1
|
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.
Collapse
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
| |
Collapse
|
2
|
Yang H, Pacheco J, Kim K, Ebrahimi D, Ito F, Chen XS. Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584510. [PMID: 38559028 PMCID: PMC10980023 DOI: 10.1101/2024.03.11.584510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
APOBEC3G (A3G) belongs to the AID/APOBEC cytidine deaminase family and is essential for antiviral immunity. It contains two zinc-coordinated cytidine-deaminase (CD) domains. The N-terminal CD1 domain is non-catalytic but has a strong affinity for nucleic acids, whereas the C-terminal CD2 domain catalyzes C-to-U editing in single-stranded DNA. The interplay between the two domains in DNA binding and editing is not fully understood. Here, our studies on rhesus macaque A3G (rA3G) show that the DNA editing function in linear and hairpin loop DNA is greatly enhanced by AA or GA dinucleotide motifs present downstream (in the 3'-direction) but not upstream (in the 5'-direction) of the target-C editing sites. The effective distance between AA/GA and the target-C sites depends on the local DNA secondary structure. We present two co-crystal structures of rA3G bound to ssDNA containing AA and GA, revealing the contribution of the non-catalytic CD1 domain in capturing AA/GA DNA and explaining our biochemical observations. Our structural and biochemical findings elucidate the molecular mechanism underlying the cooperative function between the non-catalytic and the catalytic domains of A3G, which is critical for its antiviral role and its contribution to genome mutations in cancer.
Collapse
Affiliation(s)
- Hanjing Yang
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Josue Pacheco
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Kyumin Kim
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Diako Ebrahimi
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Fumiaki Ito
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA90095, USA
| | - Xiaojiang S. Chen
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
- Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089, USA
| |
Collapse
|
3
|
Budzko L, Hoffa-Sobiech K, Jackowiak P, Figlerowicz M. Engineered deaminases as a key component of DNA and RNA editing tools. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102062. [PMID: 38028200 PMCID: PMC10661471 DOI: 10.1016/j.omtn.2023.102062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Over recent years, zinc-dependent deaminases have attracted increasing interest as key components of nucleic acid editing tools that can generate point mutations at specific sites in either DNA or RNA by combining a targeting module (such as a catalytically impaired CRISPR-Cas component) and an effector module (most often a deaminase). Deaminase-based molecular tools are already being utilized in a wide spectrum of therapeutic and research applications; however, their medical and biotechnological potential seems to be much greater. Recent reports indicate that the further development of nucleic acid editing systems depends largely on our ability to engineer the substrate specificity and catalytic activity of the editors themselves. In this review, we summarize the current trends and achievements in deaminase engineering. The presented data indicate that the potential of these enzymes has not yet been fully revealed or understood. Several examples show that even relatively minor changes in the structure of deaminases can give them completely new and unique properties.
Collapse
Affiliation(s)
- Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Karolina Hoffa-Sobiech
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| |
Collapse
|
4
|
Dudley JP. APOBECs: Our fickle friends? PLoS Pathog 2023; 19:e1011364. [PMID: 37200235 DOI: 10.1371/journal.ppat.1011364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Affiliation(s)
- Jaquelin P Dudley
- Department of Molecular Biosciences and LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, United States of America
| |
Collapse
|
5
|
Butler K, Banday AR. APOBEC3-mediated mutagenesis in cancer: causes, clinical significance and therapeutic potential. J Hematol Oncol 2023; 16:31. [PMID: 36978147 PMCID: PMC10044795 DOI: 10.1186/s13045-023-01425-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Apolipoprotein B mRNA-editing enzyme, catalytic polypeptides (APOBECs) are cytosine deaminases involved in innate and adaptive immunity. However, some APOBEC family members can also deaminate host genomes to generate oncogenic mutations. The resulting mutations, primarily signatures 2 and 13, occur in many tumor types and are among the most common mutational signatures in cancer. This review summarizes the current evidence implicating APOBEC3s as major mutators and outlines the exogenous and endogenous triggers of APOBEC3 expression and mutational activity. The review also discusses how APOBEC3-mediated mutagenesis impacts tumor evolution through both mutagenic and non-mutagenic pathways, including by inducing driver mutations and modulating the tumor immune microenvironment. Moving from molecular biology to clinical outcomes, the review concludes by summarizing the divergent prognostic significance of APOBEC3s across cancer types and their therapeutic potential in the current and future clinical landscapes.
Collapse
Affiliation(s)
- Kelly Butler
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A Rouf Banday
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
6
|
Specialized DNA Structures Act as Genomic Beacons for Integration by Evolutionarily Diverse Retroviruses. Viruses 2023; 15:v15020465. [PMID: 36851678 PMCID: PMC9962126 DOI: 10.3390/v15020465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Retroviral integration site targeting is not random and plays a critical role in expression and long-term survival of the integrated provirus. To better understand the genomic environment surrounding retroviral integration sites, we performed a meta-analysis of previously published integration site data from evolutionarily diverse retroviruses, including new experimental data from HIV-1 subtypes A, B, C and D. We show here that evolutionarily divergent retroviruses exhibit distinct integration site profiles with strong preferences for integration near non-canonical B-form DNA (non-B DNA). We also show that in vivo-derived HIV-1 integration sites are significantly more enriched in transcriptionally silent regions and transcription-silencing non-B DNA features of the genome compared to in vitro-derived HIV-1 integration sites. Integration sites from individuals infected with HIV-1 subtype A, B, C or D viruses exhibited different preferences for common genomic and non-B DNA features. In addition, we identified several integration site hotspots shared between different HIV-1 subtypes, all of which were located in the non-B DNA feature slipped DNA. Together, these data show that although evolutionarily divergent retroviruses exhibit distinct integration site profiles, they all target non-B DNA for integration. These findings provide new insight into how retroviruses integrate into genomes for long-term survival.
Collapse
|
7
|
Influence of viral genome properties on polymerase fidelity. Trends Genet 2023; 39:9-14. [PMID: 36402624 DOI: 10.1016/j.tig.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/27/2022] [Accepted: 10/30/2022] [Indexed: 11/17/2022]
Abstract
The first step of viral evolution takes place during genome replication via the error-prone viral polymerase. Among the mutants that arise through this process, only a few well-adapted variants will be selected by natural selection, renewing the viral genome population. Viral polymerase-mediated errors are thought to occur stochastically. However, accumulating evidence suggests that viral polymerase-mediated mutations are heterogeneously distributed throughout the viral genome. Here, we review work that supports this concept and provides mechanistic insights into how specific features of the viral genome could modulate viral polymerase-mediated errors. A predisposition to accumulate viral polymerase-mediated errors at specific loci in the viral genome may guide evolution to specific pathways, thus opening new directions of research to better understand viral evolutionary dynamics.
Collapse
|
8
|
Yang H, Kim K, Li S, Pacheco J, Chen XS. Structural basis of sequence-specific RNA recognition by the antiviral factor APOBEC3G. Nat Commun 2022; 13:7498. [PMID: 36470880 PMCID: PMC9722718 DOI: 10.1038/s41467-022-35201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
An essential step in restricting HIV infectivity by the antiviral factor APOBEC3G is its incorporation into progeny virions via binding to HIV RNA. However, the mechanism of APOBEC3G capturing viral RNA is unknown. Here, we report crystal structures of a primate APOBEC3G bound to different types of RNAs, revealing that APOBEC3G specifically recognizes unpaired 5'-AA-3' dinucleotides, and to a lesser extent, 5'-GA-3' dinucleotides. APOBEC3G binds to the common 3'A in the AA/GA motifs using an aromatic/hydrophobic pocket in the non-catalytic domain. It binds to the 5'A or 5'G in the AA/GA motifs using an aromatic/hydrophobic groove conformed between the non-catalytic and catalytic domains. APOBEC3G RNA binding property is distinct from that of the HIV nucleocapsid protein recognizing unpaired guanosines. Our findings suggest that the sequence-specific RNA recognition is critical for APOBEC3G virion packaging and restricting HIV infectivity.
Collapse
Affiliation(s)
- Hanjing Yang
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA
| | - Kyumin Kim
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA
| | - Shuxing Li
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA ,grid.42505.360000 0001 2156 6853Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089 USA
| | - Josue Pacheco
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA
| | - Xiaojiang S. Chen
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA ,grid.42505.360000 0001 2156 6853Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089 USA ,grid.42505.360000 0001 2156 6853Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, Los Angeles, CA 90033 USA ,grid.42505.360000 0001 2156 6853Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033 USA
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Abstract
The AID/APOBEC polynucleotide cytidine deaminases have historically been classified as either DNA mutators or RNA editors based on their first identified nucleic acid substrate preference. DNA mutators can generate functional diversity at antibody genes but also cause genomic instability in cancer. RNA editors can generate informational diversity in the transcriptome of innate immune cells, and of cancer cells. Members of both classes can act as antiviral restriction factors. Recent structural work has illuminated differences and similarities between AID/APOBEC enzymes that can catalyse DNA mutation, RNA editing or both, suggesting that the strict functional classification of members of this family should be reconsidered. As many of these enzymes have been employed for targeted genome (or transcriptome) editing, a more holistic understanding will help improve the design of therapeutically relevant programmable base editors. In this Perspective, Pecori et al. provide an overview of the AID/APOBEC cytidine deaminase family, discussing key structural features, how they contribute to viral and tumour evolution and how they can be harnessed for (potentially therapeutic) base-editing purposes.
Collapse
|
11
|
Differential Activity of APOBEC3F, APOBEC3G, and APOBEC3H in the Restriction of HIV-2. J Mol Biol 2022; 434:167355. [PMID: 34774569 PMCID: PMC8752514 DOI: 10.1016/j.jmb.2021.167355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 02/01/2023]
Abstract
Human immunodeficiency virus (HIV) mutagenesis is driven by a variety of internal and external sources, including the host APOBEC3 (apolipoprotein B mRNA editing enzyme catalytic polypetide-like 3; A3) family of mutagenesis factors, which catalyze G-to-A transition mutations during virus replication. HIV-2 replication is characterized by a relative lack of G-to-A mutations, suggesting infrequent mutagenesis by A3 proteins. To date, the activity of the A3 repertoire against HIV-2 has remained largely uncharacterized, and the mutagenic activity of these proteins against HIV-2 remains to be elucidated. In this study, we provide the first comprehensive characterization of the restrictive capacity of A3 proteins against HIV-2 in cell culture using a dual fluorescent reporter HIV-2 vector virus. We found that A3F, A3G, and A3H restricted HIV-2 infectivity in the absence of Vif and were associated with significant increases in the frequency of viral mutants. These proteins increased the frequency of G-to-A mutations within the proviruses of infected cells as well. A3G and A3H also reduced HIV-2 infectivity via inhibition of reverse transcription and the accumulation of DNA products during replication. In contrast, A3D did not exhibit any restrictive activity against HIV-2, even at higher expression levels. Taken together, these results provide evidence that A3F, A3G, and A3H, but not A3D, are capable of HIV-2 restriction. Differences in A3-mediated restriction of HIV-1 and HIV-2 may serve to provide new insights in the observed mutation profiles of these viruses.
Collapse
|
12
|
Wei Y, Silke JR, Aris P, Xia X. Coronavirus genomes carry the signatures of their habitats. PLoS One 2020; 15:e0244025. [PMID: 33351847 PMCID: PMC7755226 DOI: 10.1371/journal.pone.0244025] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/01/2020] [Indexed: 12/15/2022] Open
Abstract
Coronaviruses such as SARS-CoV-2 regularly infect host tissues that express antiviral proteins (AVPs) in abundance. Understanding how they evolve to adapt or evade host immune responses is important in the effort to control the spread of infection. Two AVPs that may shape viral genomes are the zinc finger antiviral protein (ZAP) and the apolipoprotein B mRNA editing enzyme-catalytic polypeptide-like 3 (APOBEC3). The former binds to CpG dinucleotides to facilitate the degradation of viral transcripts while the latter frequently deaminates C into U residues which could generate notable viral sequence variations. We tested the hypothesis that both APOBEC3 and ZAP impose selective pressures that shape the genome of an infecting coronavirus. Our investigation considered a comprehensive number of publicly available genomes for seven coronaviruses (SARS-CoV-2, SARS-CoV, and MERS infecting Homo sapiens, Bovine CoV infecting Bos taurus, MHV infecting Mus musculus, HEV infecting Sus scrofa, and CRCoV infecting Canis lupus familiaris). We show that coronaviruses that regularly infect tissues with abundant AVPs have CpG-deficient and U-rich genomes; whereas those that do not infect tissues with abundant AVPs do not share these sequence hallmarks. Among the coronaviruses surveyed herein, CpG is most deficient in SARS-CoV-2 and a temporal analysis showed a marked increase in C to U mutations over four months of SARS-CoV-2 genome evolution. Furthermore, the preferred motifs in which these C to U mutations occur are the same as those subjected to APOBEC3 editing in HIV-1. These results suggest that both ZAP and APOBEC3 shape the SARS-CoV-2 genome: ZAP imposes a strong CpG avoidance, and APOBEC3 constantly edits C to U. Evolutionary pressures exerted by host immune systems onto viral genomes may motivate novel strategies for SARS-CoV-2 vaccine development.
Collapse
Affiliation(s)
- Yulong Wei
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Jordan R. Silke
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Parisa Aris
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
13
|
Hakata Y, Miyazawa M. Deaminase-Independent Mode of Antiretroviral Action in Human and Mouse APOBEC3 Proteins. Microorganisms 2020; 8:microorganisms8121976. [PMID: 33322756 PMCID: PMC7764128 DOI: 10.3390/microorganisms8121976] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023] Open
Abstract
Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3) proteins (APOBEC3s) are deaminases that convert cytosines to uracils predominantly on a single-stranded DNA, and function as intrinsic restriction factors in the innate immune system to suppress replication of viruses (including retroviruses) and movement of retrotransposons. Enzymatic activity is supposed to be essential for the APOBEC3 antiviral function. However, it is not the only way that APOBEC3s exert their biological function. Since the discovery of human APOBEC3G as a restriction factor for HIV-1, the deaminase-independent mode of action has been observed. At present, it is apparent that both the deaminase-dependent and -independent pathways are tightly involved not only in combating viruses but also in human tumorigenesis. Although the deaminase-dependent pathway has been extensively characterized so far, understanding of the deaminase-independent pathway remains immature. Here, we review existing knowledge regarding the deaminase-independent antiretroviral functions of APOBEC3s and their molecular mechanisms. We also discuss the possible unidentified molecular mechanism for the deaminase-independent antiretroviral function mediated by mouse APOBEC3.
Collapse
Affiliation(s)
- Yoshiyuki Hakata
- Department of Immunology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan;
- Correspondence: ; Tel.: +81-72-367-7660
| | - Masaaki Miyazawa
- Department of Immunology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan;
- Kindai University Anti-Aging Center, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| |
Collapse
|
14
|
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.
Collapse
|
15
|
Shi MJ, Meng XY, Fontugne J, Chen CL, Radvanyi F, Bernard-Pierrot I. Identification of new driver and passenger mutations within APOBEC-induced hotspot mutations in bladder cancer. Genome Med 2020; 12:85. [PMID: 32988402 PMCID: PMC7646471 DOI: 10.1186/s13073-020-00781-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 09/11/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND APOBEC-driven mutagenesis and functional positive selection of mutated genes may synergistically drive the higher frequency of some hotspot driver mutations compared to other mutations within the same gene, as we reported for FGFR3 S249C. Only a few APOBEC-associated driver hotspot mutations have been identified in bladder cancer (BCa). Here, we systematically looked for and characterised APOBEC-associated hotspots in BCa. METHODS We analysed 602 published exome-sequenced BCas, for part of which gene expression data were also available. APOBEC-associated hotspots were identified by motif-mapping, mutation signature fitting and APOBEC-mediated mutagenesis comparison. Joint analysis of DNA hairpin stability and gene expression was performed to predict driver or passenger hotspots. Aryl hydrocarbon receptor (AhR) activity was calculated based on its target genes expression. Effects of AhR knockout/inhibition on BCa cell viability were analysed. RESULTS We established a panel of 44 APOBEC-associated hotspot mutations in BCa, which accounted for about half of the hotspot mutations. Fourteen of them overlapped with the hotspots found in other cancer types with high APOBEC activity. They mostly occurred in the DNA lagging-strand templates and the loop of DNA hairpins. APOBEC-associated hotspots presented systematically a higher prevalence than the other mutations within each APOBEC-target gene, independently of their functional impact. A combined analysis of DNA loop stability and gene expression allowed to distinguish known passenger from known driver hotspot mutations in BCa, including loss-of-function mutations affecting tumour suppressor genes, and to predict new candidate drivers, such as AHR Q383H. We further characterised AHR Q383H as an activating driver mutation associated with high AhR activity in luminal tumours. High AhR activity was also found in tumours presenting amplifications of AHR and its co-receptor ARNT. We finally showed that BCa cells presenting those different genetic alterations were sensitive to AhR inhibition. CONCLUSIONS Our study identified novel potential drivers within APOBEC-associated hotspot mutations in BCa reinforcing the importance of APOBEC mutagenesis in BCa. It could allow a better understanding of BCa biology and aetiology and have clinical implications such as AhR as a potential therapeutic target. Our results also challenge the dogma that all hotspot mutations are drivers and mostly gain-of-function mutations affecting oncogenes.
Collapse
Affiliation(s)
- Ming-Jun Shi
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Institut Curie, CNRS, UMR144, Molecular Oncology team, PSL Research University, 26 Rue d'Ulm, 75005, Paris, France
- Paris-Saclay University, Paris, France
| | - Xiang-Yu Meng
- Institut Curie, CNRS, UMR144, Molecular Oncology team, PSL Research University, 26 Rue d'Ulm, 75005, Paris, France.
- Paris-Saclay University, Paris, France.
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Jacqueline Fontugne
- Institut Curie, CNRS, UMR144, Molecular Oncology team, PSL Research University, 26 Rue d'Ulm, 75005, Paris, France
- Paris-Saclay University, Paris, France
| | - Chun-Long Chen
- Institut Curie, CNRS, UMR3244, PSL Research University, Paris, France
- Sorbonne Université, Paris, France
| | - François Radvanyi
- Institut Curie, CNRS, UMR144, Molecular Oncology team, PSL Research University, 26 Rue d'Ulm, 75005, Paris, France
| | - Isabelle Bernard-Pierrot
- Institut Curie, CNRS, UMR144, Molecular Oncology team, PSL Research University, 26 Rue d'Ulm, 75005, Paris, France.
| |
Collapse
|
16
|
Mas-Ponte D, Supek F. DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers. Nat Genet 2020; 52:958-968. [PMID: 32747826 PMCID: PMC7610516 DOI: 10.1038/s41588-020-0674-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 06/30/2020] [Indexed: 01/12/2023]
Abstract
Certain mutagens, including the APOBEC3 (A3) cytosine deaminase enzymes, can create multiple genetic changes in a single event. Activity of A3s results in striking 'mutation showers' occurring near DNA breakpoints; however, less is known about the mechanisms underlying the majority of A3 mutations. We classified the diverse patterns of clustered mutagenesis in tumor genomes, which identified a new A3 pattern: nonrecurrent, diffuse hypermutation (omikli). This mechanism occurs independently of the known focal hypermutation (kataegis), and is associated with activity of the DNA mismatch-repair pathway, which can provide the single-stranded DNA substrate needed by A3, and contributes to a substantial proportion of A3 mutations genome wide. Because mismatch repair is directed towards early-replicating, gene-rich chromosomal domains, A3 mutagenesis has a high propensity to generate impactful mutations, which exceeds that of other common carcinogens such as tobacco smoke and ultraviolet exposure. Cells direct their DNA repair capacity towards more important genomic regions; thus, carcinogens that subvert DNA repair can be remarkably potent.
Collapse
Affiliation(s)
- David Mas-Ponte
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fran Supek
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| |
Collapse
|
17
|
Delviks-Frankenberry KA, Desimmie BA, Pathak VK. Structural Insights into APOBEC3-Mediated Lentiviral Restriction. Viruses 2020; 12:E587. [PMID: 32471198 PMCID: PMC7354603 DOI: 10.3390/v12060587] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 01/18/2023] Open
Abstract
Mammals have developed clever adaptive and innate immune defense mechanisms to protect against invading bacterial and viral pathogens. Human innate immunity is continuously evolving to expand the repertoire of restriction factors and one such family of intrinsic restriction factors is the APOBEC3 (A3) family of cytidine deaminases. The coordinated expression of seven members of the A3 family of cytidine deaminases provides intrinsic immunity against numerous foreign infectious agents and protects the host from exogenous retroviruses and endogenous retroelements. Four members of the A3 proteins-A3G, A3F, A3H, and A3D-restrict HIV-1 in the absence of virion infectivity factor (Vif); their incorporation into progeny virions is a prerequisite for cytidine deaminase-dependent and -independent activities that inhibit viral replication in the host target cell. HIV-1 encodes Vif, an accessory protein that antagonizes A3 proteins by targeting them for polyubiquitination and subsequent proteasomal degradation in the virus producing cells. In this review, we summarize our current understanding of the role of human A3 proteins as barriers against HIV-1 infection, how Vif overcomes their antiviral activity, and highlight recent structural and functional insights into A3-mediated restriction of lentiviruses.
Collapse
Affiliation(s)
| | | | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA; (K.A.D.-F.); (B.A.D.)
| |
Collapse
|
18
|
McDaniel YZ, Wang D, Love RP, Adolph MB, Mohammadzadeh N, Chelico L, Mansky LM. Deamination hotspots among APOBEC3 family members are defined by both target site sequence context and ssDNA secondary structure. Nucleic Acids Res 2020; 48:1353-1371. [PMID: 31943071 PMCID: PMC7026630 DOI: 10.1093/nar/gkz1164] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 12/26/2022] Open
Abstract
The human apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3, A3) family member proteins can deaminate cytosines in single-strand (ss) DNA, which restricts human immunodeficiency virus type 1 (HIV-1), retrotransposons, and other viruses such as hepatitis B virus, but can cause a mutator phenotype in many cancers. While structural information exists for several A3 proteins, the precise details regarding deamination target selection are not fully understood. Here, we report the first parallel, comparative analysis of site selection of A3 deamination using six of the seven purified A3 member enzymes, oligonucleotides having 5'TC3' or 5'CT3' dinucleotide target sites, and different flanking bases within diverse DNA secondary structures. A3A, A3F and A3H were observed to have strong preferences toward the TC target flanked by A or T, while all examined A3 proteins did not show a preference for a TC target flanked by a G. We observed that the TC target was strongly preferred in ssDNA regions rather than dsDNA, loop or bulge regions, with flanking bases influencing the degree of preference. CT was also shown to be a potential deamination target. Taken together, our observations provide new insights into A3 enzyme target site selection and how A3 mutagenesis impacts mutation rates.
Collapse
Affiliation(s)
- Yumeng Z McDaniel
- Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455 USA
| | - Dake Wang
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455 USA
- Pharmacology Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
| | - Robin P Love
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Madison B Adolph
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Nazanin Mohammadzadeh
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Linda Chelico
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Louis M Mansky
- Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455 USA
- Pharmacology Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455 USA
- Department of Microbiology & Immunology, University of Minnesota, Minneapolis, MN 55455 USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| |
Collapse
|
19
|
Barzak FM, Harjes S, Kvach MV, Kurup HM, Jameson GB, Filichev VV, Harjes E. Selective inhibition of APOBEC3 enzymes by single-stranded DNAs containing 2'-deoxyzebularine. Org Biomol Chem 2019; 17:9435-9441. [PMID: 31603457 DOI: 10.1039/c9ob01781j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
To restrict pathogens, in a normal human cell, APOBEC3 enzymes mutate cytosine to uracil in foreign single-stranded DNAs. However, in cancer cells, APOBEC3B (one of seven APOBEC3 enzymes) has been identified as the primary source of genetic mutations. As such, APOBEC3B promotes evolution and progression of cancers and leads to development of drug resistance in multiple cancers. As APOBEC3B is a non-essential protein, its inhibition can be used to suppress emergence of drug resistance in existing anti-cancer therapies. Because of the vital role of APOBEC3 enzymes in innate immunity, selective inhibitors targeting only APOBEC3B are required. Here, we use the discriminative properties of wild-type APOBEC3A, APOBEC3B and APOBEC3G to deaminate different cytosines in the CCC-recognition motif in order to best place the cytidine analogue 2'-deoxyzebularine (dZ) in the CCC-motif. Using several APOBEC3 variants that mimic deamination patterns of wild-type enzymes, we demonstrate that selective inhibition of APOBEC3B in preference to other APOBEC3 constructs is feasible for the dZCC motif. This work is an important step towards development of in vivo tools to inhibit APOBEC3 enzymes in living cells by using short, chemically modified oligonucleotides.
Collapse
Affiliation(s)
- Fareeda M Barzak
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | | | | | | | | | | | | |
Collapse
|
20
|
Role of co-expressed APOBEC3F and APOBEC3G in inducing HIV-1 drug resistance. Heliyon 2019; 5:e01498. [PMID: 31025011 PMCID: PMC6475876 DOI: 10.1016/j.heliyon.2019.e01498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/24/2019] [Accepted: 04/05/2019] [Indexed: 01/04/2023] Open
Abstract
The APOBEC3 enzymes can induce mutagenesis of HIV-1 proviral DNA through the deamination of cytosine. HIV-1 overcomes this restriction through the viral protein Vif that induces APOBEC3 proteasomal degradation. Within this dynamic host-pathogen relationship, the APOBEC3 enzymes have been found to be beneficial, neutral, or detrimental to HIV-1 biology. Here, we assessed the ability of co-expressed APOBEC3F and APOBEC3G to induce HIV-1 resistance to antiviral drugs. We found that co-expression of APOBEC3F and APOBEC3G enabled partial resistance of APOBEC3F to Vif-mediated degradation with a corresponding increase in APOBEC3F-induced deaminations in the presence of Vif, in addition to APOBEC3G-induced deaminations. We recovered HIV-1 drug resistant variants resulting from APOBEC3-induced mutagenesis, but these variants were less able to replicate than drug resistant viruses derived from RT-induced mutations alone. The data support a model in which APOBEC3 enzymes cooperate to restrict HIV-1, promoting viral inactivation over evolution to drug resistance.
Collapse
|
21
|
Borzooee F, Larijani M. Pichia pastoris as a host for production and isolation of mutagenic AID/APOBEC enzymes involved in cancer and immunity. N Biotechnol 2019; 51:67-79. [PMID: 30822538 DOI: 10.1016/j.nbt.2019.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 12/14/2022]
Abstract
AID/APOBEC3 enzymes are cytidine deaminases that mutate antibody and retroviral genes and also mediate extensive tumor genome mutagenesis. The study of purified AID/APOBEC3 proteins is challenged by difficulties with their expression and purification arising from genotoxicity in expression hosts, extensive non-specific protein-protein/DNA/RNA interactions and haphazard oligomerization. To date, expression hosts for purification of AID/APOBEC3 enzymes include bacteria, insect and mammalian cells. Here the establishment and optimization of a yeast expression/secretion system for AID/APOBEC3s are reported, followed by comparison with the same enzymes expressed in bacterial and mammalian hosts. AID and APOBEC3G were expressed successfully in Pichia pastoris, each either with an N-terminal GST tag, C-terminal V5-His tag or as untagged native form. It was verified that the yeast-expressed enzymes exhibit identical biochemical properties to those reported using bacterial and mammalian expression, indicating high fidelity of protein folding. It was demonstrated that the system can be adapted for secretion of the enzymes into the media which was used directly in various enzyme assays. The system is also amenable to elimination of bulky fusion tags, providing native untagged enzymes. Thus, P. pastoris is an advantageous expression factory for AID/APOBEC3 enzymes, considering the cost, time, efficiency and quality of the obtained enzymes. The first report is also provided here of a functionally active, untagged, secreted AID, which may become a useful research reagent. A comprehensive comparison is made of the effect of fusion tags and expression hosts on the biochemical actions of AID and APOBEC3G.
Collapse
Affiliation(s)
- Faezeh Borzooee
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, Canada.
| | - Mani Larijani
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, Canada.
| |
Collapse
|
22
|
Borzooee F, Joris KD, Grant MD, Larijani M. APOBEC3G Regulation of the Evolutionary Race Between Adaptive Immunity and Viral Immune Escape Is Deeply Imprinted in the HIV Genome. Front Immunol 2019; 9:3032. [PMID: 30687306 PMCID: PMC6338068 DOI: 10.3389/fimmu.2018.03032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 12/07/2018] [Indexed: 12/16/2022] Open
Abstract
APOBEC3G (A3G) is a host enzyme that mutates the genomes of retroviruses like HIV. Since A3G is expressed pre-infection, it has classically been considered an agent of innate immunity. We and others previously showed that the impact of A3G-induced mutations on the HIV genome extends to adaptive immunity also, by generating cytotoxic T cell (CTL) escape mutations. Accordingly, HIV genomic sequences encoding CTL epitopes often contain A3G-mutable “hotspot” sequence motifs, presumably to channel A3G action toward CTL escape. Here, we studied the depths and consequences of this apparent viral genome co-evolution with A3G. We identified all potential CTL epitopes in Gag, Pol, Env, and Nef restricted to several HLA class I alleles. We simulated A3G-induced mutations within CTL epitope-encoding sequences, and flanking regions. From the immune recognition perspective, we analyzed how A3G-driven mutations are predicted to impact CTL-epitope generation through modulating proteasomal processing and HLA class I binding. We found that A3G mutations were most often predicted to result in diminishing/abolishing HLA-binding affinity of peptide epitopes. From the viral genome evolution perspective, we evaluated enrichment of A3G hotspots at sequences encoding CTL epitopes and included control sequences in which the HIV genome was randomly shuffled. We found that sequences encoding immunogenic epitopes exhibited a selective enrichment of A3G hotspots, which were strongly biased to translate to non-synonymous amino acid substitutions. When superimposed on the known mutational gradient across the entire length of the HIV genome, we observed a gradient of A3G hotspot enrichment, and an HLA-specific pattern of the potential of A3G hotspots to lead to CTL escape mutations. These data illuminate the depths and extent of the co-evolution of the viral genome to subvert the host mutator A3G.
Collapse
Affiliation(s)
- Faezeh Borzooee
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Krista D Joris
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Michael D Grant
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Mani Larijani
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| |
Collapse
|
23
|
Poulos RC, Wong YT, Ryan R, Pang H, Wong JWH. Analysis of 7,815 cancer exomes reveals associations between mutational processes and somatic driver mutations. PLoS Genet 2018; 14:e1007779. [PMID: 30412573 PMCID: PMC6249022 DOI: 10.1371/journal.pgen.1007779] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/21/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023] Open
Abstract
Driver mutations are the genetic variants responsible for oncogenesis, but how specific somatic mutational events arise in cells remains poorly understood. Mutational signatures derive from the frequency of mutated trinucleotides in a given cancer sample, and they provide an avenue for investigating the underlying mutational processes that operate in cancer. Here we analyse somatic mutations from 7,815 cancer exomes from The Cancer Genome Atlas (TCGA) across 26 cancer types. We curate a list of 50 known cancer driver mutations by analysing recurrence in our cohort and annotations of known cancer-associated genes from the Cancer Gene Census, IntOGen database and Cancer Genome Interpreter. We then use these datasets to perform binary univariate logistic regression and establish the statistical relationship between individual driver mutations and known mutational signatures across different cancer types. Our analysis led to the identification of 39 significant associations between driver mutations and mutational signatures (P < 0.004, with a false discovery rate of < 5%). We first validate our methodology by establishing statistical links for known and novel associations between driver mutations and the mutational signature arising from Polymerase Epsilon proofreading deficiency. We then examine associations between driver mutations and mutational signatures for AID/APOBEC enzyme activity and deficient mismatch repair. We also identify negative associations (odds ratio < 1) between mutational signatures and driver mutations, and here we examine the role of aging and cigarette smoke mutagenesis in the generation of driver mutations in IDH1 and KRAS in brain cancers and lung adenocarcinomas respectively. Our study provides statistical foundations for hypothesised links between otherwise independent biological processes and we uncover previously unexplored relationships between driver mutations and mutagenic processes during cancer development. These associations give insights into how cancers acquire advantageous mutations and can provide direction to guide further mechanistic studies into cancer pathogenesis. Cancer develops when cells acquire somatic driver mutations that confer a growth advantage. The origins underlying the development of many of these mutations remain largely unknown. Mutational signatures represent the frequency of different somatic mutations across a genome and can be used to characterise the mutational processes that have operated over time within an individual cancer. In this study, we use mutational signatures as a tool to identify associations between mutational processes and cancer-causing mutations known as drivers. We hypothesised that in some cases a driver mutation would be the underlying cause of an associated signature. In other cases, the altered trinucleotide preferences arising from a signature would have increased the likelihood of the associated driver mutation arising. We determine which scenario is most likely to be the case by examining the trinucleotide context of each driver mutation. Here we identify 39 significant associations using a cohort of 7,815 cancer exomes. We examine known and novel associations between driver mutations and mutational signatures arising from processes such as defective proofreading during DNA replication, AID/APOBEC enzyme-associated mutagenesis and deficient mismatch repair. Our study explores important relationships that can inform our understanding of the complex pathogenic history associated with cancer development.
Collapse
Affiliation(s)
- Rebecca C. Poulos
- Prince of Wales Clinical School and Lowy Cancer Research Centre, Faculty of Medicine, UNSW Sydney, NSW, Australia
- Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Yuen T. Wong
- Prince of Wales Clinical School and Lowy Cancer Research Centre, Faculty of Medicine, UNSW Sydney, NSW, Australia
| | - Regina Ryan
- Prince of Wales Clinical School and Lowy Cancer Research Centre, Faculty of Medicine, UNSW Sydney, NSW, Australia
| | - Herbert Pang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Jason W. H. Wong
- Prince of Wales Clinical School and Lowy Cancer Research Centre, Faculty of Medicine, UNSW Sydney, NSW, Australia
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- * E-mail:
| |
Collapse
|
24
|
Strategy of Human Cytomegalovirus To Escape Interferon Beta-Induced APOBEC3G Editing Activity. J Virol 2018; 92:JVI.01224-18. [PMID: 30045985 DOI: 10.1128/jvi.01224-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 01/26/2023] Open
Abstract
The apolipoprotein B editing enzyme catalytic subunit 3 (APOBEC3) is a family of DNA cytosine deaminases that mutate and inactivate viral genomes by single-strand DNA editing, thus providing an innate immune response against a wide range of DNA and RNA viruses. In particular, APOBEC3A (A3A), a member of the APOBEC3 family, is induced by human cytomegalovirus (HCMV) in decidual tissues where it efficiently restricts HCMV replication, thereby acting as an intrinsic innate immune effector at the maternal-fetal interface. However, the widespread incidence of congenital HCMV infection implies that HCMV has evolved to counteract APOBEC3-induced mutagenesis through mechanisms that still remain to be fully established. Here, we have assessed gene expression and deaminase activity of various APOBEC3 gene family members in HCMV-infected primary human foreskin fibroblasts (HFFs). Specifically, we show that APOBEC3G (A3G) gene products and, to a lesser degree, those of A3F but not of A3A, are upregulated in HCMV-infected HFFs. We also show that HCMV-mediated induction of A3G expression is mediated by interferon beta (IFN-β), which is produced early during HCMV infection. However, knockout or overexpression of A3G does not affect HCMV replication, indicating that A3G is not a restriction factor for HCMV. Finally, through a bioinformatics approach, we show that HCMV has evolved mutational robustness against IFN-β by limiting the presence of A3G hot spots in essential open reading frames (ORFs) of its genome. Overall, our findings uncover a novel immune evasion strategy by HCMV with profound implications for HCMV infections.IMPORTANCE APOBEC3 family of proteins plays a pivotal role in intrinsic immunity defense mechanisms against multiple viral infections, including retroviruses, through the deamination activity. However, the currently available data on APOBEC3 editing mechanisms upon HCMV infection remain unclear. In the present study, we show that particularly the APOBEC3G (A3G) member of the deaminase family is strongly induced upon infection with HCMV in fibroblasts and that its upregulation is mediated by IFN-β. Furthermore, we were able to demonstrate that neither A3G knockout nor A3G overexpression appears to modulate HCMV replication, indicating that A3G does not inhibit HCMV replication. This may be explained by HCMV escape strategy from A3G activity through depletion of the preferred nucleotide motifs (hot spots) from its genome. The results may shed light on antiviral potential of APOBEC3 activity during HCMV infection, as well as the viral counteracting mechanisms under A3G-mediated selective pressure.
Collapse
|
25
|
Szlachta K, Thys RG, Atkin ND, Pierce LCT, Bekiranov S, Wang YH. Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human. Genome Biol 2018; 19:89. [PMID: 30001206 PMCID: PMC6042338 DOI: 10.1186/s13059-018-1463-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/13/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Alternative DNA secondary structures can arise from single-stranded DNA when duplex DNA is unwound during DNA processes such as transcription, resulting in the regulation or perturbation of these processes. We identify sites of high propensity to form stable DNA secondary structure across the human genome using Mfold and ViennaRNA programs with parameters for analyzing DNA. RESULTS The promoter-proximal regions of genes with paused transcription are significantly and energetically more favorable to form DNA secondary structure than non-paused genes or genes without RNA polymerase II (Pol II) binding. Using Pol II ChIP-seq, GRO-seq, NET-seq, and mNET-seq data, we arrive at a robust set of criteria for Pol II pausing, independent of annotation, and find that a highly stable secondary structure is likely to form about 10-50 nucleotides upstream of a Pol II pausing site. Structure probing data confirm the existence of DNA secondary structures enriched at the promoter-proximal regions of paused genes in human cells. Using an in vitro transcription assay, we demonstrate that Pol II pausing at HSPA1B, a human heat shock gene, is affected by manipulating DNA secondary structure upstream of the pausing site. CONCLUSIONS Our results indicate alternative DNA secondary structure formation as a mechanism for how GC-rich sequences regulate RNA Pol II promoter-proximal pausing genome-wide.
Collapse
Affiliation(s)
- Karol Szlachta
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA
| | - Ryan G Thys
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA
| | - Naomi D Atkin
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA
| | | | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA.
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA.
| |
Collapse
|
26
|
Temerozo JR, de Azevedo SSD, Insuela DBR, Vieira RC, Ferreira PLC, Carvalho VF, Bello G, Bou-Habib DC. The Neuropeptides Vasoactive Intestinal Peptide and Pituitary Adenylate Cyclase-Activating Polypeptide Control HIV-1 Infection in Macrophages Through Activation of Protein Kinases A and C. Front Immunol 2018; 9:1336. [PMID: 29951068 PMCID: PMC6008521 DOI: 10.3389/fimmu.2018.01336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/29/2018] [Indexed: 12/19/2022] Open
Abstract
Vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide (PACAP) are highly similar neuropeptides present in several tissues, endowed with immunoregulatory functions and other systemic effects. We previously reported that both neuropeptides reduce viral production in HIV-1-infected primary macrophages, with the participation of β-chemokines and IL-10, and now we describe molecular mechanisms engaged in this activity. Macrophages exposed to VIP or PACAP before HIV-1 infection showed resistance to viral replication, comparable to that observed when the cells were treated after infection. Also, multiple treatments with a suboptimal dose of VIP or PACAP after macrophage infection resulted in a decline of virus production similar to the inhibition promoted by a single exposure to the optimal inhibitory concentration. Cellular signaling pathways involving cAMP production and activation of protein kinases A and C were critical components of the VIP and PACAP anti-HIV-1 effects. Analysis of the transcription factors and the transcriptional/cell cycle regulators showed that VIP and PACAP induced cAMP response element-binding protein activation, inhibited NF-kB, and reduced Cyclin D1 levels in HIV-1-infected cells. Remarkably, VIP and PACAP promoted G-to-A mutations in the HIV-1 provirus, matching those derived from the activity of the APOBEC family of viral restriction factors, and reduced viral infectivity. In conclusion, our findings strengthen the antiretroviral potential of VIP and PACAP and point to new therapeutic approaches to control the progression of HIV-1 infection.
Collapse
Affiliation(s)
- Jairo R Temerozo
- Laboratory on Thymus Research, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil.,National Institute of Science and Technology on Neuroimmunomodulation, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| | - Suwellen S D de Azevedo
- Laboratory of AIDS and Molecular Immunology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| | - Daniella B R Insuela
- Laboratory of Inflammation, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| | - Rhaíssa C Vieira
- Laboratory on Thymus Research, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| | - Pedro L C Ferreira
- Laboratory on Thymus Research, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| | - Vinícius F Carvalho
- National Institute of Science and Technology on Neuroimmunomodulation, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil.,Laboratory of Inflammation, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratory of AIDS and Molecular Immunology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| | - Dumith Chequer Bou-Habib
- Laboratory on Thymus Research, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil.,National Institute of Science and Technology on Neuroimmunomodulation, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| |
Collapse
|
27
|
Salter JD, Smith HC. Modeling the Embrace of a Mutator: APOBEC Selection of Nucleic Acid Ligands. Trends Biochem Sci 2018; 43:606-622. [PMID: 29803538 PMCID: PMC6073885 DOI: 10.1016/j.tibs.2018.04.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 12/17/2022]
Abstract
The 11-member APOBEC (apolipoprotein B mRNA editing catalytic polypeptide-like) family of zinc-dependent cytidine deaminases bind to RNA and single-stranded DNA (ssDNA) and, in specific contexts, modify select (deoxy)cytidines to (deoxy)uridines. In this review, we describe advances made through high-resolution co-crystal structures of APOBECs bound to mono- or oligonucleotides that reveal potential substrate-specific binding sites at the active site and non-sequence-specific nucleic acid binding sites distal to the active site. We also discuss the effect of APOBEC oligomerization on functionality. Future structural studies will need to address how ssDNA binding away from the active site may enhance catalysis and the mechanism by which RNA binding may modulate catalytic activity on ssDNA. APOBEC proteins catalyze deamination of cytidine or deoxycytidine in either a sequence-specific or semi-specific manner on either DNA or RNA. APOBECs each possess the cytidine deaminase core fold, but sequence and structural differences among loops surrounding the zinc-dependent active site impart differences in sequence-dependent target preferences, binding affinity, catalytic rate, and regulation of substrate access to the active site among the 11 family members. APOBECs also regulate the deamination reaction through additional nucleic acid substrate binding sites located within surface grooves or patches of positive electrostatic potential that are distal to the active site but may do so nonspecifically. Binding of nonsubstrate RNA and RNA-mediated oligomerization by APOBECs that deaminate ssDNA downregulates catalytic activity but also controls APOBEC subcellular or virion localization. The presence of a second, though noncatalytic, cytidine deaminase domain for some APOBECs and the ability of some APOBECs to oligomerize add additional molecular surfaces for positive or negative regulation of catalysis through nucleic acid binding.
Collapse
Affiliation(s)
- Jason D Salter
- OyaGen, Inc., 77 Ridgeland Road, Rochester, NY 14623, USA.
| | - Harold C Smith
- OyaGen, Inc., 77 Ridgeland Road, Rochester, NY 14623, USA; University of Rochester, School of Medicine and Dentistry, Department of Biochemistry and Biophysics, 601 Elmwood Avenue, Rochester, NY 14642, USA.
| |
Collapse
|
28
|
Ledesma-Feliciano C, Hagen S, Troyer R, Zheng X, Musselman E, Slavkovic Lukic D, Franke AM, Maeda D, Zielonka J, Münk C, Wei G, VandeWoude S, Löchelt M. Replacement of feline foamy virus bet by feline immunodeficiency virus vif yields replicative virus with novel vaccine candidate potential. Retrovirology 2018; 15:38. [PMID: 29769087 PMCID: PMC5956581 DOI: 10.1186/s12977-018-0419-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/03/2018] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Hosts are able to restrict viral replication to contain virus spread before adaptive immunity is fully initiated. Many viruses have acquired genes directly counteracting intrinsic restriction mechanisms. This phenomenon has led to a co-evolutionary signature for both the virus and host which often provides a barrier against interspecies transmission events. Through different mechanisms of action, but with similar consequences, spumaviral feline foamy virus (FFV) Bet and lentiviral feline immunodeficiency virus (FIV) Vif counteract feline APOBEC3 (feA3) restriction factors that lead to hypermutation and degradation of retroviral DNA genomes. Here we examine the capacity of vif to substitute for bet function in a chimeric FFV to assess the transferability of anti-feA3 factors to allow viral replication. RESULTS We show that vif can replace bet to yield replication-competent chimeric foamy viruses. An in vitro selection screen revealed that an engineered Bet-Vif fusion protein yields suboptimal protection against feA3. After multiple passages through feA3-expressing cells, however, variants with optimized replication competence emerged. In these variants, Vif was expressed independently from an N-terminal Bet moiety and was stably maintained. Experimental infection of immunocompetent domestic cats with one of the functional chimeras resulted in seroconversion against the FFV backbone and the heterologous FIV Vif protein, but virus could not be detected unambiguously by PCR. Inoculation with chimeric virus followed by wild-type FFV revealed that repeated administration of FVs allowed superinfections with enhanced antiviral antibody production and detection of low level viral genomes, indicating that chimeric virus did not induce protective immunity against wild-type FFV. CONCLUSIONS Unrelated viral antagonists of feA3 cellular restriction factors can be exchanged in FFV, resulting in replication competence in vitro that was attenuated in vivo. Bet therefore may have additional functions other than A3 antagonism that are essential for successful in vivo replication. Immune reactivity was mounted against the heterologous Vif protein. We conclude that Vif-expressing FV vaccine vectors may be an attractive tool to prevent or modulate lentivirus infections with the potential option to induce immunity against additional lentivirus antigens.
Collapse
Affiliation(s)
- Carmen Ledesma-Feliciano
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Sarah Hagen
- Department of Molecular Diagnostics of Oncogenic Infections, Research Program Infection, Inflammation and Cancer, German Cancer Research Center, (Deutsches Krebsforschungszentrum Heidelberg, DKFZ), Im Neuenheimer Feld 242, 69120, Heidelberg, Germany
| | - Ryan Troyer
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Xin Zheng
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Esther Musselman
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Dragana Slavkovic Lukic
- Department of Molecular Diagnostics of Oncogenic Infections, Research Program Infection, Inflammation and Cancer, German Cancer Research Center, (Deutsches Krebsforschungszentrum Heidelberg, DKFZ), Im Neuenheimer Feld 242, 69120, Heidelberg, Germany.,Department of Internal Medicine II, Division of Hematology, University Hospital of Würzburg, Würzburg, Germany
| | - Ann-Mareen Franke
- Department of Molecular Diagnostics of Oncogenic Infections, Research Program Infection, Inflammation and Cancer, German Cancer Research Center, (Deutsches Krebsforschungszentrum Heidelberg, DKFZ), Im Neuenheimer Feld 242, 69120, Heidelberg, Germany.,Roche Pharma AG, Grenzach-Wyhlen, Germany
| | - Daniel Maeda
- Department of Molecular Diagnostics of Oncogenic Infections, Research Program Infection, Inflammation and Cancer, German Cancer Research Center, (Deutsches Krebsforschungszentrum Heidelberg, DKFZ), Im Neuenheimer Feld 242, 69120, Heidelberg, Germany.,University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Jörg Zielonka
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.,Roche Glycart AG, Schlieren, 8952, Switzerland
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Guochao Wei
- Department of Molecular Diagnostics of Oncogenic Infections, Research Program Infection, Inflammation and Cancer, German Cancer Research Center, (Deutsches Krebsforschungszentrum Heidelberg, DKFZ), Im Neuenheimer Feld 242, 69120, Heidelberg, Germany.,Division of Infectious Disease, University of Colorado, Anschutz Medical Campus, Aurora, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Martin Löchelt
- Department of Molecular Diagnostics of Oncogenic Infections, Research Program Infection, Inflammation and Cancer, German Cancer Research Center, (Deutsches Krebsforschungszentrum Heidelberg, DKFZ), Im Neuenheimer Feld 242, 69120, Heidelberg, Germany.
| |
Collapse
|
29
|
Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions. Sci Rep 2018; 8:7511. [PMID: 29760455 PMCID: PMC5951847 DOI: 10.1038/s41598-018-25881-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/30/2018] [Indexed: 12/31/2022] Open
Abstract
The APOBEC3 (A3) family of human cytidine deaminases is renowned for providing a first line of defense against many exogenous and endogenous retroviruses. However, the ability of these proteins to deaminate deoxycytidines in ssDNA makes A3s a double-edged sword. When overexpressed, A3s can mutate endogenous genomic DNA resulting in a variety of cancers. Although the sequence context for mutating DNA varies among A3s, the mechanism for substrate sequence specificity is not well understood. To characterize substrate specificity of A3A, a systematic approach was used to quantify the affinity for substrate as a function of sequence context, length, secondary structure, and solution pH. We identified the A3A ssDNA binding motif as (T/C)TC(A/G), which correlated with enzymatic activity. We also validated that A3A binds RNA in a sequence specific manner. A3A bound tighter to substrate binding motif within a hairpin loop compared to linear oligonucleotide, suggesting A3A affinity is modulated by substrate structure. Based on these findings and previously published A3A–ssDNA co-crystal structures, we propose a new model with intra-DNA interactions for the molecular mechanism underlying A3A sequence preference. Overall, the sequence and structural preferences identified for A3A leads to a new paradigm for identifying A3A’s involvement in mutation of endogenous or exogenous DNA.
Collapse
|
30
|
Borzooee F, Asgharpour M, Quinlan E, Grant MD, Larijani M. Viral subversion of APOBEC3s: Lessons for anti-tumor immunity and tumor immunotherapy. Int Rev Immunol 2018; 37:151-164. [PMID: 29211501 DOI: 10.1080/08830185.2017.1403596] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
APOBEC3s (A3) are endogenous DNA-editing enzymes that are expressed in immune cells including T lymphocytes. A3s target and mutate the genomes of retroviruses that infect immune tissues such as the human immunodeficiency virus (HIV). Therefore, A3s were classically defined as host anti-viral innate immune factors. In contrast, we and others showed that A3s can also benefit the virus by mediating escape from adaptive immune recognition and drugs. Crucially, whether A3-mediated mutations help or hinder HIV, is not up to chance. Rather, the virus has evolved multiple mechanisms to actively and maximally subvert A3 activity. More recently, extensive A3 mutational footprints in tumor genomes have been observed in many different cancers. This suggests a role for A3s in cancer initiation and progression. On the other hand, multiple anti-tumor activities of A3s have also come to light, including impact on immune checkpoint molecules and possible generation of tumor neo-antigens. Here, we review the studies that reshaped the view of A3s from anti-viral innate immune agents to host factors exploited by HIV to escape from immune recognition. Viruses and tumors share many attributes, including rapid evolution and adeptness at exploiting mutations. Given this parallel, we then discuss the pro- and anti-tumor roles of A3s, and suggest that lessons learned from studying A3s in the context of anti-viral immunity can be applied to tumor immunotherapy.
Collapse
Affiliation(s)
- Faezeh Borzooee
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Mahdi Asgharpour
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Emma Quinlan
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Michael D Grant
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Mani Larijani
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| |
Collapse
|
31
|
Asymmetric Modification of Hepatitis B Virus (HBV) Genomes by an Endogenous Cytidine Deaminase inside HBV Cores Informs a Model of Reverse Transcription. J Virol 2018; 92:JVI.02190-17. [PMID: 29491156 DOI: 10.1128/jvi.02190-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 02/20/2018] [Indexed: 02/07/2023] Open
Abstract
Cytidine deaminases inhibit replication of a broad range of DNA viruses by deaminating cytidines on single-stranded DNA (ssDNA) to generate uracil. While several lines of evidence have revealed hepatitis B virus (HBV) genome editing by deamination, it is still unclear which nucleic acid intermediate of HBV is modified. Hepatitis B virus has a relaxed circular double-stranded DNA (rcDNA) genome that is reverse transcribed within virus cores from a RNA template. The HBV genome also persists as covalently closed circular DNA (cccDNA) in the nucleus of an infected cell. In the present study, we found that in HBV-producing HepAD38 and HepG2.2.15 cell lines, endogenous cytidine deaminases edited 10 to 25% of HBV rcDNA genomes, asymmetrically with almost all mutations on the 5' half of the minus strand. This region corresponds to the last half of the minus strand to be protected by plus-strand synthesis. Within this half of the genome, the number of mutations peaks in the middle. Overexpressed APOBEC3A and APOBEC3G could be packaged in HBV capsids but did not change the amount or distribution of mutations. We found no deamination on pregenomic RNA (pgRNA), indicating that an intact genome is encapsidated and deaminated during or after reverse transcription. The deamination pattern suggests a model of rcDNA synthesis in which pgRNA and then newly synthesized minus-sense single-stranded DNA are protected from deaminase by interaction with the virus capsid; during plus-strand synthesis, when enough dsDNA has been synthesized to displace the remaining minus strand from the capsid surface, the single-stranded DNA becomes deaminase sensitive.IMPORTANCE Host-induced mutation of the HBV genome by APOBEC proteins may be a path to clearing the virus. We examined cytidine-to-thymidine mutations in the genomes of HBV particles grown in the presence or absence of overexpressed APOBEC proteins. We found that genomes were subjected to deamination activity during reverse transcription, which takes place within the virus capsid. These observations provide a direct insight into the mechanics of reverse transcription, suggesting that newly synthesized dsDNA displaces ssDNA from the capsid walls, making the ssDNA accessible to deaminase activity.
Collapse
|
32
|
APOBEC Enzymes as Targets for Virus and Cancer Therapy. Cell Chem Biol 2017; 25:36-49. [PMID: 29153851 DOI: 10.1016/j.chembiol.2017.10.007] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/11/2017] [Accepted: 10/18/2017] [Indexed: 01/08/2023]
Abstract
Human DNA cytosine-to-uracil deaminases catalyze mutations in both pathogen and cellular genomes. APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H restrict human immunodeficiency virus 1 (HIV-1) infection in cells deficient in the viral infectivity factor (Vif), and have the potential to catalyze sublethal levels of mutation in viral genomes in Vif-proficient cells. At least two APOBEC3 enzymes, and in particular APOBEC3B, are sources of somatic mutagenesis in cancer cells that drive tumor evolution and may manifest clinically as recurrence, metastasis, and/or therapy resistance. Consequently, APOBEC3 enzymes are tantalizing targets for developing chemical probes and therapeutic molecules to harness mutational processes in human disease. This review highlights recent efforts to chemically manipulate APOBEC3 activities.
Collapse
|
33
|
Biochemical Regulatory Features of Activation-Induced Cytidine Deaminase Remain Conserved from Lampreys to Humans. Mol Cell Biol 2017; 37:MCB.00077-17. [PMID: 28716949 DOI: 10.1128/mcb.00077-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/10/2017] [Indexed: 01/17/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) is a genome-mutating enzyme that initiates class switch recombination and somatic hypermutation of antibodies in jawed vertebrates. We previously described the biochemical properties of human AID and found that it is an unusual enzyme in that it exhibits binding affinities for its substrate DNA and catalytic rates several orders of magnitude higher and lower, respectively, than a typical enzyme. Recently, we solved the functional structure of AID and demonstrated that these properties are due to nonspecific DNA binding on its surface, along with a catalytic pocket that predominantly assumes a closed conformation. Here we investigated the biochemical properties of AID from a sea lamprey, nurse shark, tetraodon, and coelacanth: representative species chosen because their lineages diverged at the earliest critical junctures in evolution of adaptive immunity. We found that these earliest-diverged AID orthologs are active cytidine deaminases that exhibit unique substrate specificities and thermosensitivities. Significant amino acid sequence divergence among these AID orthologs is predicted to manifest as notable structural differences. However, despite major differences in sequence specificities, thermosensitivities, and structural features, all orthologs share the unusually high DNA binding affinities and low catalytic rates. This absolute conservation is evidence for biological significance of these unique biochemical properties.
Collapse
|
34
|
Jaguva Vasudevan AA, Hofmann H, Willbold D, Häussinger D, Koenig BW, Münk C. Enhancing the Catalytic Deamination Activity of APOBEC3C Is Insufficient to Inhibit Vif-Deficient HIV-1. J Mol Biol 2017; 429:1171-1191. [DOI: 10.1016/j.jmb.2017.03.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/08/2017] [Accepted: 03/08/2017] [Indexed: 12/17/2022]
|
35
|
Shi K, Carpenter M, Banerjee S, Shaban N, Kurahashi K, Salamango D, McCann J, Starrett G, Duffy J, Demir Ö, Amaro R, Harki D, Harris R, Aihara H. Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat Struct Mol Biol 2017; 24:131-139. [PMID: 27991903 PMCID: PMC5296220 DOI: 10.1038/nsmb.3344] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/16/2016] [Indexed: 12/17/2022]
Abstract
APOBEC-catalyzed cytosine-to-uracil deamination of single-stranded DNA (ssDNA) has beneficial functions in immunity and detrimental effects in cancer. APOBEC enzymes have intrinsic dinucleotide specificities that impart hallmark mutation signatures. Although numerous structures have been solved, mechanisms for global ssDNA recognition and local target-sequence selection remain unclear. Here we report crystal structures of human APOBEC3A and a chimera of human APOBEC3B and APOBEC3A bound to ssDNA at 3.1-Å and 1.7-Å resolution, respectively. These structures reveal a U-shaped DNA conformation, with the specificity-conferring -1 thymine flipped out and the target cytosine inserted deep into the zinc-coordinating active site pocket. The -1 thymine base fits into a groove between flexible loops and makes direct hydrogen bonds with the protein, accounting for the strong 5'-TC preference. These findings explain both conserved and unique properties among APOBEC family members, and they provide a basis for the rational design of inhibitors to impede the evolvability of viruses and tumors.
Collapse
Affiliation(s)
- K. Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - M.A. Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - S. Banerjee
- Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, Illinois, USA, 60439
| | - N.M. Shaban
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - K. Kurahashi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - D.J. Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - J.L. McCann
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - G.J. Starrett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - J.V. Duffy
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Ö. Demir
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093
| | - R.E. Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093
| | - D.A. Harki
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - R.S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - H. Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| |
Collapse
|
36
|
Sanjuán R, Domingo-Calap P. Mechanisms of viral mutation. Cell Mol Life Sci 2016; 73:4433-4448. [PMID: 27392606 PMCID: PMC5075021 DOI: 10.1007/s00018-016-2299-6] [Citation(s) in RCA: 473] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 02/08/2023]
Abstract
The remarkable capacity of some viruses to adapt to new hosts and environments is highly dependent on their ability to generate de novo diversity in a short period of time. Rates of spontaneous mutation vary amply among viruses. RNA viruses mutate faster than DNA viruses, single-stranded viruses mutate faster than double-strand virus, and genome size appears to correlate negatively with mutation rate. Viral mutation rates are modulated at different levels, including polymerase fidelity, sequence context, template secondary structure, cellular microenvironment, replication mechanisms, proofreading, and access to post-replicative repair. Additionally, massive numbers of mutations can be introduced by some virus-encoded diversity-generating elements, as well as by host-encoded cytidine/adenine deaminases. Our current knowledge of viral mutation rates indicates that viral genetic diversity is determined by multiple virus- and host-dependent processes, and that viral mutation rates can evolve in response to specific selective pressures.
Collapse
Affiliation(s)
- Rafael Sanjuán
- Department of Genetics and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, C/Catedrático José Beltrán 2, 46980, Paterna, Valencia, Spain.
| | - Pilar Domingo-Calap
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire OMICARE, Centre de Recherche d'Immunologie et d'Hématologie, Strasbourg, France
| |
Collapse
|
37
|
Morganella S, Alexandrov LB, Glodzik D, Zou X, Davies H, Staaf J, Sieuwerts AM, Brinkman AB, Martin S, Ramakrishna M, Butler A, Kim HY, Borg Å, Sotiriou C, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Stunnenberg HG, van de Vijver MJ, Martens JWM, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Sale J, Rada C, Stratton MR, Birney E, Nik-Zainal S. The topography of mutational processes in breast cancer genomes. Nat Commun 2016; 7:11383. [PMID: 27136393 PMCID: PMC5001788 DOI: 10.1038/ncomms11383] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/18/2016] [Indexed: 12/28/2022] Open
Abstract
Somatic mutations in human cancers show unevenness in genomic distribution that correlate with aspects of genome structure and function. These mutations are, however, generated by multiple mutational processes operating through the cellular lineage between the fertilized egg and the cancer cell, each composed of specific DNA damage and repair components and leaving its own characteristic mutational signature on the genome. Using somatic mutation catalogues from 560 breast cancer whole-genome sequences, here we show that each of 12 base substitution, 2 insertion/deletion (indel) and 6 rearrangement mutational signatures present in breast tissue, exhibit distinct relationships with genomic features relating to transcription, DNA replication and chromatin organization. This signature-based approach permits visualization of the genomic distribution of mutational processes associated with APOBEC enzymes, mismatch repair deficiency and homologous recombinational repair deficiency, as well as mutational processes of unknown aetiology. Furthermore, it highlights mechanistic insights including a putative replication-dependent mechanism of APOBEC-related mutagenesis.
Collapse
Affiliation(s)
- Sandro Morganella
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Cambridgeshire
CB10 1SD, UK
| | - Ludmil B. Alexandrov
- Wellcome Trust Sanger Institute, Cambridge
CB10 1SA, UK
- Theoretical Biology and Biophysics (T-6), Los Alamos National
Laboratory, Los Alamos
NM 87545, New Mexico, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory,
Los Alamos
NM 87545, New Mexico, USA
| | | | - Xueqing Zou
- Wellcome Trust Sanger Institute, Cambridge
CB10 1SA, UK
| | - Helen Davies
- Wellcome Trust Sanger Institute, Cambridge
CB10 1SA, UK
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences
Lund, Lund University, Lund
SE-223 81, Sweden
| | - Anieta M. Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute and
Cancer Genomics Netherlands, Erasmus University Medical Center,
Rotterdam
3015CN, The Netherlands
| | - Arie B. Brinkman
- Radboud University, Faculty of Science, Department of Molecular
Biology, 6525GA
Nijmegen, The Netherlands
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Cambridge
CB10 1SA, UK
| | | | - Adam Butler
- Wellcome Trust Sanger Institute, Cambridge
CB10 1SA, UK
| | - Hyung-Yong Kim
- Department of Pathology, College of Medicine, Hanyang
University, Seoul
133-791, South Korea
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences
Lund, Lund University, Lund
SE-223 81, Sweden
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Université
Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121,
B-1000
Brussels, Belgium
| | - P. Andrew Futreal
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Cambridgeshire
CB10 1SD, UK
- Department of Genomic Medicine, UT MD Anderson Cancer
Center, Houston, Texas
77230, USA
| | | | - Paul N. Span
- Department of Radiation Oncology, and department of Laboratory
Medicine, Radboud university medical center, Nijmegen
6525GA, The Netherlands
| | - Steven Van Laere
- Translational Cancer Research Unit, GZA Hospitals Sint-Augustinus,
Wilrijk, Belgium and Center for Oncological Research, University of Antwerp,
Antwerp
B-2610, Belgium
| | - Sunil R. Lakhani
- Centre for Clinical Research and School of Medicine, University of
Queensland, Brisbane, Queensland
4059, Australia
- Pathology Queensland, The Royal Brisbane and Women's
Hospital, Brisbane, Queensland
4029, Australia
| | - Jorunn E. Eyfjord
- Cancer Research Laboratory, Faculty of Medicine, University of
Iceland, 101
Reykjavik, Iceland
| | - Alastair M. Thompson
- Department of Breast Surgical Oncology, University of Texas MD
Anderson Cancer Center, 1400 Pressler
Street,Houston, Texas
77030, USA
- Department of Surgical Oncology, University of Dundee,
Dundee
DD1 9SY, UK
| | - Hendrik G. Stunnenberg
- Radboud University, Faculty of Science, Department of Molecular
Biology, 6525GA
Nijmegen, The Netherlands
| | - Marc J. van de Vijver
- Department of Pathology, Academic Medical Center,
Meibergdreef 9, 1105 AZ
Amsterdam, The Netherlands
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute and
Cancer Genomics Netherlands, Erasmus University Medical Center,
Rotterdam
3015CN, The Netherlands
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo
University Hospital, The Norwegian Radium Hospital, Oslo
0310, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for
Clinical Medicine, University of Oslo, Oslo
0310, Norway
| | - Andrea L. Richardson
- Department of Pathology, Brigham and Women's Hospital,
Boston, Massachusetts
02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, Massachusetts
02215, USA
| | - Gu Kong
- Department of Pathology, College of Medicine, Hanyang
University, Seoul
133-791, South Korea
| | - Gilles Thomas
- Synergie Lyon Cancer, Centre Léon Bérard,
28 rue Laënnec, Lyon
Cedex 08, France
| | - Julian Sale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge
CB2 0QH, UK
| | - Cristina Rada
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge
CB2 0QH, UK
| | | | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Cambridgeshire
CB10 1SD, UK
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Cambridge
CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University
Hospitals NHS Foundation Trust, Cambridge
CB2 9NB, UK
| |
Collapse
|
38
|
Delviks-Frankenberry KA, Nikolaitchik OA, Burdick RC, Gorelick RJ, Keele BF, Hu WS, Pathak VK. Minimal Contribution of APOBEC3-Induced G-to-A Hypermutation to HIV-1 Recombination and Genetic Variation. PLoS Pathog 2016; 12:e1005646. [PMID: 27186986 PMCID: PMC4871359 DOI: 10.1371/journal.ppat.1005646] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/28/2016] [Indexed: 11/19/2022] Open
Abstract
Although the predominant effect of host restriction APOBEC3 proteins on HIV-1 infection is to block viral replication, they might inadvertently increase retroviral genetic variation by inducing G-to-A hypermutation. Numerous studies have disagreed on the contribution of hypermutation to viral genetic diversity and evolution. Confounding factors contributing to the debate include the extent of lethal (stop codon) and sublethal hypermutation induced by different APOBEC3 proteins, the inability to distinguish between G-to-A mutations induced by APOBEC3 proteins and error-prone viral replication, the potential impact of hypermutation on the frequency of retroviral recombination, and the extent to which viral recombination occurs in vivo, which can reassort mutations in hypermutated genomes. Here, we determined the effects of hypermutation on the HIV-1 recombination rate and its contribution to genetic variation through recombination to generate progeny genomes containing portions of hypermutated genomes without lethal mutations. We found that hypermutation did not significantly affect the rate of recombination, and recombination between hypermutated and wild-type genomes only increased the viral mutation rate by 3.9 × 10-5 mutations/bp/replication cycle in heterozygous virions, which is similar to the HIV-1 mutation rate. Since copackaging of hypermutated and wild-type genomes occurs very rarely in vivo, recombination between hypermutated and wild-type genomes does not significantly contribute to the genetic variation of replicating HIV-1. We also analyzed previously reported hypermutated sequences from infected patients and determined that the frequency of sublethal mutagenesis for A3G and A3F is negligible (4 × 10-21 and1 × 10-11, respectively) and its contribution to viral mutations is far below mutations generated during error-prone reverse transcription. Taken together, we conclude that the contribution of APOBEC3-induced hypermutation to HIV-1 genetic variation is substantially lower than that from mutations during error-prone replication.
Collapse
Affiliation(s)
- Krista A. Delviks-Frankenberry
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Olga A. Nikolaitchik
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Ryan C. Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Lab, Frederick, Maryland, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Lab, Frederick, Maryland, United States of America
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| |
Collapse
|
39
|
Knisbacher BA, Gerber D, Levanon EY. DNA Editing by APOBECs: A Genomic Preserver and Transformer. Trends Genet 2016; 32:16-28. [PMID: 26608778 DOI: 10.1016/j.tig.2015.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/18/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
Information warfare is not limited to the cyber world because it is waged within our cells as well. The unique AID (activation-induced cytidine deaminase)/APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide) family comprises proteins that alter DNA sequences by converting deoxycytidines to deoxyuridines through deamination. This C-to-U DNA editing enables them to inhibit parasitic viruses and retrotransposons by disrupting their genomic content. In addition to attacking genomic invaders, APOBECs can target their host genome, which can be beneficial by initiating processes that create antibody diversity needed for the immune system or by accelerating the rate of evolution. AID can also alter gene regulation by removing epigenetic modifications from genomic DNA. However, when uncontrolled, these powerful agents of change can threaten genome stability and eventually lead to cancer.
Collapse
Affiliation(s)
- Binyamin A Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Doron Gerber
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel.
| |
Collapse
|
40
|
Contribution of APOBEC3G/F activity to the development of low-abundance drug-resistant human immunodeficiency virus type 1 variants. Clin Microbiol Infect 2015; 22:191-200. [PMID: 26482266 DOI: 10.1016/j.cmi.2015.10.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 09/07/2015] [Accepted: 10/03/2015] [Indexed: 11/20/2022]
Abstract
Plasma drug-resistant minority human immunodeficiency virus type 1 variants (DRMVs) increase the risk of virological failure to first-line non-nucleoside reverse transcriptase inhibitor antiretroviral therapy (ART). The origin of DRMVs in ART-naive patients, however, remains unclear. In a large pan-European case-control study investigating the clinical relevance of pre-existing DRMVs using 454 pyrosequencing, the six most prevalent plasma DRMVs detected corresponded to G-to-A nucleotide mutations (V90I, V106I, V108I, E138K, M184I and M230I). Here, we evaluated if such DRMVs could have emerged from apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3G/F (APOBEC3G/F) activity. Out of 236 ART-naive subjects evaluated, APOBEC3G/F hypermutation signatures were detected in plasma viruses of 14 (5.9%) individuals. Samples with minority E138K, M184I, and M230I mutations, but not those with V90I, V106I or V108I, were significantly associated with APOBEC3G/F activity (Fisher's P < 0.005), defined as the presence of > 0.5% of sample sequences with an APOBEC3G/F signature. Mutations E138K, M184I and M230I co-occurred in the same sequence as APOBEC3G/F signatures in 3/9 (33%), 5/11 (45%) and 4/8 (50%) of samples, respectively; such linkage was not found for V90I, V106I or V108I. In-frame STOP codons were observed in 1.5% of all clonal sequences; 14.8% of them co-occurred with APOBEC3G/F signatures. APOBEC3G/F-associated E138K, M184I and M230I appeared within clonal sequences containing in-frame STOP codons in 2/3 (66%), 5/5 (100%) and 4/4 (100%) of the samples. In a re-analysis of the parent case control study, the presence of APOBEC3G/F signatures was not associated with virological failure. In conclusion, the contribution of APOBEC3G/F editing to the development of DRMVs is very limited and does not affect the efficacy of non-nucleoside reverse transcriptase inhibitor ART.
Collapse
|
41
|
Rawson JMO, Landman SR, Reilly CS, Mansky LM. HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation. Retrovirology 2015; 12:60. [PMID: 26160407 PMCID: PMC4496919 DOI: 10.1186/s12977-015-0180-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 06/08/2015] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 2 (HIV-2) is often distinguished clinically by lower viral loads, reduced transmissibility, and longer asymptomatic periods than for human immunodeficiency virus type 1 (HIV-1). Differences in the mutation frequencies of HIV-1 and HIV-2 have been hypothesized to contribute to the attenuated progression of HIV-2 observed clinically. RESULTS To address this hypothesis, we performed Illumina sequencing of multiple amplicons prepared from cells infected with HIV-1 or HIV-2, resulting in ~4.7 million read pairs and the identification of ~200,000 mutations after data processing. We observed that: (1) HIV-2 displayed significantly lower total mutation, substitution, and transition mutation frequencies than that of HIV-1, along with a mutation spectrum markedly less biased toward G-to-A transitions, (2) G-to-A hypermutation consistent with the activity of APOBEC3 proteins was observed for both HIV-1 and HIV-2 despite the presence of Vif, (3) G-to-A hypermutation was significantly higher for HIV-1 than for HIV-2, and (4) HIV-1 and HIV-2 total mutation frequencies were not significantly different in the absence of G-to-A hypermutants. CONCLUSIONS Taken together, these data demonstrate that HIV-2 exhibits a distinct mutational spectrum and a lower mutation frequency relative to HIV-1. However, the observed differences were primarily due to reduced levels of G-to-A hypermutation for HIV-2. These findings suggest that HIV-2 may be less susceptible than HIV-1 to APOBEC3-mediated hypermutation, but that the fidelities of other mutational sources (such as reverse transcriptase) are relatively similar for HIV-1 and HIV-2. Overall, these data imply that differences in replication fidelity are likely not a major contributing factor to the unique clinical features of HIV-2 infection.
Collapse
Affiliation(s)
- Jonathan M O Rawson
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.
- Molecular, Cellular, Developmental Biology and Genetics Graduate Program, University of Minnesota, Minneapolis, MN, USA.
| | - Sean R Landman
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.
| | - Cavan S Reilly
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA.
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA.
- Department of Microbiology, University of Minnesota, Minneapolis, MN, USA.
- Molecular, Cellular, Developmental Biology and Genetics Graduate Program, University of Minnesota, Minneapolis, MN, USA.
| |
Collapse
|
42
|
Martin-Gayo E, Buzon MJ, Ouyang Z, Hickman T, Cronin J, Pimenova D, Walker BD, Lichterfeld M, Yu XG. Potent Cell-Intrinsic Immune Responses in Dendritic Cells Facilitate HIV-1-Specific T Cell Immunity in HIV-1 Elite Controllers. PLoS Pathog 2015; 11:e1004930. [PMID: 26067651 PMCID: PMC4466270 DOI: 10.1371/journal.ppat.1004930] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/01/2015] [Indexed: 12/29/2022] Open
Abstract
The majority of HIV-1 elite controllers (EC) restrict HIV-1 replication through highly functional HIV-1-specific T cell responses, but mechanisms supporting the evolution of effective HIV-1-specific T cell immunity in these patients remain undefined. Cytosolic immune recognition of HIV-1 in conventional dendritic cells (cDC) can facilitate priming and expansion of HIV-1-specific T cells; however, HIV-1 seems to be able to avoid intracellular immune recognition in cDCs in most infected individuals. Here, we show that exposure of cDCs from EC to HIV-1 leads to a rapid and sustained production of type I interferons and upregulation of several interferon-stimulated effector genes. Emergence of these cell-intrinsic immune responses was associated with a reduced induction of SAMHD1 and LEDGF/p75, and an accumulation of viral reverse transcripts, but inhibited by pharmacological blockade of viral reverse transcription or siRNA-mediated silencing of the cytosolic DNA sensor cGAS. Importantly, improved cell-intrinsic immune recognition of HIV-1 in cDCs from elite controllers translated into stronger abilities to stimulate and expand HIV-1-specific CD8 T cell responses. These data suggest an important role of cell-intrinsic type I interferon secretion in dendritic cells for the induction of effective HIV-1-specific CD8 T cells, and may be helpful for eliciting functional T cell immunity against HIV-1 for preventative or therapeutic clinical purposes.
Collapse
Affiliation(s)
- Enrique Martin-Gayo
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
| | - Maria Jose Buzon
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
- Infectious Disease Division, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Zhengyu Ouyang
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
| | - Taylor Hickman
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
| | - Jacqueline Cronin
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
| | - Dina Pimenova
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
- Infectious Disease Division, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
43
|
Harris RS, Dudley JP. APOBECs and virus restriction. Virology 2015; 479-480:131-45. [PMID: 25818029 PMCID: PMC4424171 DOI: 10.1016/j.virol.2015.03.012] [Citation(s) in RCA: 365] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 02/10/2015] [Accepted: 03/04/2015] [Indexed: 12/22/2022]
Abstract
The APOBEC family of single-stranded DNA cytosine deaminases comprises a formidable arm of the vertebrate innate immune system. Pre-vertebrates express a single APOBEC, whereas some mammals produce as many as 11 enzymes. The APOBEC3 subfamily displays both copy number variation and polymorphisms, consistent with ongoing pathogenic pressures. These enzymes restrict the replication of many DNA-based parasites, such as exogenous viruses and endogenous transposable elements. APOBEC1 and activation-induced cytosine deaminase (AID) have specialized functions in RNA editing and antibody gene diversification, respectively, whereas APOBEC2 and APOBEC4 appear to have different functions. Nevertheless, the APOBEC family protects against both periodic viral zoonoses as well as exogenous and endogenous parasite replication. This review highlights viral pathogens that are restricted by APOBEC enzymes, but manage to escape through unique mechanisms. The sensitivity of viruses that lack counterdefense measures highlights the need to develop APOBEC-enabling small molecules as a new class of anti-viral drugs.
Collapse
Affiliation(s)
- Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Center for Genome Engineering, and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, United States.
| | - Jaquelin P Dudley
- Department of Molecular Biosciences, Center for Infectious Disease, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States.
| |
Collapse
|
44
|
Sharma S, Patnaik SK, Taggart RT, Kannisto ED, Enriquez SM, Gollnick P, Baysal BE. APOBEC3A cytidine deaminase induces RNA editing in monocytes and macrophages. Nat Commun 2015; 6:6881. [PMID: 25898173 PMCID: PMC4411297 DOI: 10.1038/ncomms7881] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/10/2015] [Indexed: 01/01/2023] Open
Abstract
The extent, regulation and enzymatic basis of RNA editing by cytidine deamination are incompletely understood. Here we show that transcripts of hundreds of genes undergo site-specific C>U RNA editing in macrophages during M1 polarization and in monocytes in response to hypoxia and interferons. This editing alters the amino acid sequences for scores of proteins, including many that are involved in pathogenesis of viral diseases. APOBEC3A, which is known to deaminate cytidines of single-stranded DNA and to inhibit viruses and retrotransposons, mediates this RNA editing. Amino acid residues of APOBEC3A that are known to be required for its DNA deamination and anti-retrotransposition activities were also found to affect its RNA deamination activity. Our study demonstrates the cellular RNA editing activity of a member of the APOBEC3 family of innate restriction factors and expands the understanding of C>U RNA editing in mammals. Aberrant RNA editing is linked to a range of neuropsychiatric and chronic diseases. Here Sharma et al. show that APOBEC3A can function as an RNA editing protein in response to physiological stimuli, significantly expanding our understanding of RNA editing and the role this may play in diseases.
Collapse
Affiliation(s)
- Shraddha Sharma
- Department of Pathology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, New York 14203, USA
| | - Santosh K Patnaik
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, New York 14203, USA
| | - R Thomas Taggart
- Department of Pathology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, New York 14203, USA
| | - Eric D Kannisto
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, New York 14203, USA
| | - Sally M Enriquez
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - Paul Gollnick
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - Bora E Baysal
- Department of Pathology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, New York 14203, USA
| |
Collapse
|
45
|
Helleday T, Eshtad S, Nik-Zainal S. Mechanisms underlying mutational signatures in human cancers. Nat Rev Genet 2014; 15:585-98. [PMID: 24981601 DOI: 10.1038/nrg3729] [Citation(s) in RCA: 561] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The collective somatic mutations observed in a cancer are the outcome of multiple mutagenic processes that have been operative over the lifetime of a patient. Each process leaves a characteristic imprint--a mutational signature--on the cancer genome, which is defined by the type of DNA damage and DNA repair processes that result in base substitutions, insertions and deletions or structural variations. With the advent of whole-genome sequencing, researchers are identifying an increasing array of these signatures. Mutational signatures can be used as a physiological readout of the biological history of a cancer and also have potential use for discerning ongoing mutational processes from historical ones, thus possibly revealing new targets for anticancer therapies.
Collapse
Affiliation(s)
- Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Saeed Eshtad
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Serena Nik-Zainal
- 1] Wellcome Trust Sanger Institute, Hinxton Genome Campus, Cambridge CB10 1SA, UK. [2] East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Trust, Cambridge CB2 2QQ, UK
| |
Collapse
|
46
|
Nowarski R, Prabhu P, Kenig E, Smith Y, Britan-Rosich E, Kotler M. APOBEC3G inhibits HIV-1 RNA elongation by inactivating the viral trans-activation response element. J Mol Biol 2014; 426:2840-53. [PMID: 24859335 DOI: 10.1016/j.jmb.2014.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 10/25/2022]
Abstract
Deamination of cytidine residues in viral DNA is a major mechanism by which APOBEC3G (A3G) inhibits vif-deficient human immunodeficiency virus type 1 (HIV-1) replication. dC-to-dU transition following RNase-H activity leads to viral cDNA degradation, production of non-functional proteins, formation of undesired stop codons and decreased viral protein synthesis. Here, we demonstrate that A3G provides an additional layer of defense against HIV-1 infection dependent on inhibition of proviral transcription. HIV-1 transcription elongation is regulated by the trans-activation response (TAR) element, a short stem-loop RNA structure required for elongation factors binding. Vif-deficient HIV-1-infected cells accumulate short viral transcripts and produce lower amounts of full-length HIV-1 transcripts due to A3G deamination of the TAR apical loop cytidine, highlighting the requirement for TAR loop integrity in HIV-1 transcription. We further show that free single-stranded DNA (ssDNA) termini are not essential for A3G activity and a gap of CCC motif blocked with juxtaposed DNA or RNA on either or 3'+5' ends is sufficient for A3G deamination. These results identify A3G as an efficient mutator and that deamination of (-)SSDNA results in an early block of HIV-1 transcription.
Collapse
Affiliation(s)
- Roni Nowarski
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel
| | - Ponnandy Prabhu
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel
| | - Edan Kenig
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel
| | - Yoav Smith
- Genomic Data Analysis Unit, The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
| | - Elena Britan-Rosich
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel
| | - Moshe Kotler
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel.
| |
Collapse
|
47
|
Nik-Zainal S, Wedge DC, Alexandrov LB, Petljak M, Butler AP, Bolli N, Davies HR, Knappskog S, Martin S, Papaemmanuil E, Ramakrishna M, Shlien A, Simonic I, Xue Y, Tyler-Smith C, Campbell PJ, Stratton MR. Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer. Nat Genet 2014; 46:487-91. [PMID: 24728294 PMCID: PMC4137149 DOI: 10.1038/ng.2955] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 03/06/2014] [Indexed: 12/13/2022]
Abstract
The somatic mutations in a cancer genome are the aggregate outcome of one or more mutational processes operative through the lifetime of the individual with cancer. Each mutational process leaves a characteristic mutational signature determined by the mechanisms of DNA damage and repair that constitute it. A role was recently proposed for the APOBEC family of cytidine deaminases in generating particular genome-wide mutational signatures and a signature of localized hypermutation called kataegis. A germline copy number polymorphism involving APOBEC3A and APOBEC3B, which effectively deletes APOBEC3B, has been associated with modestly increased risk of breast cancer. Here we show that breast cancers in carriers of the deletion show more mutations of the putative APOBEC-dependent genome-wide signatures than cancers in non-carriers. The results suggest that the APOBEC3A-APOBEC3B germline deletion allele confers cancer susceptibility through increased activity of APOBEC-dependent mutational processes, although the mechanism by which this increase in activity occurs remains unknown.
Collapse
Affiliation(s)
- Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Medical Genetics, Box 134, Addenbrooke’s Hospital NHS Trust, Hills Road, Cambridge CB2 0QQ
| | - David C. Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Ludmil B. Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Mia Petljak
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Adam P. Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Niccolo Bolli
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK
| | - Helen R. Davies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Stian Knappskog
- Section of Oncology, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Sancha Martin
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Manasa Ramakrishna
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Adam Shlien
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Ingrid Simonic
- Regional Genetics Laboratories, Box 143, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0QQ
| | - Yali Xue
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Chris Tyler-Smith
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Peter J. Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK
| | - Michael R. Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| |
Collapse
|
48
|
Desimmie BA, Delviks-Frankenberrry KA, Burdick RC, Qi D, Izumi T, Pathak VK. Multiple APOBEC3 restriction factors for HIV-1 and one Vif to rule them all. J Mol Biol 2014; 426:1220-45. [PMID: 24189052 PMCID: PMC3943811 DOI: 10.1016/j.jmb.2013.10.033] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/25/2013] [Accepted: 10/28/2013] [Indexed: 12/11/2022]
Abstract
Several members of the APOBEC3 family of cellular restriction factors provide intrinsic immunity to the host against viral infection. Specifically, APOBEC3DE, APOBEC3F, APOBEC3G, and APOBEC3H haplotypes II, V, and VII provide protection against HIV-1Δvif through hypermutation of the viral genome, inhibition of reverse transcription, and inhibition of viral DNA integration into the host genome. HIV-1 counteracts APOBEC3 proteins by encoding the viral protein Vif, which contains distinct domains that specifically interact with these APOBEC3 proteins to ensure their proteasomal degradation, allowing virus replication to proceed. Here, we review our current understanding of APOBEC3 structure, editing and non-editing mechanisms of APOBEC3-mediated restriction, Vif-APOBEC3 interactions that trigger APOBEC3 degradation, and the contribution of APOBEC3 proteins to restriction and control of HIV-1 replication in infected patients.
Collapse
Affiliation(s)
- Belete A Desimmie
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | | | - Ryan C Burdick
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - DongFei Qi
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Taisuke Izumi
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
| |
Collapse
|