1
|
Chen YC, Liao YC, Mao YC, Yeh TK, Liu PY. Tracing the footprints of MPXV in Asia: phylogenetic insights and lineage dynamics. Sex Transm Infect 2024; 100:384-387. [PMID: 38914476 DOI: 10.1136/sextrans-2024-056119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/29/2024] [Indexed: 06/26/2024] Open
Abstract
OBJECTIVES The 2022 global outbreak of monkeypox virus (MPXV), previously confined to Central and West Africa, necessitates an enhanced understanding of its spread. Comprehensive genomic surveillance to understand the virus's evolution and spread is needed, particularly in Asia. METHODS Genomic data from 169 MPXV genome sequences in Asia were analysed. Through advanced genomic sequencing of clinical samples, we analysed the distribution and mutations of MPXV lineages in Asia. RESULTS Phylogenetic analysis revealed a distinct clustering of C.1 strains rise in Northeast Asia in 2023, while genomic examination identified specific consensus mutations like R84K, R665C and L16F in C.1 strains. The mutations, coupled with an increased rate of apolipoprotein B mRNA-editing catalytic polypeptide-like 3 motif G-to-A mutations in C.1 (OR 24.87±8.81), indicate a potential adaptation mechanism. CONCLUSIONS Our findings underscore the need for ongoing surveillance and provide vital insights into MPXV's evolving dynamics, aiding in public health strategy formulation against this emerging infectious threat.
Collapse
Affiliation(s)
- Yung-Chun Chen
- Division of Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Yan-Chiao Mao
- Division of Clinical Toxicology, Department of Emergency Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Defense Medical Center, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Ting-Kuang Yeh
- Division of Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Po-Yu Liu
- Division of Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
| |
Collapse
|
2
|
Begum MSTM, Bokani A, Rajib SA, Soleimanpour M, Maeda Y, Yoshimura K, Satou Y, Ebrahimi D, Ikeda T. Potential Role of APOBEC3 Family Proteins in SARS-CoV-2 Replication. Viruses 2024; 16:1141. [PMID: 39066304 PMCID: PMC11281575 DOI: 10.3390/v16071141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has acquired multiple mutations since its emergence. Analyses of the SARS-CoV-2 genomes from infected patients exhibit a bias toward C-to-U mutations, which are suggested to be caused by the apolipoprotein B mRNA editing enzyme polypeptide-like 3 (APOBEC3, A3) cytosine deaminase proteins. However, the role of A3 enzymes in SARS-CoV-2 replication remains unclear. To address this question, we investigated the effect of A3 family proteins on SARS-CoV-2 replication in the myeloid leukemia cell line THP-1 lacking A3A to A3G genes. The Wuhan, BA.1, and BA.5 variants had comparable viral replication in parent and A3A-to-A3G-null THP-1 cells stably expressing angiotensin-converting enzyme 2 (ACE2) protein. On the other hand, the replication and infectivity of these variants were abolished in A3A-to-A3G-null THP-1-ACE2 cells in a series of passage experiments over 20 days. In contrast to previous reports, we observed no evidence of A3-induced SARS-CoV-2 mutagenesis in the passage experiments. Furthermore, our analysis of a large number of publicly available SARS-CoV-2 genomes did not reveal conclusive evidence for A3-induced mutagenesis. Our studies suggest that A3 family proteins can positively contribute to SARS-CoV-2 replication; however, this effect is deaminase-independent.
Collapse
Affiliation(s)
- MST Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Ayub Bokani
- School of Engineering and Technology, CQ University, Sydney, NSW 2000, Australia
| | - Samiul Alam Rajib
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| | | | - Yosuke Maeda
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Department of Nursing, Kibi International University, Takahashi 716-8508, Japan
| | | | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Diako Ebrahimi
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| |
Collapse
|
3
|
McCool MA, Bryant CJ, Abriola L, Surovtseva YV, Baserga SJ. The cytidine deaminase APOBEC3A regulates nucleolar function to promote cell growth and ribosome biogenesis. PLoS Biol 2024; 22:e3002718. [PMID: 38976757 PMCID: PMC11257408 DOI: 10.1371/journal.pbio.3002718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 07/18/2024] [Accepted: 06/20/2024] [Indexed: 07/10/2024] Open
Abstract
Cancer initiates as a consequence of genomic mutations and its subsequent progression relies in part on increased production of ribosomes to maintain high levels of protein synthesis for unchecked cell growth. Recently, cytidine deaminases have been uncovered as sources of mutagenesis in cancer. In an attempt to form a connection between these 2 cancer driving processes, we interrogated the cytidine deaminase family of proteins for potential roles in human ribosome biogenesis. We identified and validated APOBEC3A and APOBEC4 as novel ribosome biogenesis factors through our laboratory's established screening platform for the discovery of regulators of nucleolar function in MCF10A cells. Through siRNA depletion experiments, we highlight APOBEC3A's requirement in making ribosomes and specific role within the processing and maturation steps that form the large subunit 5.8S and 28S ribosomal (r)RNAs. We demonstrate that a subset of APOBEC3A resides within the nucleolus and associates with critical ribosome biogenesis factors. Mechanistic insight was revealed by transient overexpression of both wild-type and a catalytically dead mutated APOBEC3A, which both increase cell growth and protein synthesis. Through an innovative nuclear RNA sequencing methodology, we identify only modest predicted APOBEC3A C-to-U target sites on the pre-rRNA and pre-mRNAs. Our work reveals a potential direct role for APOBEC3A in ribosome biogenesis likely independent of its editing function. More broadly, we found an additional function of APOBEC3A in cancer pathology through its function in ribosome biogenesis, expanding its relevance as a target for cancer therapeutics.
Collapse
Affiliation(s)
- Mason A. McCool
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Carson J. Bryant
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, Connecticut, United States of America
| | - Yulia V. Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, Connecticut, United States of America
| | - Susan J. Baserga
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| |
Collapse
|
4
|
Dhivahar J, Parthasarathy A, Krishnan K, Kovi BS, Pandian GN. Bat-associated microbes: Opportunities and perils, an overview. Heliyon 2023; 9:e22351. [PMID: 38125540 PMCID: PMC10730444 DOI: 10.1016/j.heliyon.2023.e22351] [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: 07/14/2022] [Revised: 09/21/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023] Open
Abstract
The potential biotechnological uses of bat-associated bacteria are discussed briefly, indicating avenues for biotechnological applications of bat-associated microbes. The uniqueness of bats in terms of their lifestyle, genomes and molecular immunology may predispose bats to act as disease reservoirs. Molecular phylogenetic analysis has shown several instances of bats harbouring the ancestral lineages of bacterial (Bartonella), protozoal (Plasmodium, Trypanosoma cruzi) and viral (SARS-CoV2) pathogens infecting humans. Along with the transmission of viruses from bats, we also discuss the potential roles of bat-associated bacteria, fungi, and protozoan parasites in emerging diseases. Current evidence suggests that environmental changes and interactions between wildlife, livestock, and humans contribute to the spill-over of infectious agents from bats to other hosts. Domestic animals including livestock may act as intermediate amplifying hosts for bat-origin pathogens to transmit to humans. An increasing number of studies investigating bat pathogen diversity and infection dynamics have been published. However, whether or how these infectious agents are transmitted both within bat populations and to other hosts, including humans, often remains unknown. Metagenomic approaches are uncovering the dynamics and distribution of potential pathogens in bat microbiomes, which might improve the understanding of disease emergence and transmission. Here, we summarize the current knowledge on bat zoonoses of public health concern and flag the gaps in the knowledge to enable further research and allocation of resources for tackling future outbreaks.
Collapse
Affiliation(s)
- J. Dhivahar
- Research Department of Zoology, St. Johns College, Palayamkottai, 627002, India
- Department of Plant Biology and Biotechnology, Laboratory of Microbial Ecology, Loyola College, Chennai, 600034, India
- Department of Biotechnology, Laboratory of Virology, University of Madras, Chennai, 600025, India
| | - Anutthaman Parthasarathy
- Department of Chemistry and Biosciences, Richmond Building, University of Bradford, Bradford, West Yorkshire, BD7 1DP, United Kingdom
| | - Kathiravan Krishnan
- Department of Biotechnology, Laboratory of Virology, University of Madras, Chennai, 600025, India
| | - Basavaraj S. Kovi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Yoshida Ushinomiyacho, 69, Sakyo Ward, 606-8501, Kyoto, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Yoshida Ushinomiyacho, 69, Sakyo Ward, 606-8501, Kyoto, Japan
| |
Collapse
|
5
|
Delamonica B, Davalos L, Larijani M, Anthony SJ, Liu J, MacCarthy T. Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes. Virus Evol 2023; 9:vead047. [PMID: 37577211 PMCID: PMC10422979 DOI: 10.1093/ve/vead047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/27/2023] [Accepted: 07/26/2023] [Indexed: 08/15/2023] Open
Abstract
APOBEC3, an enzyme subfamily that plays a role in virus restriction by generating mutations at particular DNA motifs or mutational 'hotspots', can drive viral mutagenesis with host-specific preferential hotspot mutations contributing to pathogen variation. While previous analysis of viral genomes from the 2022 Mpox (formerly Monkeypox) disease outbreak has shown a high frequency of C>T mutations at TC motifs, suggesting recent mutations are human APOBEC3-mediated, how emerging monkeypox virus (MPXV) strains will evolve as a consequence of APOBEC3-mediated mutations remains unknown. By measuring hotspot under-representation, depletion at synonymous sites, and a combination of the two, we analyzed APOBEC3-driven evolution in human poxvirus genomes, finding varying hotspot under-representation patterns. While the native poxvirus molluscum contagiosum exhibits a signature consistent with extensive coevolution with human APOBEC3, including depletion of TC hotspots, variola virus shows an intermediate effect consistent with ongoing evolution at the time of eradication. MPXV, likely the result of recent zoonosis, showed many genes with more TC hotspots than expected by chance (over-representation) and fewer GC hotspots than expected (under-representation). These results suggest the MPXV genome: (1) may have evolved in a host with a particular APOBEC GC hotspot preference, (2) has inverted terminal repeat (ITR) regions-which may be exposed to APOBEC3 for longer during viral replication-and longer genes likely to evolve faster, and therefore (3) has a heightened potential for future human APOBEC3-meditated evolution as the virus spreads in the human population. Our predictions of MPXV mutational potential can both help guide future vaccine development and identification of putative drug targets and add urgency to the task of containing human Mpox disease transmission and uncovering the ecology of the virus in its reservoir host.
Collapse
Affiliation(s)
- Brenda Delamonica
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Liliana Davalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mani Larijani
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Department of Pathology, Microbiology, and Immunology, University of California-Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California-Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Jia Liu
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR 72205, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| |
Collapse
|
6
|
Delamonica B, Davalos L, Larijani M, Anthony SJ, Liu J, MacCarthy T. Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546779. [PMID: 37425914 PMCID: PMC10326987 DOI: 10.1101/2023.06.27.546779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
APOBEC3, an enzyme subfamily that plays a role in virus restriction by generating mutations at particular DNA motifs or mutational "hotspots," can drive viral mutagenesis with host-specific preferential hotspot mutations contributing to pathogen variation. While previous analysis of viral genomes from the 2022 Mpox (formerly Monkeypox) disease outbreak has shown a high frequency of C>T mutations at T C motifs, suggesting recent mutations are human APOBEC3-mediated, how emerging monkeypox virus (MPXV) strains will evolve as a consequence of APOBEC3-mediated mutations remains unknown. By measuring hotspot under-representation, depletion at synonymous sites, and a combination of the two, we analyzed APOBEC3-driven evolution in human poxvirus genomes, finding varying hotspot under-representation patterns. While the native poxvirus molluscum contagiosum exhibits a signature consistent with extensive coevolution with human APOBEC3, including depletion of T C hotspots, variola virus shows an intermediate effect consistent with ongoing evolution at the time of eradication. MPXV, likely the result of recent zoonosis, showed many genes with more T C hotspots than expected by chance (over-representation) and fewer G C hotspots than expected (under-representation). These results suggest the MPXV genome: 1) may have evolved in a host with a particular APOBEC G C hotspot preference, 2) has inverted terminal repeat (ITR) regions -which may be exposed to APOBEC3 for longer during viral replication- and longer genes likely to evolve faster, and therefore 3) has a heightened potential for future human APOBEC3-meditated evolution as the virus spreads in the human population. Our predictions of MPXV mutational potential can both help guide future vaccine development and identification of putative drug targets and add urgency to the task of containing human Mpox disease transmission and uncovering the ecology of the virus in its reservoir host.
Collapse
Affiliation(s)
- Brenda Delamonica
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Liliana Davalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA; Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Mani Larijani
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada; Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California-Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Jia Liu
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| |
Collapse
|
7
|
Aroldi A, Angaroni F, D’Aliberti D, Spinelli S, Crespiatico I, Crippa V, Piazza R, Graudenzi A, Ramazzotti D. Characterization of SARS-CoV-2 Mutational Signatures from 1.5+ Million Raw Sequencing Samples. Viruses 2022; 15:7. [PMID: 36680048 PMCID: PMC9864147 DOI: 10.3390/v15010007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/01/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
We present a large-scale analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) substitutions, considering 1,585,456 high-quality raw sequencing samples, aimed at investigating the existence and quantifying the effect of mutational processes causing mutations in SARS-CoV-2 genomes when interacting with the human host. As a result, we confirmed the presence of three well-differentiated mutational processes likely ruled by reactive oxygen species (ROS), apolipoprotein B editing complex (APOBEC), and adenosine deaminase acting on RNA (ADAR). We then evaluated the activity of these mutational processes in different continental groups, showing that some samples from Africa present a significantly higher number of substitutions, most likely due to higher APOBEC activity. We finally analyzed the activity of mutational processes across different SARS-CoV-2 variants, and we found a significantly lower number of mutations attributable to APOBEC activity in samples assigned to the Omicron variant.
Collapse
Affiliation(s)
- Andrea Aroldi
- Hematology and Clinical Research Unit, San Gerardo Hospital, Via G. B. Pergolesi 33, 20900 Monza, Italy
- Department of Medicine and Surgery, Università degli Studi di Milano-Bicocca, Via Cadore 48, 20900 Monza, Italy
| | - Fabrizio Angaroni
- Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Viale Sarca 336, 20100 Milano, Italy
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milano, Italy
| | - Deborah D’Aliberti
- Department of Medicine and Surgery, Università degli Studi di Milano-Bicocca, Via Cadore 48, 20900 Monza, Italy
| | - Silvia Spinelli
- Department of Medicine and Surgery, Università degli Studi di Milano-Bicocca, Via Cadore 48, 20900 Monza, Italy
| | - Ilaria Crespiatico
- Department of Medicine and Surgery, Università degli Studi di Milano-Bicocca, Via Cadore 48, 20900 Monza, Italy
| | - Valentina Crippa
- Department of Medicine and Surgery, Università degli Studi di Milano-Bicocca, Via Cadore 48, 20900 Monza, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, Università degli Studi di Milano-Bicocca, Via Cadore 48, 20900 Monza, Italy
- Bicocca Bioinformatics, Biostatistics and Bioimaging Center—B4, Via Follereau 3, 20854 Vedano al Lambro, Italy
| | - Alex Graudenzi
- Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Viale Sarca 336, 20100 Milano, Italy
- Bicocca Bioinformatics, Biostatistics and Bioimaging Center—B4, Via Follereau 3, 20854 Vedano al Lambro, Italy
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, Università degli Studi di Milano-Bicocca, Via Cadore 48, 20900 Monza, Italy
| |
Collapse
|
8
|
Reggiani A, Rugna G, Bonilauri P. SARS-CoV-2 and animals, a long story that doesn't have to end now: What we need to learn from the emergence of the Omicron variant. Front Vet Sci 2022; 9:1085613. [PMID: 36590812 PMCID: PMC9798331 DOI: 10.3389/fvets.2022.1085613] [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: 10/31/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
OIE, the world organization for animal health, recently released an update on the state of the art of knowledge regarding SARS-CoV-2 in animals. For farmed animals, ferrets and minks were found to be highly susceptible to the virus and develop symptomatic disease both in natural conditions and in experimental infections. Lagomorphs of the species Oryctolagus cuniculus are indicated as highly susceptible to the virus under experimental conditions, but show no symptoms of the disease and do not transmit the virus between conspecifics, unlike raccoon dogs (Nyctereutes procyonoides), which in addition to being highly susceptible to the virus under experimental conditions, can also transmit the virus between conspecifics. Among felines, the circulation of the virus has reached a level of cases such as sometimes suggests the experimental use of vaccines for human use or treatments with monoclonal antibodies. But even among wild animals, several species (White-tailed deer, Egyptian rousettes, and minks) have now been described as potential natural reservoirs of the virus. This proven circulation of SARS-CoV-2 among animals has not been accompanied by the development of an adequate surveillance system that allows following the evolution of the virus among its natural hosts. This will be all the more relevant as the surveillance system in humans inevitably drops and we move to surveillance by sentinels similar to the human flu virus. The lesson that we can draw from the emergence of Omicron and, more than likely, its animal origin must not be lost, and in this mini-review, we explain why.
Collapse
|
9
|
Jakobsdottir GM, Brewer DS, Cooper C, Green C, Wedge DC. APOBEC3 mutational signatures are associated with extensive and diverse genomic instability across multiple tumour types. BMC Biol 2022; 20:117. [PMID: 35597990 PMCID: PMC9124393 DOI: 10.1186/s12915-022-01316-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The APOBEC3 (apolipoprotein B mRNA editing enzyme catalytic polypeptide 3) family of cytidine deaminases is responsible for two mutational signatures (SBS2 and SBS13) found in cancer genomes. APOBEC3 enzymes are activated in response to viral infection, and have been associated with increased mutation burden and TP53 mutation. In addition to this, it has been suggested that APOBEC3 activity may be responsible for mutations that do not fall into the classical APOBEC3 signatures (SBS2 and SBS13), through generation of double strand breaks.Previous work has mainly focused on the effects of APOBEC3 within individual tumour types using exome sequencing data. Here, we use whole genome sequencing data from 2451 primary tumours from 39 different tumour types in the Pan-Cancer Analysis of Whole Genomes (PCAWG) data set to investigate the relationship between APOBEC3 and genomic instability (GI). RESULTS AND CONCLUSIONS We found that the number of classical APOBEC3 signature mutations correlates with increased mutation burden across different tumour types. In addition, the number of APOBEC3 mutations is a significant predictor for six different measures of GI. Two GI measures (INDELs attributed to INDEL signatures ID6 and ID8) strongly suggest the occurrence and error prone repair of double strand breaks, and the relationship between APOBEC3 mutations and GI remains when SNVs attributed to kataegis are excluded.We provide evidence that supports a model of cancer genome evolution in which APOBEC3 acts as a causative factor in the development of diverse and widespread genomic instability through the generation of double strand breaks. This has important implications for treatment approaches for cancers that carry APOBEC3 mutations, and challenges the view that APOBECs only act opportunistically at sites of single stranded DNA.
Collapse
Affiliation(s)
- G Maria Jakobsdottir
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
- Manchester Cancer Research Centre, University of Manchester, Wilmslow Road, Manchester, M20 4GJ, UK
| | - Daniel S Brewer
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Colin Cooper
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Catherine Green
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - David C Wedge
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK.
- Manchester Cancer Research Centre, University of Manchester, Wilmslow Road, Manchester, M20 4GJ, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, OX4 2PG, UK.
| |
Collapse
|
10
|
Liao X, Xia X, Su W, Yan H, Ma Y, Xu L, Luo H, Liu W, Yin D, Zhang WH, Chen HN, Deng Y, Ren Z, Yu Z, Liao F, Chen K, Cao M, Zhang Y, Zhang W, Wang W, Zhao JN, Xu H, Shu Y. Association of recurrent APOBEC3B alterations with the prognosis of gastric-type cervical adenocarcinoma. Gynecol Oncol 2022; 165:105-113. [DOI: 10.1016/j.ygyno.2022.01.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 12/13/2022]
|
11
|
Asaoka M, Patnaik SK, Ishikawa T, Takabe K. Different members of the APOBEC3 family of DNA mutators have opposing associations with the landscape of breast cancer. Am J Cancer Res 2021; 11:5111-5125. [PMID: 34765315 PMCID: PMC8569370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023] Open
Abstract
APOBEC enzymes are strong mutagenic factors. In breast cancer, expression of APOBEC3B is increased and associated with mutation load and poor outcome. Other APOBEC3s can also mutate DNA but their clinical significance in breast cancer and its underpinnings have not been comprehensively studied. In our examination of 1,091 breast carcinoma cases, high expression of APOBEC3A or APOBEC3B genes was associated with greater tumor burden of mutations and other genomic aberrations. Expression of none of the five APOBEC3C-H genes had any correlation with these features, including T[C-T/G]W mutations, but their high expression levels indicated a robust anti-cancer immune response within tumors, with elevated CD8+ T cell abundance, T cell receptor diversity, and immune cytolytic activity. Concordantly, survival analyses of this and two other cohorts with > 3,000 patients each showed favorable prognostic benefit of high APOBEC3C-H expression for both cancer progression and mortality. A detrimental prognostic value was observed for APOBEC3A and APOBEC3B. Single-cell data revealed cancer epithelial and stromal immune cells as major sources of APOBEC3B and APOBEC3C-H expression in tumors, respectively. These observations on opposing associations with breast cancer of different APOBEC3s highlight the contrasting roles of these enzymes, promoting cancer through mutagenesis while antagonizing it through immune response.
Collapse
Affiliation(s)
- Mariko Asaoka
- Department of Breast Surgery, Roswell Park Comprehensive Cancer CenterBuffalo, New York, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo, Japan
| | - Santosh K Patnaik
- Department of Thoracic Surgery, Roswell Park Comprehensive Cancer CenterBuffalo, New York, USA
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New YorkBuffalo, New York, USA
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo, Japan
| | - Kazuaki Takabe
- Department of Breast Surgery, Roswell Park Comprehensive Cancer CenterBuffalo, New York, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo, Japan
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New YorkBuffalo, New York, USA
- Niigata University Graduate School of Medical and Dental SciencesNiigata, Japan
- Department of Surgery, Yokohama City UniversityYokohama, Japan
| |
Collapse
|
12
|
Activation of DNA Damage Tolerance Pathways May Improve Immunotherapy of Mesothelioma. Cancers (Basel) 2021; 13:cancers13133211. [PMID: 34199066 PMCID: PMC8269013 DOI: 10.3390/cancers13133211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/14/2021] [Accepted: 06/23/2021] [Indexed: 12/20/2022] Open
Abstract
Immunotherapy based on two checkpoint inhibitors (ICI), programmed cell death 1 (PD-1, Nivolumab) and cytotoxic T-lymphocyte 4 (CTLA-4, Ipilimumab), has provided a significant improvement in overall survival for malignant mesothelioma (MM). Despite this major breakthrough, the median overall survival of patients treated with the two ICIs only reached 18.1 months vs. 14 months in standard chemotherapy. With an objective response rate of 40%, only a subset of patients benefits from immunotherapy. A critical step in the success of immunotherapy is the presentation of tumor-derived peptides by the major histocompatibility complex I (MHC-I) of tumor cells. These neoantigens are potentially immunogenic and trigger immune responses orchestrated by cytotoxic cells. In MM, tumor development is nevertheless characterized by a low mutation rate despite major structural chromosomal rearrangements driving oncogenesis (BAP1, NF2, CDKN2AB). In this opinion, we propose to investigate an approach based on the mechanisms of the DNA damage tolerance (DDT) pathways to increase the frequency of non-synonymous mutations. The idea is to transiently activate the error-prone DDT in order to generate neoantigens while preserving a fully competent antitumor immune response.
Collapse
|
13
|
Infection of Bronchial Epithelial Cells by the Human Adenoviruses A12, B3, and C2 Differently Regulates the Innate Antiviral Effector APOBEC3B. J Virol 2021; 95:e0241320. [PMID: 33853956 DOI: 10.1128/jvi.02413-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Human adenoviruses (HAdVs) are a large family of DNA viruses that include more than 100 genotypes divided into seven species (A to G) and induce respiratory tract infections, gastroenteritis, and conjunctivitis. Genetically modified adenoviruses are also used as vaccines, gene therapies, and anticancer treatments. The APOBEC3s are a family of cytidine deaminases that restrict viruses by introducing mutations in their genomes. Viruses developed different strategies to cope with the APOBEC3 selection pressure, but nothing is known on the interplay between the APOBEC3s and the HAdVs. In this study, we focused on three HAdV strains: the B3 and C2 strains, as they are very frequent, and the A12 strain, which is less common but is oncogenic in animal models. We demonstrated that the three HAdV strains induce a similar APOBEC3B upregulation at the transcriptional level. At the protein level, however, APOBEC3B is abundantly expressed during HAdV-A12 and -C2 infection and shows a nuclear distribution. On the contrary, APOBEC3B is barely detectable in HAdV-B3-infected cells. APOBEC3B deaminase activity is detected in total protein extracts upon HAdV-A12 and -C2 infection. Bioinformatic analysis demonstrates that the HAdV-A12 genome bears a stronger APOBEC3 evolutionary footprint than that of the HAdV-C2 and HAdV-B3 genomes. Our results show that HAdV infection triggers the transcriptional upregulation of the antiviral innate effector APOBEC3B. The discrepancies between the APOBEC3B mRNA and protein levels might reflect the ability of some HAdV strains to antagonize the APOBEC3B protein. These findings point toward an involvement of APOBEC3B in HAdV restriction and evolution. IMPORTANCE The APOBEC3 family of cytosine deaminases has important roles in antiviral innate immunity and cancer. Notably, APOBEC3A and APOBEC3B are actively upregulated by several DNA tumor viruses and contribute to transformation by introducing mutations in the cellular genome. Human adenoviruses (HAdVs) are a large family of DNA viruses that cause generally asymptomatic infections in immunocompetent adults. HAdVs encode several oncogenes, and some HAdV strains, like HAdV-A12, induce tumors in hamsters and mice. Here, we show that HAdV infection specifically promotes the expression of the APOBEC3B gene. We report that infection with the A12 strain induces a strong expression of an enzymatically active APOBEC3B protein in bronchial epithelial cells. We provide bioinformatic evidence that HAdVs' genomes and notably the A12 genome are under APOBEC3 selection pressure. Thus, APOBEC3B might contribute to adenoviral restriction, diversification, and oncogenic potential of particular strains.
Collapse
|
14
|
Shapiro M, Krug LT, MacCarthy T. Mutational pressure by host APOBEC3s more strongly affects genes expressed early in the lytic phase of herpes simplex virus-1 (HSV-1) and human polyomavirus (HPyV) infection. PLoS Pathog 2021; 17:e1009560. [PMID: 33930088 PMCID: PMC8115780 DOI: 10.1371/journal.ppat.1009560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 05/12/2021] [Accepted: 04/14/2021] [Indexed: 01/22/2023] Open
Abstract
Herpes-Simplex Virus 1 (HSV-1) infects most humans when they are young, sometimes with fatal consequences. Gene expression occurs in a temporal order upon lytic HSV-1 infection: immediate early (IE) genes are expressed, then early (E) genes, followed by late (L) genes. During this infection cycle, the HSV-1 genome has the potential for exposure to APOBEC3 (A3) proteins, a family of cytidine deaminases that cause C>U mutations on single-stranded DNA (ssDNA), often resulting in a C>T transition. We developed a computational model for the mutational pressure of A3 on the lytic cycle of HSV-1 to determine which viral kinetic gene class is most vulnerable to A3 mutations. Using in silico stochastic methods, we simulated the infectious cycle under varying intensities of A3 mutational pressure. We found that the IE and E genes are more vulnerable to A3 than L genes. We validated this model by analyzing the A3 evolutionary footprints in 25 HSV-1 isolates. We find that IE and E genes have evolved to underrepresent A3 hotspot motifs more so than L genes, consistent with greater selection pressure on IE and E genes. We extend this model to two-step infections, such as those of polyomavirus, and find that the same pattern holds for over 25 human Polyomavirus (HPyVs) genomes. Genes expressed earlier during infection are more vulnerable to mutations than those expressed later.
Collapse
Affiliation(s)
- Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
| | - Laurie T. Krug
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, United States of America
| |
Collapse
|
15
|
Insights into the Structures and Multimeric Status of APOBEC Proteins Involved in Viral Restriction and Other Cellular Functions. Viruses 2021; 13:v13030497. [PMID: 33802945 PMCID: PMC8002816 DOI: 10.3390/v13030497] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 12/16/2022] Open
Abstract
Apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) proteins belong to a family of deaminase proteins that can catalyze the deamination of cytosine to uracil on single-stranded DNA or/and RNA. APOBEC proteins are involved in diverse biological functions, including adaptive and innate immunity, which are critical for restricting viral infection and endogenous retroelements. Dysregulation of their functions can cause undesired genomic mutations and RNA modification, leading to various associated diseases, such as hyper-IgM syndrome and cancer. This review focuses on the structural and biochemical data on the multimerization status of individual APOBECs and the associated functional implications. Many APOBECs form various multimeric complexes, and multimerization is an important way to regulate functions for some of these proteins at several levels, such as deaminase activity, protein stability, subcellular localization, protein storage and activation, virion packaging, and antiviral activity. The multimerization of some APOBECs is more complicated than others, due to the associated complex RNA binding modes.
Collapse
|
16
|
Mika T, Ladigan-Badura S, Maghnouj A, Mustafa B, Klein-Scory S, Baraniskin A, Döhring S, Fuchs I, Ehl S, Hahn SA, Schroers R. Altered T-Lymphocyte Biology Following High-Dose Melphalan and Autologous Stem Cell Transplantation With Implications for Adoptive T-Cell Therapy. Front Oncol 2020; 10:568056. [PMID: 33363008 PMCID: PMC7759611 DOI: 10.3389/fonc.2020.568056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/20/2020] [Indexed: 01/18/2023] Open
Abstract
In relapsed and refractory multiple myeloma (MM), adoptive cell therapies (ACT) including CAR-T-cells are under clinical investigation. However, relapse due to T-cell exhaustion or limited persistence is an obstacle. Before ACT are considered in MM, high-dose (HD) melphalan followed by autologous stem-cell transplantation (autoSCT) has been administered in most clinical situations. Yet, the impact of HD chemotherapy on T-cells in MM with respect to ACT is unclear. In this study, T-lymphocytes’ phenotypes, expansion properties, lentiviral transduction efficacy, and gene expression were examined with special respect to patients following HD melphalan. Significant impairment of T-cells’ expansion and transduction rates could be demonstrated. Expansion was diminished due to inherent disadvantages of the predominant T-cell phenotype but restored over time. The quantitative fraction of CD27−/CD28− T-cells before expansion was predictive of T-cell yield. Following autoSCT, the transduction efficacy was reduced by disturbed lentiviral genome integration. Moreover, an unfavorable T-cell phenotype after expansion was demonstrated. In initial analyses of CD107a degranulation impaired T-cell cytotoxicity was detected in one patient following melphalan and autoSCT. The findings of our study have potential implications regarding the time point of leukapheresis for CAR-T-cell manufacturing. Our results point to a preferred interval of more than 3 months until patients should undergo cell separation for CAR-T therapy in the specific situation post-HD melphalan/autoSCT. Monitoring of CD27−/CD28− T-cells, has the potential to influence clinical decision making before apheresis in MM.
Collapse
Affiliation(s)
- Thomas Mika
- Department of Medicine, Hematology and Oncology, Ruhr-University Bochum, Bochum, Germany.,Department of Molecular Gastrointestinal Oncology, Ruhr-University Bochum, Bochum, Germany
| | - Swetlana Ladigan-Badura
- Department of Medicine, Hematology and Oncology, Ruhr-University Bochum, Bochum, Germany.,Department of Molecular Gastrointestinal Oncology, Ruhr-University Bochum, Bochum, Germany
| | - Abdelouahid Maghnouj
- Department of Molecular Gastrointestinal Oncology, Ruhr-University Bochum, Bochum, Germany
| | - Bakr Mustafa
- Department of Molecular Gastrointestinal Oncology, Ruhr-University Bochum, Bochum, Germany
| | - Susanne Klein-Scory
- Department of Medicine, Hematology and Oncology, Ruhr-University Bochum, Bochum, Germany
| | - Alexander Baraniskin
- Department of Medicine, Hematology and Oncology, Ruhr-University Bochum, Bochum, Germany
| | - Sascha Döhring
- Department of Molecular Gastrointestinal Oncology, Ruhr-University Bochum, Bochum, Germany
| | - Ilka Fuchs
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Stephan Ehl
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Stephan A Hahn
- Department of Molecular Gastrointestinal Oncology, Ruhr-University Bochum, Bochum, Germany
| | - Roland Schroers
- Department of Medicine, Hematology and Oncology, Ruhr-University Bochum, Bochum, Germany
| |
Collapse
|
17
|
Revathidevi S, Murugan AK, Nakaoka H, Inoue I, Munirajan AK. APOBEC: A molecular driver in cervical cancer pathogenesis. Cancer Lett 2020; 496:104-116. [PMID: 33038491 PMCID: PMC7539941 DOI: 10.1016/j.canlet.2020.10.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/16/2020] [Accepted: 10/04/2020] [Indexed: 02/09/2023]
Abstract
Cervical cancer is one of the foremost common cancers in women. Human papillomavirus (HPV) infection remains a major risk factor of cervical cancer. In addition, numerous other genetic and epigenetic factors also are involved in the underlying pathogenesis of cervical cancer. Recently, it has been reported that apolipoprotein B mRNA editing enzyme catalytic polypeptide like (APOBEC), DNA-editing protein plays an important role in the molecular pathogenesis of cancer. Particularly, the APOBEC3 family was shown to induce tumor mutations by aberrant DNA editing mechanism. In general, APOBEC3 enzymes play a pivotal role in the deamination of cytidine to uridine in DNA and RNA to control diverse biological processes such as regulation of protein expression, innate immunity, and embryonic development. Innate antiviral activity of the APOBEC3 family members restrict retroviruses, endogenous retro-element, and DNA viruses including the HPV that is the leading risk factor for cervical cancer. This review briefly describes the pathogenesis of cervical cancer and discusses in detail the recent findings on the role of APOBEC in the molecular pathogenesis of cervical cancer. APOBEC enzymes deaminate cytidine to uridine and control diverse biological processes including viral restriction. APOBEC3, DNA/RNA-editing enzyme plays an important role in the molecular pathogenesis of cervical cancer. APOBEC3-mediated DNA editing leads to the accumulation of somatic mutations in tumors and HPV genome. Deregulation of APOBEC3 family genes cause genomic instability and result in drug resistance, and immune-evasion in tumors.
Collapse
Affiliation(s)
- Sundaramoorthy Revathidevi
- Department of Genetics, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, 600113, India; Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Avaniyapuram Kannan Murugan
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Hirofumi Nakaoka
- Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan; Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, 101-0062, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Arasambattu Kannan Munirajan
- Department of Genetics, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, 600113, India.
| |
Collapse
|
18
|
Poulain F, Lejeune N, Willemart K, Gillet NA. Footprint of the host restriction factors APOBEC3 on the genome of human viruses. PLoS Pathog 2020; 16:e1008718. [PMID: 32797103 PMCID: PMC7449416 DOI: 10.1371/journal.ppat.1008718] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 08/26/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
APOBEC3 enzymes are innate immune effectors that introduce mutations into viral genomes. These enzymes are cytidine deaminases which transform cytosine into uracil. They preferentially mutate cytidine preceded by thymidine making the 5'TC motif their favored target. Viruses have evolved different strategies to evade APOBEC3 restriction. Certain viruses actively encode viral proteins antagonizing the APOBEC3s, others passively face the APOBEC3 selection pressure thanks to a depleted genome for APOBEC3-targeted motifs. Hence, the APOBEC3s left on the genome of certain viruses an evolutionary footprint. The aim of our study is the identification of these viruses having a genome shaped by the APOBEC3s. We analyzed the genome of 33,400 human viruses for the depletion of APOBEC3-favored motifs. We demonstrate that the APOBEC3 selection pressure impacts at least 22% of all currently annotated human viral species. The papillomaviridae and polyomaviridae are the most intensively footprinted families; evidencing a selection pressure acting genome-wide and on both strands. Members of the parvoviridae family are differentially targeted in term of both magnitude and localization of the footprint. Interestingly, a massive APOBEC3 footprint is present on both strands of the B19 erythroparvovirus; making this viral genome one of the most cleaned sequences for APOBEC3-favored motifs. We also identified the endemic coronaviridae as significantly footprinted. Interestingly, no such footprint has been detected on the zoonotic MERS-CoV, SARS-CoV-1 and SARS-CoV-2 coronaviruses. In addition to viruses that are footprinted genome-wide, certain viruses are footprinted only on very short sections of their genome. That is the case for the gamma-herpesviridae and adenoviridae where the footprint is localized on the lytic origins of replication. A mild footprint can also be detected on the negative strand of the reverse transcribing HIV-1, HIV-2, HTLV-1 and HBV viruses. Together, our data illustrate the extent of the APOBEC3 selection pressure on the human viruses and identify new putatively APOBEC3-targeted viruses.
Collapse
Affiliation(s)
- Florian Poulain
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
| | - Noémie Lejeune
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
| | - Kévin Willemart
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
| | - Nicolas A. Gillet
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
| |
Collapse
|
19
|
Martinez T, Shapiro M, Bhaduri-McIntosh S, MacCarthy T. Evolutionary effects of the AID/APOBEC family of mutagenic enzymes on human gamma-herpesviruses. Virus Evol 2019; 5:vey040. [PMID: 30792902 PMCID: PMC6371749 DOI: 10.1093/ve/vey040] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The human gamma-herpesviruses, Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus, establish lifelong latency in B cells and are associated with multiple malignancies. Virus-host coevolution often drive changes in both host immunity and in the viral genome. We consider one host immune mechanism, the activation-induced deaminase (AID)/APOBEC family of cytidine deaminases, that induces mutations in viral DNA. AID, the ancestral gene in the family has a conserved role in somatic hypermutation, a key step in antibody affinity maturation. The APOBEC3 subfamily, of which there are seven genes in human, have evolved antiviral functions and have diversified in terms of their expression pattern, subcellular localization, and DNA mutation motifs (hotspots). In this study, we investigated how the human gamma-herpesviruses have evolved to avoid the action of the AID/APOBEC enzymes and determine if these enzymes are contributing to the ongoing evolution of the viruses. We used computational methods to evaluate observed versus expected frequency of AID/APOBEC hotspots in viral genomes and found that the viruses have evolved to limit the representation of AID and certain APOBEC3 motifs. At the same time, the remaining hotspots were highly likely to cause amino acid changes, suggesting prolonged evolutionary pressure of the enzymes on the viruses. To study current hypermutation, as opposed to historical mutation processes, we also analyzed putative mutations derived from alignments of published viral genomes and found again that AID and APOBEC3 appear to target the genome most frequently. New protein variants resulting from AID/APOBEC activity may have important consequences in health, including vaccine development (epitope evolution) and host immune evasion.
Collapse
Affiliation(s)
- Teresa Martinez
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Sumita Bhaduri-McIntosh
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| |
Collapse
|
20
|
Expansions, diversification, and interindividual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys. Proc Natl Acad Sci U S A 2018; 115:E3211-E3220. [PMID: 29555777 PMCID: PMC5889659 DOI: 10.1073/pnas.1720871115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cytidine deaminases of the AID/APOBEC family mutate the genetic material of pathogens or contribute to the generation and diversification of antibody repertoires in jawed vertebrates. In the extant jawless vertebrate, the lamprey, two members of the AID/APOBEC family are implicated in the somatic diversification of variable lymphocyte receptor (VLR) repertoires. We discovered an unexpected diversity of cytidine deaminase genes within and among lamprey species. The cytidine deaminases with features comparable to jawed vertebrate AID are always present, suggesting that they are involved in essential processes, such as VLR assembly. In contrast, other genes show a remarkable copy number variation, like the APOBEC3 genes in mammals. This suggests an unexpected similarity in functional deployment of AID/APOBEC cytidine deaminases across all vertebrates. Cytidine deaminases of the AID/APOBEC family catalyze C-to-U nucleotide transitions in mRNA or DNA. Members of the APOBEC3 branch are involved in antiviral defense, whereas AID contributes to diversification of antibody repertoires in jawed vertebrates via somatic hypermutation, gene conversion, and class switch recombination. In the extant jawless vertebrate, the lamprey, two members of the AID/APOBEC family are implicated in the generation of somatic diversity of the variable lymphocyte receptors (VLRs). Expression studies linked CDA1 and CDA2 genes to the assembly of VLRA/C genes in T-like cells and the VLRB genes in B-like cells, respectively. Here, we identify and characterize several CDA1-like genes in the larvae of different lamprey species and demonstrate that these encode active cytidine deaminases. Structural comparisons of the CDA1 variants highlighted substantial differences in surface charge; this observation is supported by our finding that the enzymes require different conditions and substrates for optimal activity in vitro. Strikingly, we also found that the number of CDA-like genes present in individuals of the same species is variable. Nevertheless, irrespective of the number of different CDA1-like genes present, all lamprey larvae have at least one functional CDA1-related gene encoding an enzyme with predicted structural and chemical features generally comparable to jawed vertebrate AID. Our findings suggest that, similar to APOBEC3 branch expansion in jawed vertebrates, the AID/APOBEC family has undergone substantial diversification in lamprey, possibly indicative of multiple distinct biological roles.
Collapse
|
21
|
HPV11 E6 mutation by overexpression of APOBEC3A and effects of interferon-ω on APOBEC3s and HPV11 E6 expression in HPV11.HaCaT cells. Virol J 2017; 14:211. [PMID: 29100527 PMCID: PMC5670706 DOI: 10.1186/s12985-017-0878-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/27/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Condyloma acuminatum, infected by low-risk human papillomaviruses (e.g., HPV6 and HPV11), is one of the most widespread sexually transmitted diseases. Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 proteins (APOBEC3s, A3s) are cellular cytidine deaminases acting as antiviral factors through hypermutation of viral genome. However, it remains unknown whether A3s results in HPV11 gene mutations and interferon-ω (IFN-ω) exhibits antiviral activities through the A3s system. Here we investigated whether enhanced APOBEC3A (A3A) resulted in the E6 gene mutations and explore the effects of recombinant human interferon-ω (rhIFN-ω) on A3s/E6 expression in HaCaT keratinocytes containing the genome of HPV 11 (HPV11.HaCaT cells). METHODS A3A-overexpressed HPV11.HaCaT (A3A-HPV11.HaCaT) cells were established by lentiviral infection and verified by immunofluorescence and western-blotting. Cell cycle, E6 gene mutations, APOBEC3s/E6 gene expression and subcellular localization were detected by FACS, 3D-PCR and sequencing, qRT-PCR and immunofluorescence respectively. RESULTS The results suggested that A3A-HPV11.HaCaT cells were successfully established. Enhanced A3A induced S-phase arrest, G > A/C > T mutations and obvious reduction of E6 mRNA expression. A3A/A3B mRNA expression was up-regulated at 6 h and 12 h and obvious A3A staining existed throughout HPV11.HaCaT cells after rhIFN-ω treatment. RhIFN-ω could also inhibit mRNA expression of HPV11 E6 significantly. CONCLUSIONS Enhanced A3A repressed HPV11 E6 expression through gene hypermutation, and rhIFN-ω might be an effective agent against HPV11 infection by up-regulation of A3A.
Collapse
|
22
|
Fountzilas G, Psyrri A, Giannoulatou E, Tikas I, Manousou K, Rontogianni D, Ciuleanu E, Ciuleanu T, Resiga L, Zaramboukas T, Papadopoulou K, Bobos M, Chrisafi S, Tsolaki E, Markou K, Giotakis E, Koutras A, Psoma E, Kalogera-Fountzila A, Skondra M, Bamia C, Pectasides D, Kotoula V. Prevalent somaticBRCA1mutations shape clinically relevant genomic patterns of nasopharyngeal carcinoma in Southeast Europe. Int J Cancer 2017; 142:66-80. [DOI: 10.1002/ijc.31023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/01/2017] [Indexed: 12/16/2022]
Affiliation(s)
- George Fountzilas
- Laboratory of Molecular Oncology; Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki; Thessaloniki Greece
- Faculty of Medicine, School of Health Sciences; Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Amanda Psyrri
- Division of Oncology, Second Department of Internal Medicine; Attikon University Hospital; Athens Greece
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute; Darlinghurst NSW Australia
- The University of New South Wales; Kensington NSW Australia
| | - Ioannis Tikas
- Laboratory of Molecular Oncology; Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Kyriaki Manousou
- Section of Biostatistics, Hellenic Cooperative Oncology Group; Data Office; Athens Greece
| | | | | | - Tudor Ciuleanu
- Institute of Oncology Ion Chiricuta and UMF Iuliu Hatieganu; Cluj-Napoca Romania
| | - Liliana Resiga
- Department of Pathology; Ion Chiricuta Cancer Institute; Cluj Romania
| | - Thomas Zaramboukas
- Department of Pathology; School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology; Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Mattheos Bobos
- Laboratory of Molecular Oncology; Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Sofia Chrisafi
- Laboratory of Molecular Oncology; Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Eleftheria Tsolaki
- Laboratory of Molecular Oncology; Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Konstantinos Markou
- First Department of Otorhinolaryngology; AHEPA Hospital, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Evangelos Giotakis
- Department of Otolaryngology Head and Neck Surgery; Hippokration Hospital, National and Kapodistrian University of Athens; Athens Greece
| | - Angelos Koutras
- Division of Oncology, Department of Medicine; University Hospital, University of Patras Medical School; Patras Greece
| | - Elsa Psoma
- Department of Radiology; AHEPA Hospital, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Anna Kalogera-Fountzila
- Department of Radiology; AHEPA Hospital, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Maria Skondra
- Oncology Section, Second Department of Internal Medicine; Hippokration Hospital; Athens
| | - Christina Bamia
- Department of Hygiene, Epidemiology and Medical Statistics; National and Kapodistrian University of Athens, Medical School; Athens Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine; Hippokration Hospital; Athens
| | - Vassiliki Kotoula
- Laboratory of Molecular Oncology; Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki; Thessaloniki Greece
- Department of Pathology; School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki; Thessaloniki Greece
| |
Collapse
|
23
|
Sharma S, Wang J, Cortes Gomez E, Taggart RT, Baysal BE. Mitochondrial complex II regulates a distinct oxygen sensing mechanism in monocytes. Hum Mol Genet 2017; 26:1328-1339. [PMID: 28204537 DOI: 10.1093/hmg/ddx041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/25/2017] [Indexed: 01/28/2023] Open
Abstract
Mutations in mitochondrial complex II (succinate dehydrogenase; SDH) genes predispose to paraganglioma tumors that show constitutive activation of hypoxia responses. We recently showed that SDHB mRNAs in hypoxic monocytes gain a stop codon mutation by APOBEC3A-mediated C-to-U RNA editing. Here, we test the hypothesis that inhibition of complex II facilitates hypoxic gene expression in monocytes using an integrative experimental approach. By RNA sequencing, we show that specific inhibition of complex II by atpenin A5 in normoxic conditions mimics hypoxia and induces hypoxic transcripts as well as APOBEC3A-mediated RNA editing in human monocytes. Myxothiazol, a complex III inhibitor, has similar effects in normoxic monocytes. Atpenin A5 partially inhibits oxygen consumption, and neither hypoxia nor atpenin A5 in normoxia robustly stabilizes hypoxia-inducible factor (HIF)-1α in primary monocytes. Several earlier studies in transformed cell lines suggested that normoxic stabilization of HIF-1α explains the persistent expression of hypoxic genes upon complex II inactivation. On the contrary, we find that atpenin A5 antagonizes the stabilization of HIF-1α and reduces hypoxic gene expression in transformed cell lines. Accordingly, compound germline heterozygosity of mouse Sdhb/Sdhc/Sdhd null alleles blunts chronic hypoxia-induced increases in hemoglobin levels, an adaptive response mainly regulated by HIF-2α. In contrast, atpenin A5 or myxothiazol does not reduce hypoxia-induced gene expression or RNA editing in monocytes. These results reveal a novel role for mitochondrial respiratory inhibition in induction of the hypoxic transcriptome in monocytes and suggest that inhibition of complex II activates a distinct hypoxia signaling pathway in a cell-type specific manner.
Collapse
Affiliation(s)
| | - Jianming Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Eduardo Cortes Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | | | | |
Collapse
|
24
|
Chen J, MacCarthy T. The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes. PLoS Comput Biol 2017; 13:e1005471. [PMID: 28362825 PMCID: PMC5391955 DOI: 10.1371/journal.pcbi.1005471] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 04/14/2017] [Accepted: 03/21/2017] [Indexed: 12/22/2022] Open
Abstract
The AID / APOBEC genes are a family of cytidine deaminases that have evolved in vertebrates, and particularly mammals, to mutate RNA and DNA at distinct preferred nucleotide contexts (or “hotspots”) on foreign genomes such as viruses and retrotransposons. These enzymes play a pivotal role in intrinsic immunity defense mechanisms, often deleteriously mutating invading retroviruses or retrotransposons and, in the case of AID, changing antibody sequences to drive affinity maturation. We investigate the strength of various hotspots on their known biological targets by evaluating the potential impact of mutations on the DNA coding sequences of these targets, and compare these results to hypothetical hotspots that did not evolve. We find that the existing AID / APOBEC hotspots have a large impact on retrotransposons and non-mammalian viruses while having a much smaller effect on vital mammalian genes, suggesting co-evolution with AID / APOBECs may have had an impact on the genomes of the viruses we analyzed. We determine that GC content appears to be a significant, but not sole, factor in resistance to deaminase activity. We discuss possible mechanisms AID and APOBEC viral targets have adopted to escape the impacts of deamination activity, including changing the GC content of the genome. The APOBEC family of cytidine deaminases are important enzymes in most vertebrates. The ancestral member of this gene family is activation induced deaminase (AID), which mutates the Immunoglobulin loci in B Cells during antibody affinity maturation in jawed vertebrates. The APOBEC family has expanded particularly in the mammals and in primates, where they have evolved roles in restriction of viruses and retrotransposons. Biochemical studies have established that AID preferentially targets “hotspots” such as AGC and avoids “coldspots” such as CCC. Other APOBECs have evolved distinct hotspots. For example, APOBEC3G, which targets retroviruses including HIV, has evolved to target the motif CCC as a hotspot, but it is unclear why. Here we ask why the AID/APOBEC cytidine deaminases evolved their particular mutational hotspots. Our results show that a wide range of unrelated genes including mammalian LINE1 ORFs and non- mammalian (ancestral-like) viruses are highly susceptible to mutations in APOBEC hotspots and less susceptible to the hypothetical non-APOBEC hotspots. On the other hand, mammalian viruses tend to exhibit low susceptibility to the same APOBEC hotspots, suggesting these viruses have co-evolved to minimize potential damaging mutations, and that the native GC content plays a large role in this behavior.
Collapse
Affiliation(s)
- Jeffrey Chen
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Book, New York, United States of America
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Book, New York, United States of America
- * E-mail:
| |
Collapse
|
25
|
Nakashima M, Tsuzuki S, Awazu H, Hamano A, Okada A, Ode H, Maejima M, Hachiya A, Yokomaku Y, Watanabe N, Akari H, Iwatani Y. Mapping Region of Human Restriction Factor APOBEC3H Critical for Interaction with HIV-1 Vif. J Mol Biol 2017; 429:1262-1276. [PMID: 28336404 DOI: 10.1016/j.jmb.2017.03.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 11/30/2022]
Abstract
The APOBEC3 (A3) family of cellular cytidine deaminases comprises seven members (A, B, C, D, F, G, and H) that potently inhibit retroviral replication. Human immunodeficiency virus type 1 (HIV-1) Vif is a small pleiotropic protein that specifically inactivates these enzymes, targeting them for ubiquitin-mediated proteasomal degradation. A3 Vif-interaction sites are presumed to fall into three distinct types: A3C/D/F, A3G, and A3H. To date, two types of A3G and A3C/D/F sites have been well characterized, whereas the A3H Vif-binding site remains poorly defined. Here, we explore the residues critical for the A3H-type Vif interaction. To avoid technical difficulties in performing experiments with human A3H haplotype II (hapII), which is relatively resistant to HIV-1 Vif, we employed its ortholog chimpanzee A3H (cA3H), which displays high Vif sensitivity, for a comparison of sensitivity with that of A3H hapII. The Vif susceptibility of A3H hapII-cA3H chimeras and their substitution mutants revealed a single residue at position 97 as a major determinant for the difference in their Vif sensitivities. We further surveyed critical residues by structure-guided mutagenesis using an A3H structural model and thus identified eight additional residues important for Vif sensitivity, which mapped to the α3 and α4 helices of A3H. Interestingly, this area is located on a surface adjacent to the A3G and A3C/D/F interfaces and is composed of negatively charged and hydrophobic patches. These findings suggest that HIV-1 Vif has evolved to utilize three dispersed surfaces for recognizing three types of interfaces on A3 proteins under certain structural constraints.
Collapse
Affiliation(s)
- Masaaki Nakashima
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Shinya Tsuzuki
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan; Department of Biotechnology, Nagoya University Graduate School of Engineering, Nagoya, Aichi 464-8603, Japan
| | - Hiroaki Awazu
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan; Department of Biotechnology, Nagoya University Graduate School of Engineering, Nagoya, Aichi 464-8603, Japan
| | - Akiko Hamano
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Ayaka Okada
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Masami Maejima
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Atsuko Hachiya
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Nobuhisa Watanabe
- Department of Biotechnology, Nagoya University Graduate School of Engineering, Nagoya, Aichi 464-8603, Japan; Synchrotron Radiation Research Center, Nagoya University, Nagoya, Aichi, 489-0965, Japan
| | - Hirofumi Akari
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan; Institute for Virus Research, Kyoto University, Kyoto, Kyoto 606-8507, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan; Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan.
| |
Collapse
|
26
|
Abstract
The AID/APOBEC family enzymes convert cytosines in single-stranded DNA to uracils, causing base substitutions and strand breaks. They are induced by cytokines produced during the body's inflammatory response to infections, and they help combat infections through diverse mechanisms. AID is essential for the maturation of antibodies and causes mutations and deletions in antibody genes through somatic hypermutation (SHM) and class-switch recombination (CSR) processes. One member of the APOBEC family, APOBEC1, edits mRNA for a protein involved in lipid transport. Members of the APOBEC3 subfamily in humans (APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H) inhibit infections of viruses such as HIV-1, HBV, and HCV, and retrotransposition of endogenous retroelements through mutagenic and nonmutagenic mechanisms. There is emerging consensus that these enzymes can cause mutations in the cellular genome at replication forks or within transcription bubbles depending on the physiological state of the cell and the phase of the cell cycle during which they are expressed. We describe here the state of knowledge about the structures of these enzymes, regulation of their expression, and both the advantageous and deleterious consequences of their expression, including carcinogenesis. We highlight similarities among them and present a holistic view of their regulation and function.
Collapse
Affiliation(s)
- Sachini U Siriwardena
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - Kang Chen
- Department of Obstetrics and Gynecology, Wayne State University , Detroit, Michigan 48201, United States
- Mucosal Immunology Studies Team, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
- Department of Immunology and Microbiology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Ashok S Bhagwat
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
- Department of Immunology and Microbiology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| |
Collapse
|
27
|
Abstract
Retrotransposons have generated about 40 % of the human genome. This review examines the strategies the cell has evolved to coexist with these genomic "parasites", focussing on the non-long terminal repeat retrotransposons of humans and mice. Some of the restriction factors for retrotransposition, including the APOBECs, MOV10, RNASEL, SAMHD1, TREX1, and ZAP, also limit replication of retroviruses, including HIV, and are part of the intrinsic immune system of the cell. Many of these proteins act in the cytoplasm to degrade retroelement RNA or inhibit its translation. Some factors act in the nucleus and involve DNA repair enzymes or epigenetic processes of DNA methylation and histone modification. RISC and piRNA pathway proteins protect the germline. Retrotransposon control is relaxed in some cell types, such as neurons in the brain, stem cells, and in certain types of disease and cancer, with implications for human health and disease. This review also considers potential pitfalls in interpreting retrotransposon-related data, as well as issues to consider for future research.
Collapse
Affiliation(s)
- John L. Goodier
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA 212051
| |
Collapse
|
28
|
Crespo H, Bertolotti L, Proffiti M, Cascio P, Cerruti F, Acutis PL, de Andrés D, Reina R, Rosati S. Low proviral small ruminant lentivirus load as biomarker of natural restriction in goats. Vet Microbiol 2016; 192:152-162. [PMID: 27527777 DOI: 10.1016/j.vetmic.2016.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 11/16/2022]
Abstract
Small ruminant lentiviruses (SRLV) globally affect welfare and production of sheep and goats and are mainly controlled through elimination of infected animals, independently of the viral kinetics within the single animal. Control programs are based on highly sensitive serological tests, however the existence of low antibody responders leads to the permanent presence of seronegative infected animals in the flock, thus perpetuating the infection. On the other hand, long-term non-progressors show a detectable antibody response not indicative of a shedding animal, suggesting immune contention of infection. In this study, we analyse two goat populations within the same herd, harbouring low or high proviral SRLV loads respectively, both showing a robust antibody response. In vivo findings were confirmed in vitro since fibroblastic cell lines obtained from one high and one low proviral load representative goats, showed respectively a high and a faint production of virus upon infection with reference and field circulating SRLV strains. Differences in virus production were relieved when strain CAEV-Co was used for experimental infection. We analysed LTR promoter activity, proviral load, entry step and production of virus and viral proteins. Intriguingly, proteasomal activity was higher in fibroblasts from low proviral load animals and proteasome inhibition increased viral production in both cell lines, suggesting the implication of active proteasome-dependent restriction factors. Among them, we analysed relative expression and sequences of TRIM5α, APOBEC3 (Z1, Z2, Z3 and Z2-Z3) and BST-2 (Tetherin) and found a global antiviral status in low proviral carriers that may confer protection against viral shedding and disease onset.
Collapse
Affiliation(s)
- Helena Crespo
- Instituto de Agrobiotecnología, UPNA-CSIC-Gob, de Navarra, Avda. Pamplona 123, 31192 Mutilva, Spain
| | - Luigi Bertolotti
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, L.go P. Braccini 2, 10095 Grugliasco (TO), Italy
| | - Margherita Proffiti
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, L.go P. Braccini 2, 10095 Grugliasco (TO), Italy
| | - Paolo Cascio
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, L.go P. Braccini 2, 10095 Grugliasco (TO), Italy
| | - Fulvia Cerruti
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, L.go P. Braccini 2, 10095 Grugliasco (TO), Italy
| | - Pier Luigi Acutis
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Torino, Italy
| | - Damián de Andrés
- Instituto de Agrobiotecnología, UPNA-CSIC-Gob, de Navarra, Avda. Pamplona 123, 31192 Mutilva, Spain
| | - Ramsés Reina
- Instituto de Agrobiotecnología, UPNA-CSIC-Gob, de Navarra, Avda. Pamplona 123, 31192 Mutilva, Spain.
| | - Sergio Rosati
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, L.go P. Braccini 2, 10095 Grugliasco (TO), Italy
| |
Collapse
|
29
|
Zhang Z, Gu Q, Jaguva Vasudevan AA, Hain A, Kloke BP, Hasheminasab S, Mulnaes D, Sato K, Cichutek K, Häussinger D, Bravo IG, Smits SHJ, Gohlke H, Münk C. Determinants of FIV and HIV Vif sensitivity of feline APOBEC3 restriction factors. Retrovirology 2016; 13:46. [PMID: 27368163 PMCID: PMC4930625 DOI: 10.1186/s12977-016-0274-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/09/2016] [Indexed: 02/07/2023] Open
Abstract
Background Feline immunodeficiency virus (FIV) is a global pathogen of Felidae species and a model system for Human immunodeficiency virus (HIV)-induced AIDS. In felids such as the domestic cat (Felis catus), APOBEC3 (A3) genes encode for single-domain A3Z2s, A3Z3 and double-domain A3Z2Z3 anti-viral cytidine deaminases. The feline A3Z2Z3 is expressed following read-through transcription and alternative splicing, introducing a previously untranslated exon in frame, encoding a domain insertion called linker. Only A3Z3 and A3Z2Z3 inhibit Vif-deficient FIV. Feline A3s also are restriction factors for HIV and Simian immunodeficiency viruses (SIV). Surprisingly, HIV-2/SIV Vifs can counteract feline A3Z2Z3. Results To identify residues in feline A3s that Vifs need for interaction and degradation, chimeric human–feline A3s were tested. Here we describe the molecular direct interaction of feline A3s with Vif proteins from cat FIV and present the first structural A3 model locating these interaction regions. In the Z3 domain we have identified residues involved in binding of FIV Vif, and their mutation blocked Vif-induced A3Z3 degradation. We further identified additional essential residues for FIV Vif interaction in the A3Z2 domain, allowing the generation of FIV Vif resistant A3Z2Z3. Mutated feline A3s also showed resistance to the Vif of a lion-specific FIV, indicating an evolutionary conserved Vif–A3 binding. Comparative modelling of feline A3Z2Z3 suggests that the residues interacting with FIV Vif have, unlike Vif-interacting residues in human A3s, a unique location at the domain interface of Z2 and Z3 and that the linker forms a homeobox-like domain protruding of the Z2Z3 core. HIV-2/SIV Vifs efficiently degrade feline A3Z2Z3 by possible targeting the linker stretch connecting both Z-domains. Conclusions Here we identified in feline A3s residues important for binding of FIV Vif and a unique protein domain insertion (linker). To understand Vif evolution, a structural model of the feline A3 was developed. Our results show that HIV Vif binds human A3s differently than FIV Vif feline A3s. The linker insertion is suggested to form a homeo-box domain, which is unique to A3s of cats and related species, and not found in human and mouse A3s. Together, these findings indicate a specific and different A3 evolution in cats and human. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0274-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zeli Zhang
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Qinyong Gu
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Ananda Ayyappan Jaguva Vasudevan
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Anika Hain
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Björn-Philipp Kloke
- Department of Medical Biotechnology, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225, Langen, Germany.,BioNTech RNA Pharmaceuticals GmbH, An der Goldgrube 12, 55131, Mainz, Germany
| | - Sascha Hasheminasab
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Daniel Mulnaes
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Kei Sato
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto, 6068507, Japan.,CREST, Japan Science and Technology Agency, Saitama, 3220012, Japan
| | - Klaus Cichutek
- Department of Medical Biotechnology, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225, Langen, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Ignacio G Bravo
- MIVEGEC (UMR CNRS 5290, IRD 224, UM), National Center of Scientific Research (CNRS), 34394, Montpellier, France
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany.
| |
Collapse
|
30
|
Rawson JMO, Roth ME, Xie J, Daly MB, Clouser CL, Landman SR, Reilly CS, Bonnac L, Kim B, Patterson SE, Mansky LM. Synergistic reduction of HIV-1 infectivity by 5-azacytidine and inhibitors of ribonucleotide reductase. Bioorg Med Chem 2016; 24:2410-2422. [PMID: 27117260 DOI: 10.1016/j.bmc.2016.03.052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/18/2016] [Accepted: 03/27/2016] [Indexed: 11/29/2022]
Abstract
Although many compounds have been approved for the treatment of human immunodeficiency type-1 (HIV-1) infection, additional anti-HIV-1 drugs (particularly those belonging to new drug classes) are still needed due to issues such as long-term drug-associated toxicities, transmission of drug-resistant variants, and development of multi-class resistance. Lethal mutagenesis represents an antiviral strategy that has not yet been clinically translated for HIV-1 and is based on the use of small molecules to induce excessive levels of deleterious mutations within the viral genome. Here, we show that 5-azacytidine (5-aza-C), a ribonucleoside analog that induces the lethal mutagenesis of HIV-1, and multiple inhibitors of the enzyme ribonucleotide reductase (RNR) interact in a synergistic fashion to more effectively reduce the infectivity of HIV-1. In these drug combinations, RNR inhibitors failed to significantly inhibit the conversion of 5-aza-C to 5-aza-2'-deoxycytidine, suggesting that 5-aza-C acts primarily as a deoxyribonucleoside even in the presence of RNR inhibitors. The mechanism of antiviral synergy was further investigated for the combination of 5-aza-C and one specific RNR inhibitor, resveratrol, as this combination improved the selectivity index of 5-aza-C to the greatest extent. Antiviral synergy was found to be primarily due to the reduced accumulation of reverse transcription products rather than the enhancement of viral mutagenesis. To our knowledge, these observations represent the first demonstration of antiretroviral synergy between a ribonucleoside analog and RNR inhibitors, and encourage the development of additional ribonucleoside analogs and RNR inhibitors with improved antiretroviral activity.
Collapse
Affiliation(s)
- Jonathan M O Rawson
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Megan E Roth
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Jiashu Xie
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Michele B Daly
- Emory Center for AIDS Research, Emory University, 1518 Clifton Road NE, Suite 8050, Atlanta, GA 30322, USA
| | - Christine L Clouser
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Sean R Landman
- Department of Computer Science and Engineering, University of Minnesota, 4-192 Keller Hall, 200 Union Street SE, Minneapolis, MN 55455, USA
| | - Cavan S Reilly
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Division of Biostatistics, School of Public Health, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Laurent Bonnac
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Baek Kim
- Emory Center for AIDS Research, Emory University, 1518 Clifton Road NE, Suite 8050, Atlanta, GA 30322, USA
| | - Steven E Patterson
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Department of Microbiology and Immunology, Medical School, University of Minnesota, 689 23rd Avenue SE, Minneapolis, MN 55455, USA; Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, 321 Church Street SE, Minneapolis, MN 55455, USA; Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street SE, Minneapolis, MN 55455, USA.
| |
Collapse
|
31
|
Sharma S, Patnaik SK, Kemer Z, Baysal BE. Transient overexpression of exogenous APOBEC3A causes C-to-U RNA editing of thousands of genes. RNA Biol 2016; 14:603-610. [PMID: 27149507 DOI: 10.1080/15476286.2016.1184387] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
APOBEC3A cytidine deaminase induces site-specific C-to-U RNA editing of hundreds of genes in monocytes exposed to hypoxia and/or interferons and in pro-inflammatory macrophages. To examine the impact of APOBEC3A overexpression, we transiently expressed APOBEC3A in HEK293T cell line and performed RNA sequencing. APOBEC3A overexpression induces C-to-U editing at more than 4,200 sites in transcripts of 3,078 genes resulting in protein recoding of 1,110 genes. We validate recoding RNA editing of genes associated with breast cancer, hematologic neoplasms, amyotrophic lateral sclerosis, Alzheimer disease and primary pulmonary hypertension. These results highlight the fundamental impact of APOBEC3A overexpression on human transcriptome by widespread RNA editing.
Collapse
Affiliation(s)
- Shraddha Sharma
- a Department of Pathology , Roswell Park Cancer Institute , Buffalo , NY , USA
| | - Santosh K Patnaik
- b Department of Thoracic Surgery , Roswell Park Cancer Institute , Buffalo , NY , USA
| | - Zeynep Kemer
- a Department of Pathology , Roswell Park Cancer Institute , Buffalo , NY , USA
| | - Bora E Baysal
- a Department of Pathology , Roswell Park Cancer Institute , Buffalo , NY , USA
| |
Collapse
|