101
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Ng JF, Fraternali F. Understanding the structural details of APOBEC3-DNA interactions using graph-based representations. Curr Res Struct Biol 2020; 2:130-143. [PMID: 34235473 PMCID: PMC8244423 DOI: 10.1016/j.crstbi.2020.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 12/22/2022] Open
Abstract
Human APOBEC3 (A3; apolipoprotein B mRNA editing catalytic polypeptide-like 3) is a family of seven enzymes involved in generating mutations in nascent reverse transcripts of many retroviruses, as well as the human genome in a range of cancer types. The structural details of the interaction between A3 proteins and DNA molecules are only available for a few family members. Here we use homology modelling techniques to address the difference in structural coverage of human A3 enzymes interacting with different DNA substrates. A3-DNA interfaces are represented as residue networks ("graphs"), based on which features at these interfaces are compared and quantified. We demonstrate that graph-based representations are effective in highlighting structural features of A3-DNA interfaces. By large-scale in silico mutagenesis of the bound DNA chain, we predicted the preference of substrate DNA sequence for multiple A3 domains. These data suggested that computational modelling approaches could contribute in the exploration of the structural basis for sequence specificity in A3 substrate selection, and demonstrated the utility of graph-based approaches in evaluating a large number of structural models generated in silico. APOBEC3(A3)-DNA structures have been resolved with modified deaminase domains. Structural modelling of interaction between wild-type A3 domains and DNA substrates. Graph-based representations reveal structural differences across A3-DNA interfaces. Using in silico mutagenesis we compared substrate preference of multiple A3 domains. Graph-based approaches can efficiently compare a large number of structural models.
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102
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Zhang D, Hussain A, Manghwar H, Xie K, Xie S, Zhao S, Larkin RM, Qing P, Jin S, Ding F. Genome editing with the CRISPR-Cas system: an art, ethics and global regulatory perspective. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1651-1669. [PMID: 32271968 PMCID: PMC7336378 DOI: 10.1111/pbi.13383] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 02/22/2020] [Accepted: 03/19/2020] [Indexed: 05/18/2023]
Abstract
Over the last three decades, the development of new genome editing techniques, such as ODM, TALENs, ZFNs and the CRISPR-Cas system, has led to significant progress in the field of plant and animal breeding. The CRISPR-Cas system is the most versatile genome editing tool discovered in the history of molecular biology because it can be used to alter diverse genomes (e.g. genomes from both plants and animals) including human genomes with unprecedented ease, accuracy and high efficiency. The recent development and scope of CRISPR-Cas system have raised new regulatory challenges around the world due to moral, ethical, safety and technical concerns associated with its applications in pre-clinical and clinical research, biomedicine and agriculture. Here, we review the art, applications and potential risks of CRISPR-Cas system in genome editing. We also highlight the patent and ethical issues of this technology along with regulatory frameworks established by various nations to regulate CRISPR-Cas-modified organisms/products.
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Affiliation(s)
- Debin Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- College of Public AdministrationHuazhong Agricultural UniversityWuhanChina
| | - Amjad Hussain
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Kabin Xie
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationWuhanChina
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationWuhanChina
| | - Robert M. Larkin
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Ping Qing
- College of Public AdministrationHuazhong Agricultural UniversityWuhanChina
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Fang Ding
- Hubei Key Laboratory of Plant PathologyCollege of Plant Sciences and TechnologyHuazhong Agricultural UniversityWuhanChina
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103
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Carlaw TM, Zhang LH, Ross CJD. CRISPR/Cas9 Editing: Sparking Discussion on Safety in Light of the Need for New Therapeutics. Hum Gene Ther 2020; 31:794-807. [PMID: 32586150 DOI: 10.1089/hum.2020.111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Recent advances in genome sequencing have greatly improved our ability to understand and identify the causes of genetic diseases. However, there remains an urgent need for innovative, safe, and effective treatments for these diseases. CRISPR-based genome editing systems have become important and powerful tools in the laboratory, and efforts are underway to translate these into patient therapies. Therapeutic base editing is one form of genome engineering that has gained much interest because of its simplicity, specificity, and effectiveness. Base editors are a fusion of a partially deactivated Cas9 enzyme with nickase function, together with a base-modifying enzyme. They are capable of precisely targeting and repairing a pathogenic mutation to restore the normal function of a gene, ideally without disturbing the rest of the genome. In the past year, research has identified new safety concerns of base editors and sparked new innovations to improve their safety. In this review, we provide an overview of the recent advances in the safety and effectiveness of therapeutic base editors and prime editing.
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Affiliation(s)
| | - Lin-Hua Zhang
- Faculty of Pharmaceutical Sciences; University of British Columbia, Vancouver, Canada
| | - Colin J D Ross
- Faculty of Pharmaceutical Sciences; University of British Columbia, Vancouver, Canada
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104
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Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots. Nat Commun 2020; 11:2971. [PMID: 32532990 PMCID: PMC7293259 DOI: 10.1038/s41467-020-16802-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/26/2020] [Indexed: 02/07/2023] Open
Abstract
APOBEC3A is a cytidine deaminase driving mutagenesis, DNA replication stress and DNA damage in cancer cells. While the APOBEC3A-induced vulnerability of cancers offers an opportunity for therapy, APOBEC3A protein and mRNA are difficult to quantify in tumors due to their low abundance. Here, we describe a quantitative and sensitive assay to measure the ongoing activity of APOBEC3A in tumors. Using hotspot RNA mutations identified from APOBEC3A-positive tumors and droplet digital PCR, we develop an assay to quantify the RNA-editing activity of APOBEC3A. This assay is superior to APOBEC3A protein- and mRNA-based assays in predicting the activity of APOBEC3A on DNA. Importantly, we demonstrate that the RNA mutation-based APOBEC3A assay is applicable to clinical samples from cancer patients. Our study presents a strategy to follow the dysregulation of APOBEC3A in tumors, providing opportunities to investigate the role of APOBEC3A in tumor evolution and to target the APOBEC3A-induced vulnerability in therapy. The DNA cytosine deaminases APOBEC3A and APOBEC3B have emerged from cancer genomics studies as drivers of mutation in cancers and tumor heterogeneity. Here the authors present a computational approach to identify the RNA mutations specifically driven by APOBEC3A, and developed an RNA mutation-based assay to quantify ongoing APOBEC3A activity in tumor cells.
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105
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Delviks-Frankenberry KA, Desimmie BA, Pathak VK. Structural Insights into APOBEC3-Mediated Lentiviral Restriction. Viruses 2020; 12:E587. [PMID: 32471198 PMCID: PMC7354603 DOI: 10.3390/v12060587] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 01/18/2023] Open
Abstract
Mammals have developed clever adaptive and innate immune defense mechanisms to protect against invading bacterial and viral pathogens. Human innate immunity is continuously evolving to expand the repertoire of restriction factors and one such family of intrinsic restriction factors is the APOBEC3 (A3) family of cytidine deaminases. The coordinated expression of seven members of the A3 family of cytidine deaminases provides intrinsic immunity against numerous foreign infectious agents and protects the host from exogenous retroviruses and endogenous retroelements. Four members of the A3 proteins-A3G, A3F, A3H, and A3D-restrict HIV-1 in the absence of virion infectivity factor (Vif); their incorporation into progeny virions is a prerequisite for cytidine deaminase-dependent and -independent activities that inhibit viral replication in the host target cell. HIV-1 encodes Vif, an accessory protein that antagonizes A3 proteins by targeting them for polyubiquitination and subsequent proteasomal degradation in the virus producing cells. In this review, we summarize our current understanding of the role of human A3 proteins as barriers against HIV-1 infection, how Vif overcomes their antiviral activity, and highlight recent structural and functional insights into A3-mediated restriction of lentiviruses.
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Affiliation(s)
| | | | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA; (K.A.D.-F.); (B.A.D.)
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106
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Hix MA, Cisneros GA. Computational Investigation of APOBEC3H Substrate Orientation and Selectivity. J Phys Chem B 2020; 124:3903-3908. [PMID: 32321250 PMCID: PMC7313631 DOI: 10.1021/acs.jpcb.0c01857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
APOBEC3H is a cytidine deaminase protein most well-known for its involvement in antiretroviral activity in humans. It acts upon a single stranded DNA (ssDNA) substrate with preferential targeting of a 5'-TCA-3' motif. Currently available crystal structures do not include the ssDNA substrate in the A3H system, nor is the mechanism of recognition for the preferred sequence known. To determine the position and orientation of the substrate in the active site, we used high-performance computing to perform molecular dynamics simulations on several systems of APOBEC3H. We examined different DNA sequences in the active site to determine the structural and chemical mechanism by which the preferred sequence is recognized. We found residues N49, K50, K51, and K52 to be relevant to the recognition of 3'-adenine and residues S86 and S87 to be relevant to the recognition of 5'-thymine, with both recognitions primarily driven by electrostatic nonbonded interactions.
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Affiliation(s)
- Mark A Hix
- Department of Chemistry, University of North Texas, Denton, Texas 76203, United States
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76203, United States
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107
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Cytosine base editors with minimized unguided DNA and RNA off-target events and high on-target activity. Nat Commun 2020; 11:2052. [PMID: 32345976 PMCID: PMC7189382 DOI: 10.1038/s41467-020-15887-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 03/30/2020] [Indexed: 11/08/2022] Open
Abstract
Cytosine base editors (CBEs) enable efficient, programmable reversion of T•A to C•G point mutations in the human genome. Recently, cytosine base editors with rAPOBEC1 were reported to induce unguided cytosine deamination in genomic DNA and cellular RNA. Here we report eight next-generation CBEs (BE4 with either RrA3F [wt, F130L], AmAPOBEC1, SsAPOBEC3B [wt, R54Q], or PpAPOBEC1 [wt, H122A, R33A]) that display comparable DNA on-target editing frequencies, whilst eliciting a 12- to 69-fold reduction in C-to-U edits in the transcriptome, and up to a 45-fold overall reduction in unguided off-target DNA deamination relative to BE4 containing rAPOBEC1. Further, no enrichment of genome-wide C•G to T•A edits are observed in mammalian cells following transfection of mRNA encoding five of these next-generation editors. Taken together, these next-generation CBEs represent a collection of base editing tools for applications in which minimized off-target and high on-target activity are required. Cytosine base editors have been reported to induce off-target mutations in DNA and RNA. Here the authors identify next-generation CBEs with reduced guide-independent off-target editing profiles and retain high on-target editing activity.
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108
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Rallapalli KL, Komor AC, Paesani F. Computer simulations explain mutation-induced effects on the DNA editing by adenine base editors. SCIENCE ADVANCES 2020; 6:eaaz2309. [PMID: 32181363 PMCID: PMC7056309 DOI: 10.1126/sciadv.aaz2309] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/11/2019] [Indexed: 06/10/2023]
Abstract
Adenine base editors, which were developed by engineering a transfer RNA adenosine deaminase enzyme (TadA) into a DNA editing enzyme (TadA*), enable precise modification of A:T to G⋮C base pairs. Here, we use molecular dynamics simulations to uncover the structural and functional roles played by the initial mutations in the onset of the DNA editing activity by TadA*. Atomistic insights reveal that early mutations lead to intricate conformational changes in the structure of TadA*. In particular, the first mutation, Asp108Asn, induces an enhancement in the binding affinity of TadA to DNA. In silico and in vivo reversion analyses verify the importance of this single mutation in imparting functional promiscuity to TadA* and demonstrate that TadA* performs DNA base editing as a monomer rather than a dimer.
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Affiliation(s)
- Kartik L. Rallapalli
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Materials Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
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109
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McCann JL, Salamango DJ, Law EK, Brown WL, Harris RS. MagnEdit-interacting factors that recruit DNA-editing enzymes to single base targets. Life Sci Alliance 2020; 3:3/4/e201900606. [PMID: 32094150 PMCID: PMC7043409 DOI: 10.26508/lsa.201900606] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 12/17/2022] Open
Abstract
This study reports a new, non-covalent strategy—called MagnEdit—that attracts the DNA cytosine deaminase APOBEC3B to a Cas9-directed site for C-to-T editing. Although CRISPR/Cas9 technology has created a renaissance in genome engineering, particularly for gene knockout generation, methods to introduce precise single base changes are also highly desirable. The covalent fusion of a DNA-editing enzyme such as APOBEC to a Cas9 nickase complex has heightened hopes for such precision genome engineering. However, current cytosine base editors are prone to undesirable off-target mutations, including, most frequently, target-adjacent mutations. Here, we report a method to “attract” the DNA deaminase, APOBEC3B, to a target cytosine base for specific editing with minimal damage to adjacent cytosine bases. The key to this system is fusing an APOBEC-interacting protein (not APOBEC itself) to Cas9n, which attracts nuclear APOBEC3B transiently to the target site for editing. Several APOBEC3B interactors were tested and one, hnRNPUL1, demonstrated proof-of-concept with successful C-to-T editing of episomal and chromosomal substrates and lower frequencies of target-adjacent events.
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Affiliation(s)
- Jennifer L McCann
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
| | - Daniel J Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Emily K Law
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
| | - William L Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA .,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
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110
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McDaniel YZ, Wang D, Love RP, Adolph MB, Mohammadzadeh N, Chelico L, Mansky LM. Deamination hotspots among APOBEC3 family members are defined by both target site sequence context and ssDNA secondary structure. Nucleic Acids Res 2020; 48:1353-1371. [PMID: 31943071 PMCID: PMC7026630 DOI: 10.1093/nar/gkz1164] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 12/26/2022] Open
Abstract
The human apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3, A3) family member proteins can deaminate cytosines in single-strand (ss) DNA, which restricts human immunodeficiency virus type 1 (HIV-1), retrotransposons, and other viruses such as hepatitis B virus, but can cause a mutator phenotype in many cancers. While structural information exists for several A3 proteins, the precise details regarding deamination target selection are not fully understood. Here, we report the first parallel, comparative analysis of site selection of A3 deamination using six of the seven purified A3 member enzymes, oligonucleotides having 5'TC3' or 5'CT3' dinucleotide target sites, and different flanking bases within diverse DNA secondary structures. A3A, A3F and A3H were observed to have strong preferences toward the TC target flanked by A or T, while all examined A3 proteins did not show a preference for a TC target flanked by a G. We observed that the TC target was strongly preferred in ssDNA regions rather than dsDNA, loop or bulge regions, with flanking bases influencing the degree of preference. CT was also shown to be a potential deamination target. Taken together, our observations provide new insights into A3 enzyme target site selection and how A3 mutagenesis impacts mutation rates.
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Affiliation(s)
- Yumeng Z McDaniel
- Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455 USA
| | - Dake Wang
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455 USA
- Pharmacology Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
| | - Robin P Love
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Madison B Adolph
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Nazanin Mohammadzadeh
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Linda Chelico
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Louis M Mansky
- Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455 USA
- Pharmacology Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455 USA
- Department of Microbiology & Immunology, University of Minnesota, Minneapolis, MN 55455 USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
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111
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Liu Z, Chen S, Shan H, Jia Y, Chen M, Song Y, Lai L, Li Z. Efficient base editing with high precision in rabbits using YFE-BE4max. Cell Death Dis 2020; 11:36. [PMID: 31959743 PMCID: PMC6971250 DOI: 10.1038/s41419-020-2244-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 02/07/2023]
Abstract
Cytidine base editors, composed of a cytidine deaminase fused to Cas9 nickase, enable efficient C-to-T conversion in various organisms. However, current base editors suffer from severe trade-off between editing efficiency and precision. Here, based on rationally mutated cytidine deaminase domain, we develop a new base editor, YFE-BE4max, effectively narrow the editing width to as little as approximately three nucleotides while maintaining high efficiency in rabbits. Moreover, YFE-BE4max successfully mediated the Tyr p. Q68Stop and Lmna p. G607G mutation in F0 rabbit with high efficiency and precision, which precisely recapitulates the pathological features of human OCA1 and HGPS, respectively. Collectively, YFE-BE4max system provide promising tools to perform efficient base editing with high precision in rabbits and enhances its capacity to precisely model human diseases.
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Affiliation(s)
- Zhiquan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Siyu Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Huanhuan Shan
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Yingqi Jia
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Mao Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Yuning Song
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Liangxue Lai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China. .,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,Guangzhou Regenerative Medicine and Health Guang Dong Laboratory (GRMH-GDL), Guangzhou, 510005, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhanjun Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China.
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112
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Shi K, Demir Ö, Carpenter MA, Banerjee S, Harki DA, Amaro RE, Harris RS, Aihara H. Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B. FASEB Bioadv 2020; 2:49-58. [PMID: 32123856 PMCID: PMC6996314 DOI: 10.1096/fba.2019-00068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 08/19/2019] [Accepted: 11/30/2019] [Indexed: 01/24/2023] Open
Abstract
The single-stranded DNA cytosine deaminase APOBEC3B (A3B) functions in innate immunity against viruses, but it is also strongly implicated in eliciting mutations in cancer genomes. Because of the critical role of A3B in promoting virus and tumor evolution, small molecule inhibitors are desirable. However, there is no reported structure for any of the APOBEC3-family enzymes in complex with a small molecule bound in the active site, which hampers the development of small molecules targeting A3B. Here we report high-resolution structures of an active A3B catalytic domain chimera with loop 7 residues exchanged with those from the corresponding region of APOBEC3G (A3G). The structures reveal novel open conformations lacking the catalytically essential zinc ion, with the highly conserved active site residues extensively rearranged. These inactive conformations are stabilized by 2-pyrimidone or an iodide ion bound in the active site. Molecular dynamics simulations corroborate the remarkable plasticity of the engineered active site and identify key interactions that stabilize the native A3B active site. These data provide insights into A3B active site dynamics and suggest possible modes of its inhibition by small molecules, which would aid in rational design of selective A3B inhibitors for constraining virus and tumor evolution.
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Affiliation(s)
- Ke Shi
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
| | - Özlem Demir
- Department of Chemistry and BiochemistryUniversity of California, San DiegoLa JollaCAUSA
| | - Michael A. Carpenter
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Howard Hughes Medical InstituteUniversity of MinnesotaMinneapolisMNUSA
| | - Surajit Banerjee
- Northeastern Collaborative Access TeamCornell UniversityLemontILUSA
| | - Daniel A. Harki
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Department of Medicinal ChemistryUniversity of MinnesotaMinneapolisMNUSA
| | - Rommie E. Amaro
- Department of Chemistry and BiochemistryUniversity of California, San DiegoLa JollaCAUSA
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Howard Hughes Medical InstituteUniversity of MinnesotaMinneapolisMNUSA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
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113
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Kvach MV, Barzak FM, Harjes S, Schares HAM, Kurup HM, Jones KF, Sutton L, Donahue J, D'Aquila RT, Jameson GB, Harki DA, Krause KL, Harjes E, Filichev VV. Differential Inhibition of APOBEC3 DNA-Mutator Isozymes by Fluoro- and Non-Fluoro-Substituted 2'-Deoxyzebularine Embedded in Single-Stranded DNA. Chembiochem 2019; 21:1028-1035. [PMID: 31633265 PMCID: PMC7142307 DOI: 10.1002/cbic.201900505] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/20/2019] [Indexed: 12/17/2022]
Abstract
The APOBEC3 (APOBEC3A‐H) enzyme family is part of the human innate immune system that restricts pathogens by scrambling pathogenic single‐stranded (ss) DNA by deamination of cytosines to produce uracil residues. However, APOBEC3‐mediated mutagenesis of viral and cancer DNA promotes its evolution, thus enabling disease progression and the development of drug resistance. Therefore, APOBEC3 inhibition offers a new strategy to complement existing antiviral and anticancer therapies by making such therapies effective for longer periods of time, thereby preventing the emergence of drug resistance. Here, we have synthesised 2′‐deoxynucleoside forms of several known inhibitors of cytidine deaminase (CDA), incorporated them into oligodeoxynucleotides (oligos) in place of 2′‐deoxycytidine in the preferred substrates of APOBEC3A, APOBEC3B, and APOBEC3G, and evaluated their inhibitory potential against these enzymes. An oligo containing a 5‐fluoro‐2′‐deoxyzebularine (5FdZ) motif exhibited an inhibition constant against APOBEC3B 3.5 times better than that of the comparable 2′‐deoxyzebularine‐containing (dZ‐containing) oligo. A similar inhibition trend was observed for wild‐type APOBEC3A. In contrast, use of the 5FdZ motif in an oligo designed for APOBEC3G inhibition resulted in an inhibitor that was less potent than the dZ‐containing oligo both in the case of APOBEC3GCTD and in that of full‐length wild‐type APOBEC3G.
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Affiliation(s)
- Maksim V Kvach
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand
| | - Fareeda M Barzak
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand
| | - Stefan Harjes
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand
| | - Henry A M Schares
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Harikrishnan M Kurup
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand
| | - Katherine F Jones
- Department of Chemistry, University of Minnesota, 207 Pleasant St SE, Minneapolis, MN, 55455, USA
| | - Lorraine Sutton
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, 21st Ave S, Nashville, TN, 37232, USA
| | - John Donahue
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, 21st Ave S, Nashville, TN, 37232, USA
| | - Richard T D'Aquila
- Division of Infectious Diseases and, Northwestern HIV Translational Research Center, Department of Medicine, Northwestern University Feinberg School of Medicine, 676 N. St. Clair Street, Suite 2330, Chicago, IL, 60611, USA
| | - Geoffrey B Jameson
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA.,Department of Chemistry, University of Minnesota, 207 Pleasant St SE, Minneapolis, MN, 55455, USA
| | - Kurt L Krause
- Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand.,Department of Biochemistry, University of Otago, P. O. Box 56, Dunedin, 9054, New Zealand
| | - Elena Harjes
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand
| | - Vyacheslav V Filichev
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand
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114
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Barzak FM, Harjes S, Kvach MV, Kurup HM, Jameson GB, Filichev VV, Harjes E. Selective inhibition of APOBEC3 enzymes by single-stranded DNAs containing 2'-deoxyzebularine. Org Biomol Chem 2019; 17:9435-9441. [PMID: 31603457 DOI: 10.1039/c9ob01781j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
To restrict pathogens, in a normal human cell, APOBEC3 enzymes mutate cytosine to uracil in foreign single-stranded DNAs. However, in cancer cells, APOBEC3B (one of seven APOBEC3 enzymes) has been identified as the primary source of genetic mutations. As such, APOBEC3B promotes evolution and progression of cancers and leads to development of drug resistance in multiple cancers. As APOBEC3B is a non-essential protein, its inhibition can be used to suppress emergence of drug resistance in existing anti-cancer therapies. Because of the vital role of APOBEC3 enzymes in innate immunity, selective inhibitors targeting only APOBEC3B are required. Here, we use the discriminative properties of wild-type APOBEC3A, APOBEC3B and APOBEC3G to deaminate different cytosines in the CCC-recognition motif in order to best place the cytidine analogue 2'-deoxyzebularine (dZ) in the CCC-motif. Using several APOBEC3 variants that mimic deamination patterns of wild-type enzymes, we demonstrate that selective inhibition of APOBEC3B in preference to other APOBEC3 constructs is feasible for the dZCC motif. This work is an important step towards development of in vivo tools to inhibit APOBEC3 enzymes in living cells by using short, chemically modified oligonucleotides.
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Affiliation(s)
- Fareeda M Barzak
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
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115
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Bohn JA, DaSilva J, Kharytonchyk S, Mercedes M, Vosters J, Telesnitsky A, Hatziioannou T, Smith JL. Flexibility in Nucleic Acid Binding Is Central to APOBEC3H Antiviral Activity. J Virol 2019; 93:e01275-19. [PMID: 31578294 PMCID: PMC6880157 DOI: 10.1128/jvi.01275-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/23/2019] [Indexed: 11/20/2022] Open
Abstract
APOBEC3 proteins APOBEC3F (A3F), APOBEC3G (A3G), and APOBEC3H (A3H) are host restriction factors that inhibit HIV-1 through DNA cytidine deaminase-dependent and -independent mechanisms and have either one (A3H) or two (A3F and A3G) zinc-binding domains. A3H antiviral activity encompasses multiple molecular functions, all of which depend on recognition of RNA or DNA. A3H crystal structures revealed an unusual interaction with RNA wherein an RNA duplex mediates dimerization of two A3H proteins. In this study, we sought to determine the importance of RNA-binding amino acids in the antiviral and biochemical properties of A3H. We show that the wild-type A3H-RNA interaction is essential for A3H antiviral activity and for two deaminase-independent processes: encapsidation into viral particles and inhibition of reverse transcription. Furthermore, an extensive mutagenesis campaign revealed distinct roles for two groups of amino acids at the RNA binding interface. C-terminal helix residues exclusively bind RNA, and loop 1 residues play a dual role in recognition of DNA substrates and in RNA binding. Weakening the interface between A3H and RNA allows DNA substrates to bind with greater affinity and enhances deamination rates, suggesting that RNA binding must be disrupted to accommodate DNA. Intriguingly, we demonstrate that A3H can deaminate overhanging DNA strands of RNA/DNA heteroduplexes, which are early intermediates during reverse transcription and may represent natural A3H substrates. Overall, we present a mechanistic model of A3H restriction and a step-by-step elucidation of the roles of RNA-binding residues in A3H activity, particle incorporation, inhibition of reverse transcriptase inhibition, and DNA cytidine deamination.IMPORTANCE APOBEC3 proteins are host factors that protect the integrity of the host genome by inhibiting retroelements as well as retroviruses, such as HIV-1. To do this, the APOBEC3H protein has evolved unique interactions with structured RNAs. Here, we studied the importance of these interactions in driving antiviral activity of APOBEC3H. Our results provide a clear picture of how RNA binding drives the ability of APOBEC3H to infiltrate new viruses and prevent synthesis of viral DNA. We also explore how RNA binding by APOBEC3H influences recognition and deamination of viral DNA and describe two possible routes by which APOBEC3H might hypermutate the HIV-1 genome. These results highlight how one protein can sense many nucleic acid species for a variety of antiviral activities.
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Affiliation(s)
- Jennifer A Bohn
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Justin DaSilva
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA
| | - Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Maria Mercedes
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA
| | - Jennifer Vosters
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Janet L Smith
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
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116
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Solomon WC, Myint W, Hou S, Kanai T, Tripathi R, Kurt Yilmaz N, Schiffer CA, Matsuo H. Mechanism for APOBEC3G catalytic exclusion of RNA and non-substrate DNA. Nucleic Acids Res 2019; 47:7676-7689. [PMID: 31424549 PMCID: PMC6698744 DOI: 10.1093/nar/gkz550] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/06/2019] [Accepted: 06/11/2019] [Indexed: 12/17/2022] Open
Abstract
The potent antiretroviral protein APOBEC3G (A3G) specifically targets and deaminates deoxycytidine nucleotides, generating deoxyuridine, in single stranded DNA (ssDNA) intermediates produced during HIV replication. A non-catalytic domain in A3G binds strongly to RNA, an interaction crucial for recruitment of A3G to the virion; yet, A3G displays no deamination activity for cytidines in viral RNA. Here, we report NMR and molecular dynamics (MD) simulation analysis for interactions between A3Gctd and multiple substrate or non-substrate DNA and RNA, in combination with deamination assays. NMR ssDNA-binding experiments revealed that the interaction with residues in helix1 and loop1 (T201-L220) distinguishes the binding mode of substrate ssDNA from non-substrate. Using 2′-deoxy-2′-fluorine substituted cytidines, we show that a 2′-endo sugar conformation of the target deoxycytidine is favored for substrate binding and deamination. Trajectories of the MD simulation indicate that a ribose 2′-hydroxyl group destabilizes the π-π stacking of the target cytosine and H257, resulting in dislocation of the target cytosine base from the catalytic position. Interestingly, APOBEC3A, which can deaminate ribocytidines, retains the ribocytidine in the catalytic position throughout the MD simulation. Our results indicate that A3Gctd catalytic selectivity against RNA is dictated by both the sugar conformation and 2′-hydroxyl group.
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Affiliation(s)
- William C Solomon
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wazo Myint
- Basic Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Shurong Hou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Tapan Kanai
- Basic Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.,Department of Chemistry, Banasthali University, Banasthali-304022, Rajasthan, India
| | - Rashmi Tripathi
- Department of Bioscience and Biotechnology, Banasthali University, Banasthali-304022, Rajasthan, India
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Hiroshi Matsuo
- Basic Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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117
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Cortez LM, Brown AL, Dennis MA, Collins CD, Brown AJ, Mitchell D, Mertz TM, Roberts SA. APOBEC3A is a prominent cytidine deaminase in breast cancer. PLoS Genet 2019; 15:e1008545. [PMID: 31841499 PMCID: PMC6936861 DOI: 10.1371/journal.pgen.1008545] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 12/30/2019] [Accepted: 12/01/2019] [Indexed: 11/19/2022] Open
Abstract
APOBEC cytidine deaminases are the second-most prominent source of mutagenesis in sequenced tumors. Previous studies have proposed that APOBEC3B (A3B) is the major source of mutagenesis in breast cancer (BRCA). We show that APOBEC3A (A3A) is the only APOBEC whose expression correlates with APOBEC-induced mutation load and that A3A expression is responsible for cytidine deamination in multiple BRCA cell lines. Comparative analysis of A3A and A3B expression by qRT-PCR, RSEM-normalized RNA-seq, and unambiguous RNA-seq validated the use of RNA-seq to measure APOBEC expression, which indicates that A3A is the primary correlate with APOBEC-mutation load in primary BRCA tumors. We also demonstrate that A3A has >100-fold more cytidine deamination activity than A3B in the presence of cellular RNA, likely explaining why higher levels of A3B expression contributes less to mutagenesis in BRCA. Our findings identify A3A as a major source of cytidine deaminase activity in breast cancer cells and possibly a prominent contributor to the APOBEC mutation signature.
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Affiliation(s)
- Luis M. Cortez
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, United States of America
| | - Amber L. Brown
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
| | - Madeline A. Dennis
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
| | - Christopher D. Collins
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
| | - Alexander J. Brown
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
- School of Molecular Biosciences, Washington State University-Vancouver, Vancouver, WA, United States of America
| | - Debra Mitchell
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
| | - Tony M. Mertz
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
| | - Steven A. Roberts
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
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118
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Liu LD, Huang M, Dai P, Liu T, Fan S, Cheng X, Zhao Y, Yeap LS, Meng FL. Intrinsic Nucleotide Preference of Diversifying Base Editors Guides Antibody Ex Vivo Affinity Maturation. Cell Rep 2019; 25:884-892.e3. [PMID: 30355495 DOI: 10.1016/j.celrep.2018.09.090] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/13/2018] [Accepted: 09/27/2018] [Indexed: 12/27/2022] Open
Abstract
Base editors (BEs) are emerging tools used for precision correction or diversifying mutation. It provides a potential way to recreate somatic hypermutations (SHM) for generating high-affinity antibody, which is usually screened from antigen-challenged animal models or synthetic combinatorial libraries. By comparing somatic mutations in the same genomic context, we screened engineered deaminases and CRISPR-deaminase coupling approaches and updated diversifying base editors (DBEs) to generate SHM. The deaminase used in DBEs retains its intrinsic nucleotide preference and mutates cytidines at its preferred motifs. DBE with AID targets the same hotspots as physiological AID does in vivo, while DBE with other deaminases generates distinct mutation profiles from the same DNA substrate. Downstream DNA repair pathways further diversified the sequence, while Cas9-nickase restricted mutation spreading. Finally, application of DBE in an antibody display system achieved antibody affinity maturation ex vivo. Our findings provide insight of DBE working mechanism and an alternative antibody engineering approach.
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Affiliation(s)
- Liu Daisy Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Min Huang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Pengfei Dai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Tingting Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Shuangshuang Fan
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Xueqian Cheng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
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119
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Ziegler SJ, Hu Y, Devarkar SC, Xiong Y. APOBEC3A Loop 1 Is a Determinant for Single-Stranded DNA Binding and Deamination. Biochemistry 2019; 58:3838-3847. [PMID: 31448897 DOI: 10.1021/acs.biochem.9b00394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3 or A3) family of proteins functions in the innate immune system. The A3 proteins are interferon inducible and hypermutate deoxycytidine to deoxyuridine in foreign single-stranded DNA (ssDNA). However, this deaminase activity cannot discriminate between foreign and host ssDNA at the biochemical level, which presents a significant danger when A3 proteins gain access to the nucleus. Interestingly, this A3 capability can be harnessed when coupled with novel CRISPR-Cas9 proteins to create a targeted base editor. Specifically, A3A has been used in vitro to revert mutations associated with disease states. Recent structural studies have shown the importance of loop regions of A3A and A3G in ssDNA recognition and positioning for deamination. In this work, we further examined loop 1 of A3A to determine how it affects substrate selection, as well as the efficiency of deamination, in the hopes of advancing the potential of A3A in base editing technology. We found that mutating residue H29 enhanced deamination activity without changing substrate specificity. Also interestingly, we found that increasing the length of loop 1 decreases substrate specificity. Overall, these results lead to a better understanding of substrate recognition and deamination by A3A and the A3 family of proteins.
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Affiliation(s)
- Samantha J Ziegler
- Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06511 , United States
| | - Yingxia Hu
- Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06511 , United States
| | - Swapnil C Devarkar
- Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06511 , United States
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06511 , United States
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120
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AID, APOBEC3A and APOBEC3B efficiently deaminate deoxycytidines neighboring DNA damage induced by oxidation or alkylation. Biochim Biophys Acta Gen Subj 2019; 1863:129415. [PMID: 31404619 DOI: 10.1016/j.bbagen.2019.129415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND AID/APOBEC3 (A3) enzymes instigate genomic mutations that are involved in immunity and cancer. Although they can deaminate any deoxycytidine (dC) to deoxyuridine (dU), each family member has a signature preference determined by nucleotides surrounding the target dC. This WRC (W = A/T, R = A/G) and YC (Y = T/C) hotspot preference is established for AID and A3A/A3B, respectively. Base alkylation and oxidation are two of the most common types of DNA damage induced environmentally or by chemotherapy. Here we examined the activity of AID, A3A and A3B on dCs neighboring such damaged bases. METHODS Substrates were designed to contain target dCs either in normal WRC/YC hotspots, or in oxidized/alkylated DNA motifs. AID, A3A and A3B were purified and deamination kinetics of each were compared between substrates containing damaged vs. normal motifs. RESULTS All three enzymes efficiently deaminated dC when common damaged bases were present in the -2 or -1 positions. Strikingly, some damaged motifs supported comparable or higher catalytic efficiencies by AID, A3A and A3B than the WRC/YC motifs which are their most favored normal sequences. Based on the resolved interactions of AID, A3A and A3B with DNA, we modeled interactions with alkylated or oxidized bases. Corroborating the enzyme assay data, the surface regions that recognize normal bases are predicted to also interact robustly with oxidized and alkylated bases. CONCLUSIONS AID, A3A and A3B can efficiently recognize and deaminate dC whose neighbouring nucleotides are damaged. GENERAL SIGNIFICANCE Beyond AID/A3s initiating DNA damage, some forms of pre-existing damaged DNA can constitute favored targets of AID/A3s if encountered.
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121
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McCann JL, Klein MM, Leland EM, Law EK, Brown WL, Salamango DJ, Harris RS. The DNA deaminase APOBEC3B interacts with the cell-cycle protein CDK4 and disrupts CDK4-mediated nuclear import of Cyclin D1. J Biol Chem 2019; 294:12099-12111. [PMID: 31217276 PMCID: PMC6690700 DOI: 10.1074/jbc.ra119.008443] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/27/2019] [Indexed: 12/13/2022] Open
Abstract
Apolipoprotein B mRNA editing enzyme catalytic subunit-like protein 3B (APOBEC3B or A3B), as other APOBEC3 members, is a single-stranded (ss)DNA cytosine deaminase with antiviral activity. A3B is also overexpressed in multiple tumor types, such as carcinomas of the bladder, cervix, lung, head/neck, and breast. A3B generates both dispersed and clustered C-to-T and C-to-G mutations in intrinsically preferred trinucleotide motifs (TCA/TCG/TCT). A3B-catalyzed mutations are likely to promote tumor evolution and cancer progression and, as such, are associated with poor clinical outcomes. However, little is known about cellular processes that regulate A3B. Here, we used a proteomics approach involving affinity purification coupled to MS with human 293T cells to identify cellular proteins that interact with A3B. This approach revealed a specific interaction with cyclin-dependent kinase 4 (CDK4). We validated and mapped this interaction by co-immunoprecipitation experiments. Functional studies and immunofluorescence microscopy experiments in multiple cell lines revealed that A3B is not a substrate for CDK4-Cyclin D1 phosphorylation nor is its deaminase activity modulated. Instead, we found that A3B is capable of disrupting the CDK4-dependent nuclear import of Cyclin D1. We propose that this interaction may favor a more potent antiviral response and simultaneously facilitate cancer mutagenesis.
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Affiliation(s)
- Jennifer L McCann
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455; Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Madeline M Klein
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
| | - Evelyn M Leland
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
| | - Emily K Law
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455; Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota 55455
| | - William L Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455; Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Daniel J Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455; Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455.
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455; Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota 55455.
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122
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Silvas TV, Schiffer CA. APOBEC3s: DNA-editing human cytidine deaminases. Protein Sci 2019; 28:1552-1566. [PMID: 31241202 DOI: 10.1002/pro.3670] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/22/2022]
Abstract
Nucleic acid editing enzymes are essential components of the human immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins. Among these enzymes are cytidine deaminases of the apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) super family, each with unique target sequence specificity and subcellular localization. We focus on the DNA-editing APOBEC3 enzymes that have recently attracted attention because of their involvement in cancer and potential in gene-editing applications. We review and compare the crystal structures of APOBEC3 (A3) domains, binding interactions with DNA, substrate specificity, and activity. Recent crystal structures of A3A and A3G bound to ssDNA have provided insights into substrate binding and specificity determinants of these enzymes. Still many unknowns remain regarding potential cooperativity, nucleic acid interactions, and systematic quantification of substrate preference of many APOBEC3s, which are needed to better characterize the biological functions and consequences of misregulation of these gene editors.
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Affiliation(s)
- Tania V Silvas
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
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123
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Buisson R, Langenbucher A, Bowen D, Kwan EE, Benes CH, Zou L, Lawrence MS. Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features. Science 2019; 364:eaaw2872. [PMID: 31249028 PMCID: PMC6731024 DOI: 10.1126/science.aaw2872] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 05/23/2019] [Indexed: 12/12/2022]
Abstract
Cancer drivers require statistical modeling to distinguish them from passenger events, which accumulate during tumorigenesis but provide no fitness advantage to cancer cells. The discovery of driver genes and mutations relies on the assumption that exact positional recurrence is unlikely by chance; thus, the precise sharing of mutations across patients identifies drivers. Examining the mutation landscape in cancer genomes, we found that many recurrent cancer mutations previously designated as drivers are likely passengers. Our integrated bioinformatic and biochemical analyses revealed that these passenger hotspot mutations arise from the preference of APOBEC3A, a cytidine deaminase, for DNA stem-loops. Conversely, recurrent APOBEC-signature mutations not in stem-loops are enriched in well-characterized driver genes and may predict new drivers. This demonstrates that mesoscale genomic features need to be integrated into computational models aimed at identifying mutations linked to diseases.
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Affiliation(s)
- Rémi Buisson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
| | - Adam Langenbucher
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Danae Bowen
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
| | - Eugene E Kwan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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124
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Yan X, Lan W, Wang C, Cao C. Structural Investigations on the Interactions between Cytidine Deaminase Human APOBEC3G and DNA. Chem Asian J 2019; 14:2235-2241. [PMID: 31116511 DOI: 10.1002/asia.201900480] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/20/2019] [Indexed: 02/05/2023]
Abstract
Human APOBEC3G (A3G) inhibits the replication of human immunodeficiency virus-1 by deaminating cytidine at the 3'-end in the target motif 5'-CCC-3' in viral cDNA during reverse transcription. It in vitro deaminates two consecutive cytidines in a 3'->5' order. Although a crystal structure of the A3G catalytic domain (A3G-CD2) with DNA was reported, it is unknown why residues involved in enzymatic reaction are distributed widely. Here, we introduced an iodine atom into the C-5 position of cytidine (dC6 I ) in DNA 5'-ATTC4 C5 C6 I A7 ATT-3' (TCCC6 I ). It switches the deamination sequence preference from CCC to TCC, although small dC6 I deamination was observed. Solution structures of A3G-CD2 in complexes with products DNA TCUC6 I and TCUU6 I indicate that the substrate DNA binds A3G-CD2 in TCC and CCC modes. The dC6 deamination correlates with the 4th base type. The CCC mode favours dC6 deamination, while the TCC mode results in dC5 deamination. These studies present an extensive basis to design inhibitors to impede viral evolvability.
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Affiliation(s)
- Xiaoxuan Yan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, 345 Lingling Road, Shanghai, 200032, China.,University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, 345 Lingling Road, Shanghai, 200032, China
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, 345 Lingling Road, Shanghai, 200032, China
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, 345 Lingling Road, Shanghai, 200032, China.,University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing, 100049, China
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125
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Zhou C, Sun Y, Yan R, Liu Y, Zuo E, Gu C, Han L, Wei Y, Hu X, Zeng R, Li Y, Zhou H, Guo F, Yang H. Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis. Nature 2019; 571:275-278. [PMID: 31181567 DOI: 10.1038/s41586-019-1314-0] [Citation(s) in RCA: 309] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/30/2019] [Indexed: 12/21/2022]
Abstract
Recently developed DNA base editing methods enable the direct generation of desired point mutations in genomic DNA without generating any double-strand breaks1-3, but the issue of off-target edits has limited the application of these methods. Although several previous studies have evaluated off-target mutations in genomic DNA4-8, it is now clear that the deaminases that are integral to commonly used DNA base editors often bind to RNA9-13. For example, the cytosine deaminase APOBEC1-which is used in cytosine base editors (CBEs)-targets both DNA and RNA12, and the adenine deaminase TadA-which is used in adenine base editors (ABEs)-induces site-specific inosine formation on RNA9,11. However, any potential RNA mutations caused by DNA base editors have not been evaluated. Adeno-associated viruses are the most common delivery system for gene therapies that involve DNA editing; these viruses can sustain long-term gene expression in vivo, so the extent of potential RNA mutations induced by DNA base editors is of great concern14-16. Here we quantitatively evaluated RNA single nucleotide variations (SNVs) that were induced by CBEs or ABEs. Both the cytosine base editor BE3 and the adenine base editor ABE7.10 generated tens of thousands of off-target RNA SNVs. Subsequently, by engineering deaminases, we found that three CBE variants and one ABE variant showed a reduction in off-target RNA SNVs to the baseline while maintaining efficient DNA on-target activity. This study reveals a previously overlooked aspect of off-target effects in DNA editing and also demonstrates that such effects can be eliminated by engineering deaminases.
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Affiliation(s)
- Changyang Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yidi Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rui Yan
- Center for Translational Medicine, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Obstetrics and Gynecology, West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yajing Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Erwei Zuo
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Center for Animal Genomics, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chan Gu
- Center for Translational Medicine, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Obstetrics and Gynecology, West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu, China
| | - Linxiao Han
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu Wei
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinde Hu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rong Zeng
- CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Yixue Li
- Center for Translational Medicine, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Obstetrics and Gynecology, West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu, China. .,School of Life Science and Technology, Shanghai Tech University, Shanghai, China. .,Shanghai Jiao Tong University, Fudan University, Shanghai Academy of Science & Technology, Shanghai, China.
| | - Haibo Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Fan Guo
- Center for Translational Medicine, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Obstetrics and Gynecology, West China Second University Hospital, College of Life Sciences, Sichuan University, Chengdu, China.
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
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126
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Protein kinase A inhibits tumor mutator APOBEC3B through phosphorylation. Sci Rep 2019; 9:8307. [PMID: 31165764 PMCID: PMC6549188 DOI: 10.1038/s41598-019-44407-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 05/14/2019] [Indexed: 12/26/2022] Open
Abstract
APOBEC3B cytidine deaminase (A3B) catalyzes cytosine into uracil in single-strand DNA and induces C-to-T mutations in genomic DNA of various types of tumors. Accumulation of APOBEC signature mutations is correlated with a worse prognosis for patients with breast cancer or multiple myeloma, suggesting that A3B activity might be a cause of the unfavorable DNA mutations and clonal evolution in these tumors. Phosphorylation of conserved threonine residues of other cytidine deaminases, activation induced deaminase (AID) and APOBEC3G, inhibits their activity. Here we show that protein kinase A (PKA) physically binds to A3B and phosphorylates Thr214. In vitro deaminase assays and foreign DNA editing assays in cells confirm that phosphomimetic A3B mutants, T214D and T214E, completely lose deaminase activity. Molecular dynamics simulation of A3B phosphorylation reveals that Thr214 phosphorylation disrupts binding between the phospho-A3B catalytic core and ssDNA. These mutants still inhibit retroviral infectivity at least partially, and also retain full anti-retrotransposition activity. These results imply that PKA-mediated phosphorylation inhibits A3B mutagenic activity without destructing its innate immune functions. Therefore, PKA activation could reduce further accumulation of mutations in A3B overexpressing tumors.
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127
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Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE. Determinants of Oligonucleotide Selectivity of APOBEC3B. J Chem Inf Model 2019; 59:2264-2273. [PMID: 30130104 PMCID: PMC6644697 DOI: 10.1021/acs.jcim.8b00427] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
APOBEC3B (A3B) is a prominent source of mutation in many cancers. To date, it has been difficult to capture the native protein-DNA interactions that confer A3B's substrate specificity by crystallography due to the highly dynamic nature of wild-type A3B active site. We use computational tools to restore a recent crystal structure of a DNA-bound A3B C-terminal domain mutant construct to its wild type sequence, and run molecular dynamics simulations to study its substrate recognition mechanisms. Analysis of these simulations reveal dynamics of the native A3Bctd-oligonucleotide interactions, including the experimentally inaccessible loop 1-oligonucleotide interactions. A second series of simulations in which the target cytosine nucleotide was computationally mutated from a deoxyribose to a ribose show a change in sugar ring pucker, leading to a rearrangement of the binding site and revealing a potential intermediate in the binding pathway. Finally, apo simulations of A3B, starting from the DNA-bound open state, experience a rapid and consistent closure of the binding site, reaching conformations incompatible with substrate binding. This study reveals a more realistic and dynamic view of the wild type A3B binding site and provides novel insights for structure-guided design efforts for A3B.
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Affiliation(s)
- Jeffrey R Wagner
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0340 , United States
| | - Özlem Demir
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0340 , United States
| | - Michael A Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Institute for Molecular Virology , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Institute for Molecular Virology , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Daniel A Harki
- Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Institute for Molecular Virology , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Howard Hughes Medical Institute , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0340 , United States
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128
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Smith NJ, Fenton TR. The APOBEC3 genes and their role in cancer: insights from human papillomavirus. J Mol Endocrinol 2019; 62:R269-R287. [PMID: 30870810 DOI: 10.1530/jme-19-0011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/14/2019] [Indexed: 12/14/2022]
Abstract
The interaction between human papillomaviruses (HPV) and the apolipoprotein-B mRNA-editing catalytic polypeptide-like (APOBEC)3 (A3) genes has garnered increasing attention in recent years, with considerable efforts focused on understanding their apparent roles in both viral editing and in HPV-driven carcinogenesis. Here, we review these developments and highlight several outstanding questions in the field. We consider whether editing of the virus and mutagenesis of the host are linked or whether both are essentially separate events, coincidentally mediated by a common or distinct A3 enzymes. We discuss the viral mechanisms and cellular signalling pathways implicated in A3 induction in virally infected cells and examine which of the A3 enzymes might play the major role in HPV-associated carcinogenesis and in the development of therapeutic resistance. We consider the parallels between A3 induction in HPV-infected cells and what might be causing aberrant A3 activity in HPV-independent cancers such as those arising in the bladder, lung and breast. Finally, we discuss the implications of ongoing A3 activity in tumours under treatment and the therapeutic opportunities that this may present.
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Affiliation(s)
- Nicola J Smith
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, Kent, UK
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129
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Evgin L, Huff AL, Kottke T, Thompson J, Molan AM, Driscoll CB, Schuelke M, Shim KG, Wongthida P, Ilett EJ, Smith KK, Harris RS, Coffey M, Pulido JS, Pandha H, Selby PJ, Harrington KJ, Melcher A, Vile RG. Suboptimal T-cell Therapy Drives a Tumor Cell Mutator Phenotype That Promotes Escape from First-Line Treatment. Cancer Immunol Res 2019; 7:828-840. [PMID: 30940643 PMCID: PMC7003288 DOI: 10.1158/2326-6066.cir-18-0013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/14/2018] [Accepted: 03/27/2019] [Indexed: 12/19/2022]
Abstract
Antitumor T-cell responses raised by first-line therapies such as chemotherapy, radiation, tumor cell vaccines, and viroimmunotherapy tend to be weak, both quantitatively (low frequency) and qualitatively (low affinity). We show here that T cells that recognize tumor-associated antigens can directly kill tumor cells if used at high effector-to-target ratios. However, when these tumor-reactive T cells were present at suboptimal ratios, direct T-cell-mediated tumor cell killing was reduced and the ability of tumor cells to evolve away from a coapplied therapy (oncolytic or suicide gene therapy) was promoted. This T-cell-mediated increase in therapeutic resistance was associated with C to T transition mutations that are characteristic of APOBEC3 cytosine deaminase activity and was induced through a TNFα and protein kinase C-dependent pathway. Short hairpin RNA inhibition of endogenous APOBEC3 reduced rates of tumor escape from oncolytic virus or suicide gene therapy to those seen in the absence of antitumor T-cell coculture. Conversely, overexpression of human APOBEC3B in tumor cells enhanced escape from suicide gene therapy and oncolytic virus therapy both in vitro and in vivo Our data suggest that weak affinity or low frequency T-cell responses against tumor antigens may contribute to the ability of tumor cells to evolve away from first-line therapies. We conclude that immunotherapies need to be optimized as early as possible so that, if they do not kill the tumor completely, they do not promote treatment resistance.
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Affiliation(s)
- Laura Evgin
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Amanda L Huff
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Timothy Kottke
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jill Thompson
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Amy M Molan
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | | | | | - Kevin G Shim
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | | | - Elizabeth J Ilett
- Leeds Institute of Cancer and Pathology, St. James' University Hospital, Leeds, United Kingdom
| | | | - Reuben S Harris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Matt Coffey
- Oncolytics Biotech Incorporated, Calgary, Canada
| | - Jose S Pulido
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
| | - Hardev Pandha
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Peter J Selby
- Leeds Institute of Cancer and Pathology, St. James' University Hospital, Leeds, United Kingdom
| | | | - Alan Melcher
- Institute of Cancer Research, London, United Kingdom
| | - Richard G Vile
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota.
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
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130
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Wan L, Kamba K, Nagata T, Katahira M. An insight into the dependence of the deamination rate of human APOBEC3F on the length of single-stranded DNA, which is affected by the concentrations of APOBEC3F and single-stranded DNA. Biochim Biophys Acta Gen Subj 2019; 1864:129346. [PMID: 30986508 DOI: 10.1016/j.bbagen.2019.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/20/2019] [Accepted: 04/08/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND APOBEC3F (A3F), a member of the human APOBEC3 (A3) family of cytidine deaminases, acts as an anti-HIV-1 factor by deaminating deoxycytidine in the complementary DNA of the viral genome. A full understanding of the deamination behavior of A3F awaits further investigation. METHODS The real-time NMR method and uracil-DNA glycosylase assay were used to track the activities of the C-terminal domain (CTD) of A3F at different concentrations of A3F-CTD and ssDNA. The steady-state fluorescence anisotropy measurement was used to examine the binding between A3F-CTD and ssDNA with different lengths. The use of the A3F-CTD N214H mutant, having higher activity than the wild-type, facilitated the tracking of the reactions. RESULTS A3F-CTD was found to efficiently deaminate the target deoxycytidine in long ssDNA in lower ssDNA concentration conditions ([A3F-CTD] ≫ [ssDNA]), while the target deoxycytidine in short ssDNA is deaminated efficiently in higher ssDNA concentration conditions ([A3F-CTD] ≪ [ssDNA]). This property is quite different from that of the previously studied A3 family member, A3B; the concentrations of the proteins and ssDNA had no effect. CONCLUSIONS The concentrations of A3F-CTD and ssDNA substrates affect the ssDNA-length-dependence of deamination rate of the A3F-CTD. This unique property of A3F is rationally interpreted on the basis of its binding characteristics with ssDNA. GENERAL SIGNIFICANCE The discovery of the unique property of A3F regarding the deamination rate deepens the understanding of its counteraction against HIV-1. Our strategy is applicable to investigate the other aspects of the A3 activities, such as those involved in the cancer development.
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Affiliation(s)
- Li Wan
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Keisuke Kamba
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, Japan.
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, Japan.
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131
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Abstract
C-to-U RNA editing enzymatically converts the base C to U in RNA molecules and could lead to nonsynonymous changes when occurring in coding regions. Hundreds to thousands of coding sites were recently found to be C-to-U edited or editable in humans, but the biological significance of this phenomenon is elusive. Here, we test the prevailing hypothesis that nonsynonymous editing is beneficial because it provides a means for tissue- or time-specific regulation of protein function that may be hard to accomplish by mutations due to pleiotropy. The adaptive hypothesis predicts that the fraction of sites edited and the median proportion of RNA molecules edited (i.e., editing level) are both higher for nonsynonymous than synonymous editing. However, our empirical observations are opposite to these predictions. Furthermore, the frequency of nonsynonymous editing, relative to that of synonymous editing, declines as genes become functionally more important or evolutionarily more constrained, and the nonsynonymous editing level at a site is negatively correlated with the evolutionary conservation of the site. Together, these findings refute the adaptive hypothesis; they instead indicate that the reported C-to-U coding RNA editing is mostly slightly deleterious or neutral, probably resulting from off-target activities of editing enzymes. Along with similar conclusions on the more prevalent A-to-I editing and m6A modification of coding RNAs, our study suggests that, at least in humans, most events of each type of posttranscriptional coding RNA modification likely manifest cellular errors rather than adaptations, demanding a paradigm shift in the research of posttranscriptional modification.
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Affiliation(s)
- Zhen Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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132
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Rogozin IB, Roche-Lima A, Lada AG, Belinky F, Sidorenko IA, Glazko GV, Babenko VN, Cooper DN, Pavlov YI. Nucleotide Weight Matrices Reveal Ubiquitous Mutational Footprints of AID/APOBEC Deaminases in Human Cancer Genomes. Cancers (Basel) 2019; 11:cancers11020211. [PMID: 30759888 PMCID: PMC6406962 DOI: 10.3390/cancers11020211] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 01/08/2023] Open
Abstract
Cancer genomes accumulate nucleotide sequence variations that number in the tens of thousands per genome. A prominent fraction of these mutations is thought to arise as a consequence of the off-target activity of DNA/RNA editing cytosine deaminases. These enzymes, collectively called activation induced deaminase (AID)/APOBECs, deaminate cytosines located within defined DNA sequence contexts. The resulting changes of the original C:G pair in these contexts (mutational signatures) provide indirect evidence for the participation of specific cytosine deaminases in a given cancer type. The conventional method used for the analysis of mutable motifs is the consensus approach. Here, for the first time, we have adopted the frequently used weight matrix (sequence profile) approach for the analysis of mutagenesis and provide evidence for this method being a more precise descriptor of mutations than the sequence consensus approach. We confirm that while mutational footprints of APOBEC1, APOBEC3A, APOBEC3B, and APOBEC3G are prominent in many cancers, mutable motifs characteristic of the action of the humoral immune response somatic hypermutation enzyme, AID, are the most widespread feature of somatic mutation spectra attributable to deaminases in cancer genomes. Overall, the weight matrix approach reveals that somatic mutations are significantly associated with at least one AID/APOBEC mutable motif in all studied cancers.
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Affiliation(s)
- Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894-6075, USA.
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities⁻RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico 00936-5067.
| | - Artem G Lada
- Department Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.
| | - Frida Belinky
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894-6075, USA.
| | | | - Galina V Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | | | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff CF14 4AY, UK.
| | - Youri I Pavlov
- Departments of Microbiology and Pathology; Biochemistry and Molecular Biology; Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA.
- Eppley Institute for Research in Cancer and Allied Diseases, Omaha, NE 68198, USA.
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133
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Polyomavirus T Antigen Induces APOBEC3B Expression Using an LXCXE-Dependent and TP53-Independent Mechanism. mBio 2019; 10:mBio.02690-18. [PMID: 30723127 PMCID: PMC6428753 DOI: 10.1128/mbio.02690-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
APOBEC3B is a single-stranded DNA cytosine deaminase with beneficial innate antiviral functions. However, misregulated APOBEC3B can also be detrimental by inflicting APOBEC signature C-to-T and C-to-G mutations in genomic DNA of multiple cancer types. Polyomavirus and papillomavirus oncoproteins induce APOBEC3B overexpression, perhaps to their own benefit, but little is known about the cellular mechanisms hijacked by these viruses to do so. Here we investigate the molecular mechanism of APOBEC3B upregulation by the polyomavirus large T antigen. First, we demonstrate that the upregulated APOBEC3B enzyme is strongly nuclear and partially localized to virus replication centers. Second, truncated T antigen (truncT) is sufficient for APOBEC3B upregulation, and the RB-interacting motif (LXCXE), but not the p53-binding domain, is required. Third, genetic knockdown of RB1 alone or in combination with RBL1 and/or RBL2 is insufficient to suppress truncT-mediated induction of APOBEC3B Fourth, CDK4/6 inhibition by palbociclib is also insufficient to suppress truncT-mediated induction of APOBEC3B Last, global gene expression analyses in a wide range of human cancers show significant associations between expression of APOBEC3B and other genes known to be regulated by the RB/E2F axis. These experiments combine to implicate the RB/E2F axis in promoting APOBEC3B transcription, yet they also suggest that the polyomavirus RB-binding motif has at least one additional function in addition to RB inactivation for triggering APOBEC3B upregulation in virus-infected cells.IMPORTANCE The APOBEC3B DNA cytosine deaminase is overexpressed in many different cancers and correlates with elevated frequencies of C-to-T and C-to-G mutations in 5'-TC motifs, oncogene activation, acquired drug resistance, and poor clinical outcomes. The mechanisms responsible for APOBEC3B overexpression are not fully understood. Here, we show that the polyomavirus truncated T antigen (truncT) triggers APOBEC3B overexpression through its RB-interacting motif, LXCXE, which in turn likely modulates the binding of E2F family transcription factors to promote APOBEC3B expression. This work strengthens the mechanistic linkage between active cell cycling, APOBEC3B overexpression, and cancer mutagenesis. Although this mutational mechanism damages cellular genomes, viruses may leverage it to promote evolution, immune escape, and pathogenesis. The cellular portion of the mechanism may also be relevant to nonviral cancers, where genetic mechanisms often activate the RB/E2F axis and APOBEC3B mutagenesis contributes to tumor evolution.
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134
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A panel of eGFP reporters for single base editing by APOBEC-Cas9 editosome complexes. Sci Rep 2019; 9:497. [PMID: 30679582 PMCID: PMC6345908 DOI: 10.1038/s41598-018-36739-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 11/26/2018] [Indexed: 01/16/2023] Open
Abstract
The prospect of introducing a single C-to-T change at a specific genomic location has become feasible with APOBEC-Cas9 editing technologies. We present a panel of eGFP reporters for quantification and optimization of single base editing by APOBEC-Cas9 editosomes. Reporter utility is demonstrated by comparing activities of seven human APOBEC3 enzymes and rat APOBEC1 (BE3). APOBEC3A and RNA binding-defective variants of APOBEC3B and APOBEC3H display the highest single base editing efficiencies. APOBEC3B catalytic domain complexes also elicit the lowest frequencies of adjacent off-target events. However, unbiased deep-sequencing of edited reporters shows that all editosomes have some degree of local off-target editing. Thus, further optimization is required to generate true single base editors and the eGFP reporters described here have the potential to facilitate this process.
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135
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Cannataro VL, Gaffney SG, Sasaki T, Issaeva N, Grewal NKS, Grandis JR, Yarbrough WG, Burtness B, Anderson KS, Townsend JP. APOBEC-induced mutations and their cancer effect size in head and neck squamous cell carcinoma. Oncogene 2019; 38:3475-3487. [PMID: 30647454 PMCID: PMC6499643 DOI: 10.1038/s41388-018-0657-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 12/12/2022]
Abstract
Recent studies have revealed the mutational signatures underlying the somatic evolution of cancer, and the prevalences of associated somatic genetic variants. Here we estimate the intensity of positive selection that drives mutations to high frequency in tumors, yielding higher prevalences than expected on the basis of mutation and neutral drift alone. We apply this approach to a sample of 525 head and neck squamous cell carcinoma exomes, producing a rank-ordered list of gene variants by selection intensity. Our results illustrate the complementarity of calculating the intensity of selection on mutations along with tallying the prevalence of individual substitutions in cancer: while many of the most prevalently-altered genes were heavily selected, their relative importance to the cancer phenotype differs from their prevalence and from their P value, with some infrequent variants exhibiting evidence of strong positive selection. Furthermore, we extend our analysis of effect size by quantifying the degree to which mutational processes (such as APOBEC mutagenesis) contributes mutations that are highly selected, driving head and neck squamous cell carcinoma. We calculate the substitutions caused by APOBEC mutagenesis that make the greatest contribution to cancer phenotype among patients. Lastly, we demonstrate via in vitro biochemical experiments that the APOBEC3B protein can deaminate the cytosine bases at two sites whose mutant states are subject to high net realized selection intensities-PIK3CA E545K and E542K. By quantifying the effects of mutations, we deepen the molecular understanding of carcinogenesis in head and neck squamous cell carcinoma.
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Affiliation(s)
- Vincent L Cannataro
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Stephen G Gaffney
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Tomoaki Sasaki
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Natalia Issaeva
- Yale Cancer Center, Yale University, New Haven, CT, USA.,Division of Otolaryngology, Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Nicholas K S Grewal
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Jennifer R Grandis
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Wendell G Yarbrough
- Yale Cancer Center, Yale University, New Haven, CT, USA.,Division of Otolaryngology, Department of Surgery, Yale School of Medicine, New Haven, CT, USA.,Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Barbara Burtness
- Yale Cancer Center, Yale University, New Haven, CT, USA.,Department of Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Karen S Anderson
- Department of Pharmacology, Yale University, New Haven, CT, USA.,Yale Cancer Center, Yale University, New Haven, CT, USA.,Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA. .,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA. .,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.
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136
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Salter JD, Polevoda B, Bennett RP, Smith HC. Regulation of Antiviral Innate Immunity Through APOBEC Ribonucleoprotein Complexes. Subcell Biochem 2019; 93:193-219. [PMID: 31939152 DOI: 10.1007/978-3-030-28151-9_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The DNA mutagenic enzyme known as APOBEC3G (A3G) plays a critical role in innate immunity to Human Immunodeficiency Virus-1 (HIV-1 ). A3G is a zinc-dependent enzyme that mutates select deoxycytidines (dC) to deoxyuridine (dU) through deamination within nascent single stranded DNA (ssDNA) during HIV reverse transcription. This activity requires that the enzyme be delivered to viral replication complexes by redistributing from the cytoplasm of infected cells to budding virions through what appears to be an RNA-dependent process. Once inside infected cells, A3G must bind to nascent ssDNA reverse transcripts for dC to dU base modification gene editing. In this chapter we will discuss data indicating that ssDNA deaminase activity of A3G is regulated by RNA binding to A3G and ribonucleoprotein complex formation along with evidence suggesting that RNA-selective interactions with A3G are temporally and mechanistically important in this process.
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Affiliation(s)
- Jason D Salter
- OyaGen, Inc, 77 Ridgeland Road, Rochester, NY, 14623, USA
| | - Bogdan Polevoda
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Ryan P Bennett
- OyaGen, Inc, 77 Ridgeland Road, Rochester, NY, 14623, USA
| | - Harold C Smith
- OyaGen, Inc, 77 Ridgeland Road, Rochester, NY, 14623, USA. .,Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, 601 Elmwood Ave, Rochester, NY, 14642, USA.
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137
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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.
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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
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138
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Huff AL, Wongthida P, Kottke T, Thompson JM, Driscoll CB, Schuelke M, Shim KG, Harris RS, Molan A, Pulido JS, Selby PJ, Harrington KJ, Melcher A, Evgin L, Vile RG. APOBEC3 Mediates Resistance to Oncolytic Viral Therapy. Mol Ther Oncolytics 2018; 11:1-13. [PMID: 30294666 PMCID: PMC6169432 DOI: 10.1016/j.omto.2018.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/23/2018] [Indexed: 12/18/2022] Open
Abstract
Tumor cells frequently evade applied therapies through the accumulation of genomic mutations and rapid evolution. In the case of oncolytic virotherapy, understanding the mechanisms by which cancer cells develop resistance to infection and lysis is critical to the development of more effective viral-based platforms. Here, we identify APOBEC3 as an important factor that restricts the potency of oncolytic vesicular stomatitis virus (VSV). We show that VSV infection of B16 murine melanoma cells upregulated APOBEC3 in an IFN-β-dependent manner, which was responsible for the evolution of virus-resistant cell populations and suggested that APOBEC3 expression promoted the acquisition of a virus-resistant phenotype. Knockdown of APOBEC3 in B16 cells diminished their capacity to develop resistance to VSV infection in vitro and enhanced the therapeutic effect of VSV in vivo. Similarly, overexpression of human APOBEC3B promoted the acquisition of resistance to oncolytic VSV both in vitro and in vivo. Finally, we demonstrate that APOBEC3B expression had a direct effect on the fitness of VSV, an RNA virus that has not previously been identified as restricted by APOBEC3B. This research identifies APOBEC3 enzymes as key players to target in order to improve the efficacy of viral or broader nucleic acid-based therapeutic platforms.
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Affiliation(s)
- Amanda L. Huff
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Timothy Kottke
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jill M. Thompson
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | - Kevin G. Shim
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Reuben S. Harris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Amy Molan
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jose S. Pulido
- Department of Ophthalmology, Mayo Clinic, Rochester, MN 55905, USA
| | - Peter J. Selby
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James’s University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | | | | | - Laura Evgin
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Richard G. Vile
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James’s University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
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139
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Hou S, Silvas TV, Leidner F, Nalivaika EA, Matsuo H, Kurt Yilmaz N, Schiffer CA. Structural Analysis of the Active Site and DNA Binding of Human Cytidine Deaminase APOBEC3B. J Chem Theory Comput 2018; 15:637-647. [PMID: 30457868 DOI: 10.1021/acs.jctc.8b00545] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
APOBEC3 (A3) proteins, a family of human cytidine deaminases, protect the host from endogenous retro-elements and exogenous viral infections by introducing hypermutations. However, overexpressed A3s can modify genomic DNA to promote tumorigenesis, especially A3B. Despite their overall similarity, A3 proteins have distinct deamination activity. Recently determined A3 structures have revealed the molecular determinants of nucleotide specificity and DNA binding. However, for A3B, the structural basis for regulation of deamination activity and the role of active site loops in coordinating DNA had remained unknown. Using advanced molecular modeling followed by experimental mutational analysis and dynamics simulations, we investigated the molecular mechanism of DNA binding by A3B-CTD. We modeled fully native A3B-DNA structure, and we identified Arg211 in loop 1 as the gatekeeper coordinating DNA and critical residue for nucleotide specificity. We also identified a unique autoinhibited conformation in A3B-CTD that restricts access and binding of DNA to the active site. Our results reveal the structural basis for DNA binding and relatively lower catalytic activity of A3B and provide opportunities for rational design of specific inhibitors to benefit cancer therapeutics.
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Affiliation(s)
- Shurong Hou
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01655 , United States
| | - Tania V Silvas
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01655 , United States
| | - Florian Leidner
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01655 , United States
| | - Ellen A Nalivaika
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01655 , United States
| | - Hiroshi Matsuo
- Basic Research Laboratory, Leidos Biomedical Research, Inc. , Frederick National Laboratory for Cancer Research , Frederick , Maryland 21702 , United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01655 , United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01655 , United States
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140
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Kvach MV, Barzak FM, Harjes S, Schares HAM, Jameson GB, Ayoub AM, Moorthy R, Aihara H, Harris RS, Filichev VV, Harki DA, Harjes E. Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2'-Deoxyzebularine Analogues. Biochemistry 2018; 58:391-400. [PMID: 30418757 PMCID: PMC6365909 DOI: 10.1021/acs.biochem.8b00858] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
APOBEC3 enzymes form part of the innate immune system by deaminating cytosine to uracil in single-stranded DNA (ssDNA) and thereby preventing the spread of pathogenic genetic information. However, APOBEC mutagenesis is also exploited by viruses and cancer cells to increase rates of evolution, escape adaptive immune responses, and resist drugs. This raises the possibility of APOBEC3 inhibition as a strategy for augmenting existing antiviral and anticancer therapies. Here we show that, upon incorporation into short ssDNAs, the cytidine nucleoside analogue 2'-deoxyzebularine (dZ) becomes capable of inhibiting the catalytic activity of selected APOBEC variants derived from APOBEC3A, APOBEC3B, and APOBEC3G, supporting a mechanism in which ssDNA delivers dZ to the active site. Multiple experimental approaches, including isothermal titration calorimetry, fluorescence polarization, protein thermal shift, and nuclear magnetic resonance spectroscopy assays, demonstrate nanomolar dissociation constants and low micromolar inhibition constants. These dZ-containing ssDNAs constitute the first substrate-like APOBEC3 inhibitors and, together, comprise a platform for developing nucleic acid-based inhibitors with cellular activity.
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Affiliation(s)
- Maksim V Kvach
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand
| | - Fareeda M Barzak
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand
| | - Stefan Harjes
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand
| | | | - Geoffrey B Jameson
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1142 , New Zealand
| | | | | | | | - Reuben S Harris
- Howard Hughes Medical Institute , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Vyacheslav V Filichev
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1142 , New Zealand
| | | | - Elena Harjes
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1142 , New Zealand
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141
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Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with DNA. CHINESE J CHEM 2018. [DOI: 10.1002/cjoc.201800508] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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142
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APOBEC3H Subcellular Localization Determinants Define Zipcode for Targeting HIV-1 for Restriction. Mol Cell Biol 2018; 38:MCB.00356-18. [PMID: 30224517 DOI: 10.1128/mcb.00356-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 09/11/2018] [Indexed: 12/22/2022] Open
Abstract
APOBEC enzymes are DNA cytosine deaminases that normally serve as virus restriction factors, but several members, including APOBEC3H, also contribute to cancer mutagenesis. Despite their importance in multiple fields, little is known about cellular processes that regulate these DNA mutating enzymes. We show that APOBEC3H exists in two distinct subcellular compartments, cytoplasm and nucleolus, and that the structural determinants for each mechanism are genetically separable. First, native and fluorescently tagged APOBEC3Hs localize to these two compartments in multiple cell types. Second, a series of genetic, pharmacologic, and cell biological studies demonstrate active cytoplasmic and nucleolar retention mechanisms, whereas nuclear import and export occur through passive diffusion. Third, APOBEC3H cytoplasmic retention determinants relocalize APOBEC3A from a passive cell-wide state to the cytosol and, additionally, endow potent HIV-1 restriction activity. These results indicate that APOBEC3H has a structural zipcode for subcellular localization and selecting viral substrates for restriction.
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143
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Cheng AZ, Yockteng-Melgar J, Jarvis MC, Malik-Soni N, Borozan I, Carpenter MA, McCann JL, Ebrahimi D, Shaban NM, Marcon E, Greenblatt J, Brown WL, Frappier L, Harris RS. Epstein-Barr virus BORF2 inhibits cellular APOBEC3B to preserve viral genome integrity. Nat Microbiol 2018; 4:78-88. [PMID: 30420783 PMCID: PMC6294688 DOI: 10.1038/s41564-018-0284-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/08/2018] [Indexed: 12/29/2022]
Abstract
The APOBEC family of single-stranded (ss)DNA cytosine deaminases provides innate immunity against virus and transposon replication1–4. A well-studied mechanism is APOBEC3G restriction of HIV-1, which is counteracted by a virus-encoded degradation mechanism1–4. Accordingly, most work has focused on retroviruses with obligate ssDNA replication intermediates and it is unclear whether large double-stranded (ds)DNA viruses may be similarly susceptible to restriction. Here, we show that the large dsDNA herpesvirus Epstein-Barr virus (EBV), which is the causative agent of infectious mononucleosis and multiple cancers5, utilizes a two-pronged approach to counteract restriction by APOBEC3B. The large subunit of the EBV ribonucleotide reductase, BORF26,7, bound to APOBEC3B in proteomics studies and immunoprecipitation experiments. Mutagenesis mapped the interaction to the APOBEC3B catalytic domain, and biochemical studies demonstrated that BORF2 stoichiometrically inhibits APOBEC3B DNA cytosine deaminase activity. BORF2 also caused a dramatic relocalization of nuclear APOBEC3B to perinuclear bodies. Upon lytic reactivation, BORF2-null viruses were susceptible to APOBEC3B-mediated deamination as evidenced by lower viral titers, lower infectivity, and hypermutation. The Kaposi’s sarcoma herpesvirus (KSHV) homolog, ORF61, also bound APOBEC3B and mediated relocalization. These data support a model in which the genomic integrity of human γ-herpesviruses is maintained by active neutralization of the antiviral enzyme APOBEC3B.
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Affiliation(s)
- Adam Z Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | | | - Matthew C Jarvis
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Natasha Malik-Soni
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ivan Borozan
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
| | - Michael A Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
| | - Jennifer L McCann
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Diako Ebrahimi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Nadine M Shaban
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Edyta Marcon
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - William L Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Lori Frappier
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA. .,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA. .,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA. .,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA. .,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA.
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144
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Liu M, Mallinger A, Tortorici M, Newbatt Y, Richards M, Mirza A, van Montfort RLM, Burke R, Blagg J, Kaserer T. Evaluation of APOBEC3B Recognition Motifs by NMR Reveals Preferred Substrates. ACS Chem Biol 2018; 13:2427-2432. [PMID: 30130388 PMCID: PMC6430498 DOI: 10.1021/acschembio.8b00639] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 08/21/2018] [Indexed: 12/31/2022]
Abstract
APOBEC3B (A3B) deamination activity on ssDNA is considered a contributing factor to tumor heterogeneity and drug resistance in a number of human cancers. Despite its clinical impact, little is known about A3B ssDNA substrate preference. We have used nuclear magnetic resonance to monitor the catalytic turnover of A3B substrates in real-time. This study reports preferred nucleotide sequences for A3B substrates, including optimized 4-mer oligonucleotides, and reveals a breadth of substrate recognition that includes DNA sequences known to be mutated in drug-resistant cancer clones. Our results are consistent with available clinical and structural data and may inform the design of substrate-based A3B inhibitors.
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Affiliation(s)
- Manjuan Liu
- Cancer Research UK Cancer Therapeutics Unit , The Institute of Cancer Research , London SM2 5NG , U.K
| | - Aurélie Mallinger
- Cancer Research UK Cancer Therapeutics Unit , The Institute of Cancer Research , London SM2 5NG , U.K
| | - Marcello Tortorici
- Cancer Research UK Cancer Therapeutics Unit , The Institute of Cancer Research , London SM2 5NG , U.K
| | - Yvette Newbatt
- Cancer Research UK Cancer Therapeutics Unit , The Institute of Cancer Research , London SM2 5NG , U.K
| | - Meirion Richards
- Cancer Research UK Cancer Therapeutics Unit , The Institute of Cancer Research , London SM2 5NG , U.K
| | - Amin Mirza
- Cancer Research UK Cancer Therapeutics Unit , The Institute of Cancer Research , London SM2 5NG , U.K
| | - Rob L M van Montfort
- Cancer Research UK Cancer Therapeutics Unit , The Institute of Cancer Research , London SM2 5NG , U.K
| | - Rosemary Burke
- Cancer Research UK Cancer Therapeutics Unit , The Institute of Cancer Research , London SM2 5NG , U.K
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit , The Institute of Cancer Research , London SM2 5NG , U.K
| | - Teresa Kaserer
- Cancer Research UK Cancer Therapeutics Unit , The Institute of Cancer Research , London SM2 5NG , U.K
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145
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Strategy of Human Cytomegalovirus To Escape Interferon Beta-Induced APOBEC3G Editing Activity. J Virol 2018; 92:JVI.01224-18. [PMID: 30045985 DOI: 10.1128/jvi.01224-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 01/26/2023] Open
Abstract
The apolipoprotein B editing enzyme catalytic subunit 3 (APOBEC3) is a family of DNA cytosine deaminases that mutate and inactivate viral genomes by single-strand DNA editing, thus providing an innate immune response against a wide range of DNA and RNA viruses. In particular, APOBEC3A (A3A), a member of the APOBEC3 family, is induced by human cytomegalovirus (HCMV) in decidual tissues where it efficiently restricts HCMV replication, thereby acting as an intrinsic innate immune effector at the maternal-fetal interface. However, the widespread incidence of congenital HCMV infection implies that HCMV has evolved to counteract APOBEC3-induced mutagenesis through mechanisms that still remain to be fully established. Here, we have assessed gene expression and deaminase activity of various APOBEC3 gene family members in HCMV-infected primary human foreskin fibroblasts (HFFs). Specifically, we show that APOBEC3G (A3G) gene products and, to a lesser degree, those of A3F but not of A3A, are upregulated in HCMV-infected HFFs. We also show that HCMV-mediated induction of A3G expression is mediated by interferon beta (IFN-β), which is produced early during HCMV infection. However, knockout or overexpression of A3G does not affect HCMV replication, indicating that A3G is not a restriction factor for HCMV. Finally, through a bioinformatics approach, we show that HCMV has evolved mutational robustness against IFN-β by limiting the presence of A3G hot spots in essential open reading frames (ORFs) of its genome. Overall, our findings uncover a novel immune evasion strategy by HCMV with profound implications for HCMV infections.IMPORTANCE APOBEC3 family of proteins plays a pivotal role in intrinsic immunity defense mechanisms against multiple viral infections, including retroviruses, through the deamination activity. However, the currently available data on APOBEC3 editing mechanisms upon HCMV infection remain unclear. In the present study, we show that particularly the APOBEC3G (A3G) member of the deaminase family is strongly induced upon infection with HCMV in fibroblasts and that its upregulation is mediated by IFN-β. Furthermore, we were able to demonstrate that neither A3G knockout nor A3G overexpression appears to modulate HCMV replication, indicating that A3G does not inhibit HCMV replication. This may be explained by HCMV escape strategy from A3G activity through depletion of the preferred nucleotide motifs (hot spots) from its genome. The results may shed light on antiviral potential of APOBEC3 activity during HCMV infection, as well as the viral counteracting mechanisms under A3G-mediated selective pressure.
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146
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Jaguva Vasudevan AA, Kreimer U, Schulz WA, Krikoni A, Schumann GG, Häussinger D, Münk C, Goering W. APOBEC3B Activity Is Prevalent in Urothelial Carcinoma Cells and Only Slightly Affected by LINE-1 Expression. Front Microbiol 2018; 9:2088. [PMID: 30233553 PMCID: PMC6132077 DOI: 10.3389/fmicb.2018.02088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/15/2018] [Indexed: 12/20/2022] Open
Abstract
The most common mutational signature in urothelial carcinoma (UC), the most common type of urinary bladder cancer is assumed to be caused by the misdirected activity of APOBEC3 (A3) cytidine deaminases, especially A3A or A3B, which are known to normally restrict the propagation of exogenous viruses and endogenous retroelements such as LINE-1 (L1). The involvement of A3 proteins in urothelial carcinogenesis is unexpected because, to date, UC is thought to be caused by chemical carcinogens rather than viral activity. Therefore, we explored the relationship between A3 expression and L1 activity, which is generally upregulated in UC. We found that UC cell lines highly express A3B and in some cases A3G, but not A3A, and exhibit corresponding cytidine deamination activity in vitro. While we observed evidence suggesting that L1 expression has a weak positive effect on A3B and A3G expression and A3B promoter activity, neither efficient siRNA-mediated knockdown nor overexpression of functional L1 elements affected catalytic activity of A3 proteins consistently. However, L1 knockdown diminished proliferation of a UC cell line exhibiting robust endogenous L1 expression, but had little impact on a cell line with low L1 expression levels. Our results indicate that UC cells express A3B at levels exceeding A3A levels by far, making A3B the prime candidate for causing genomic mutations. Our data provide evidence that L1 activation constitutes only a minor and negligible factor involved in induction or upregulation of endogenous A3 expression in UC.
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Affiliation(s)
- Ananda Ayyappan Jaguva Vasudevan
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ulrike Kreimer
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Aikaterini Krikoni
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Wolfgang Goering
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Pathology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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147
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St. Martin A, Salamango D, Serebrenik A, Shaban N, Brown WL, Donati F, Munagala U, Conticello SG, Harris RS. A fluorescent reporter for quantification and enrichment of DNA editing by APOBEC-Cas9 or cleavage by Cas9 in living cells. Nucleic Acids Res 2018; 46:e84. [PMID: 29746667 PMCID: PMC6101615 DOI: 10.1093/nar/gky332] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 03/26/2018] [Accepted: 04/18/2018] [Indexed: 12/17/2022] Open
Abstract
Base editing is an exciting new genome engineering technology. C-to-T mutations in genomic DNA have been achieved using ribonucleoprotein complexes comprised of rat APOBEC1 single-stranded DNA deaminase, Cas9 nickase (Cas9n), uracil DNA glycosylase inhibitor (UGI), and guide (g)RNA. Here, we report the first real-time reporter system for quantification of APOBEC-mediated base editing activity in living mammalian cells. The reporter expresses eGFP constitutively as a marker for transfection or transduction, and editing restores functionality of an upstream mCherry cassette through the simultaneous processing of two gRNA binding regions that each contain an APOBEC-preferred 5'TCA target site. Using this system as both an episomal and a chromosomal editing reporter, we show that human APOBEC3A-Cas9n-UGI and APOBEC3B-Cas9n-UGI base editing complexes are more efficient than the original rat APOBEC1-Cas9n-UGI construct. We also demonstrate coincident enrichment of editing events at a heterologous chromosomal locus in reporter-edited, mCherry-positive cells. The mCherry reporter also quantifies the double-stranded DNA cleavage activity of Cas9, and may therefore be adaptable for use with many different CRISPR systems. The combination of a rapid, fluorescence-based editing reporter system and more efficient, structurally defined DNA editing enzymes broadens the versatility of the rapidly expanding toolbox of genome editing and engineering technologies.
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Affiliation(s)
- Amber St. Martin
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Center for Genome Engineering, Institute for Molecular Virology, University of Minnesota, MN 55455, USA
| | - Daniel Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Center for Genome Engineering, Institute for Molecular Virology, University of Minnesota, MN 55455, USA
| | - Artur Serebrenik
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Center for Genome Engineering, Institute for Molecular Virology, University of Minnesota, MN 55455, USA
| | - Nadine Shaban
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Center for Genome Engineering, Institute for Molecular Virology, University of Minnesota, MN 55455, USA
| | - William L Brown
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Center for Genome Engineering, Institute for Molecular Virology, University of Minnesota, MN 55455, USA
| | | | | | | | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Center for Genome Engineering, Institute for Molecular Virology, University of Minnesota, MN 55455, USA
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
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148
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Wang X, Li J, Wang Y, Yang B, Wei J, Wu J, Wang R, Huang X, Chen J, Yang L. Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion. Nat Biotechnol 2018; 36:946-949. [PMID: 30125268 DOI: 10.1038/nbt.4198] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/03/2018] [Indexed: 01/02/2023]
Abstract
Base editors (BEs) enable the generation of targeted single-nucleotide mutations, but currently used rat APOBEC1-based BEs are relatively inefficient in editing cytosines in highly methylated regions or in GpC contexts. By screening a variety of APOBEC and AID deaminases, we show that human APOBEC3A-conjugated BEs and versions we engineered to have narrower editing windows can mediate efficient C-to-T base editing in regions with high methylation levels and GpC dinucleotide content.
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Affiliation(s)
- Xiao Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jianan Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ying Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Jia Wei
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jing Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ruixuan Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jia Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Li Yang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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149
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Gehrke JM, Cervantes O, Clement MK, Wu Y, Zeng J, Bauer DE, Pinello L, Joung JK. An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat Biotechnol 2018; 36:977-982. [PMID: 30059493 PMCID: PMC6181770 DOI: 10.1038/nbt.4199] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/25/2018] [Indexed: 12/31/2022]
Abstract
Base editor (BE) technology, which uses CRISPR-Cas9 to direct cytidine deaminase enzymatic activity to specific genomic loci, enables the highly efficient introduction of precise cytidine-to-thymidine DNA alterations1–6. However, existing BEs create unwanted C to T alterations when more than one C is present in the enzyme’s five-base-pair editing window. Here we describe a strategy for reducing bystander mutations using an engineered human APOBEC3A (eA3A) domain, which preferentially deaminates cytidines in specific motifs according to a TCR>TCY>VCN hierarchy. In direct comparisons with the widely used BE3 fusion in human cells, our eA3A-BE3 fusion exhibits similar activities on cytidines in TC motifs but greatly reduced editing on cytidines in other sequence contexts. eA3A-BE3 corrects a human beta-thalassemia promoter mutation with much higher (>40-fold) precision than BE3. We also demonstrate that eA3A-BE3 shows reduced mutation frequencies on known off-target sites of BE3, even when targeting promiscuous homopolymeric sites.
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Affiliation(s)
- Jason M Gehrke
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Oliver Cervantes
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - M Kendell Clement
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Yuxuan Wu
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Luca Pinello
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
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150
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Gao J, Choudhry H, Cao W. Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like family genes activation and regulation during tumorigenesis. Cancer Sci 2018; 109:2375-2382. [PMID: 29856501 PMCID: PMC6113426 DOI: 10.1111/cas.13658] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 12/19/2022] Open
Abstract
Cancer is currently viewed as a disease of evolving genomic instability and abnormal epigenomic modifications. Most solid cancers harbor oncogenic gene mutations driven by both extrinsic and intrinsic factors. Apolipoprotein B mRNA editing catalytic polypeptide‐like family (APOBEC) enzymes have an intrinsic deamination activity to convert cytosine to uracil during RNA editing and retrovirus or retrotransposon restriction. Beyond their natural defense in innate immunity, compelling evidence showed that a subclass of APOBEC3 can cause high mutation burden in various types of cancer genomes, and high expression subtypes of APOBEC3 may contribute to drug resistance and associate with clinical outcomes. The underlying molecular mechanisms of APOBEC‐mediated hypermutation phenotype are poorly understood. In this review, we discuss the linkage of activation‐induced deaminase (AID)/APOBEC3 enzymes to tumorigenesis, highlight the dysregulatory mechanisms of APOBEC3 activities during cancer development, and propose potential approaches to targeting APOBEC3‐mediated mutagenesis for cancer interventions.
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Affiliation(s)
| | | | - Wei Cao
- Translational Medical Center, Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
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