.); (P.J.S.); (W.A.B.); (S.A.R.)
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: (A.Z.C.); (R.S.H.)
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Hirabayashi S, Shirakawa K, Horisawa Y, Matsumoto T, Matsui H, Yamazaki H, Sarca AD, Kazuma Y, Nomura R, Konishi Y, Takeuchi S, Stanford E, Kawaji H, Murakawa Y, Takaori-Kondo A. APOBEC3B is preferentially expressed at the G2/M phase of cell cycle. Biochem Biophys Res Commun 2021; 546:178-184. [PMID: 33592502 DOI: 10.1016/j.bbrc.2021.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/02/2021] [Indexed: 02/06/2023]
Abstract
APOBEC3B (A3B) is a cytosine deaminase that converts cytosine to uracil in single-stranded DNA. Cytosine-to-thymine and cytosine-to-guanine base substitution mutations in trinucleotide motifs (APOBEC mutational signatures) were found in various cancers including lymphoid hematological malignancies such as multiple myeloma and A3B has been shown to be an enzymatic source of mutations in those cancers. Although the importance of A3B is being increasingly recognized, it is unclear how A3B expression is regulated in cancer cells as well as normal cells. To answer these fundamental questions, we analyzed 1276 primary myeloma cells using single-cell RNA-sequencing (scRNA-seq) and found that A3B was preferentially expressed at the G2/M phase, in sharp contrast to the expression patterns of other APOBEC3 genes. Consistently, we demonstrated that A3B protein was preferentially expressed at the G2/M phase in myeloma cells by cell sorting. We also demonstrated that normal blood cells expressing A3B were also enriched in G2/M-phase cells by analyzing scRNA-seq data from 86,493 normal bone marrow mononuclear cells. Furthermore, we revealed that A3B was expressed mainly in plasma cells, CD10+ B cells and erythroid cells, but not in granulocyte-macrophage progenitors. A3B expression profiling in normal blood cells may contribute to understanding the defense mechanism of A3B against viruses, and partially explain the bias of APOBEC mutational signatures in lymphoid but not myeloid malignancies. This study identified the cells and cellular phase in which A3B is highly expressed, which may help reveal the mechanisms behind carcinogenesis and cancer heterogeneity, as well as the biological functions of A3B in normal blood cells.
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Affiliation(s)
- Shigeki Hirabayashi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihito Horisawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadahiko Matsumoto
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Matsui
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Yamazaki
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Anamaria Daniela Sarca
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhiro Kazuma
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryosuke Nomura
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshinobu Konishi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Suguru Takeuchi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Emani Stanford
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hideya Kawaji
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan; RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; IFOM-the FIRC Institute of Molecular Oncology, Milan, Italy; Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Institute for Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution. Virology 2021; 556:62-72. [PMID: 33545556 PMCID: PMC7831814 DOI: 10.1016/j.virol.2020.12.018] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022]
Abstract
Members of the APOBEC family of cytidine deaminases show antiviral activities in mammalian cells through lethal editing in the genomes of small DNA viruses, herpesviruses and retroviruses, and potentially those of RNA viruses such as coronaviruses. Consistent with the latter, APOBEC-like directional C→U transitions of genomic plus-strand RNA are greatly overrepresented in SARS-CoV-2 genome sequences of variants emerging during the COVID-19 pandemic. A C→U mutational process may leave evolutionary imprints on coronavirus genomes, including extensive homoplasy from editing and reversion at targeted sites and the occurrence of driven amino acid sequence changes in viral proteins. If sustained over longer periods, this process may account for the previously reported marked global depletion of C and excess of U bases in human seasonal coronavirus genomes. This review synthesizes the current knowledge on APOBEC evolution and function and the evidence of their role in APOBEC-mediated genome editing of SARS-CoV-2 and other coronaviruses. SARS-CoV-2 sequence variants contain an overabundance of C- > U transitions C- > U transitions are the hallmark of the activity of APOBEC cytosine deaminases Further work is needed to determine APOBEC's role in coronavirus evolution
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Ullah A, Mabood N, Maqbool M, Khan L, Ullah M. Cytidine deamination-induced perpetual immunity to SAR-CoV-2 infection is a potential new therapeutic target. Int J Med Sci 2021; 18:3788-3793. [PMID: 34790054 PMCID: PMC8579299 DOI: 10.7150/ijms.61779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/19/2021] [Indexed: 12/23/2022] Open
Abstract
As the world is racing to develop perpetual immunity to the SARS-CoV-2 virus. The emergence of new viral strains, together with vaccination and reinfections, are all contributing to a long-term immunity against the deadly virus that has taken over the world since its introduction to humans in late December 2019. The discovery that more than 95 percent of people who recovered from COVID-19 had long-lasting immunity and that asymptomatic people have a different immune response to SARS-CoV-2 than symptomatic people has shifted attention to how our immune system initiates such diverse responses. These findings have provided reason to believe that SARS-CoV-2 days are numbered. Hundreds of research papers have been published on the causes of long-lasting immune responses and variations in the numbers of different immune cell types in COVID 19 survivors, but the main reason of these differences has still not been adequately identified. In this article, we focus on the activation-induced cytidine deaminase (AID), which initiates molecular processes that allow our immune system to generate antibodies against SARS-CoV-2. To establish lasting immunity to SARS-CoV-2, we suggest that AID could be the key to unlocking it.
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Affiliation(s)
- Asad Ullah
- Department of Radiation Oncology, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Neelam Mabood
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Muhammad Maqbool
- Department of Clinical & Diagnostic Sciences, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Luqman Khan
- Cardiovascular Research Institute, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Mujib Ullah
- Department of Immunology and Transplantation, School of Medicine, Stanford University, Stanford, California, USA
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45
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The Role of APOBECs in Viral Replication. Microorganisms 2020; 8:microorganisms8121899. [PMID: 33266042 PMCID: PMC7760323 DOI: 10.3390/microorganisms8121899] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/14/2022] Open
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) proteins are a diverse and evolutionarily conserved family of cytidine deaminases that provide a variety of functions from tissue-specific gene expression and immunoglobulin diversity to control of viruses and retrotransposons. APOBEC family expansion has been documented among mammalian species, suggesting a powerful selection for their activity. Enzymes with a duplicated zinc-binding domain often have catalytically active and inactive domains, yet both have antiviral function. Although APOBEC antiviral function was discovered through hypermutation of HIV-1 genomes lacking an active Vif protein, much evidence indicates that APOBECs also inhibit virus replication through mechanisms other than mutagenesis. Multiple steps of the viral replication cycle may be affected, although nucleic acid replication is a primary target. Packaging of APOBECs into virions was first noted with HIV-1, yet is not a prerequisite for viral inhibition. APOBEC antagonism may occur in viral producer and recipient cells. Signatures of APOBEC activity include G-to-A and C-to-T mutations in a particular sequence context. The importance of APOBEC activity for viral inhibition is reflected in the identification of numerous viral factors, including HIV-1 Vif, which are dedicated to antagonism of these deaminases. Such viral antagonists often are only partially successful, leading to APOBEC selection for viral variants that enhance replication or avoid immune elimination.
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