1
|
Kawale AS, Zou L. Regulation, functional impact, and therapeutic targeting of APOBEC3A in cancer. DNA Repair (Amst) 2024; 141:103734. [PMID: 39047499 PMCID: PMC11330346 DOI: 10.1016/j.dnarep.2024.103734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Enzymes of the apolipoprotein B mRNA editing catalytic polypeptide like (APOBEC) family are cytosine deaminases that convert cytosine to uracil in DNA and RNA. Among these proteins, APOBEC3 sub-family members, APOBEC3A (A3A) and APOBEC3B (A3B), are prominent sources of mutagenesis in cancer cells. The aberrant expression of A3A and A3B in cancer cells leads to accumulation of mutations with specific single-base substitution (SBS) signatures, characterized by C→T and C→G changes, in a number of tumor types. In addition to fueling mutagenesis, A3A and A3B, particularly A3A, induce DNA replication stress, DNA damage, and chromosomal instability through their catalytic activities, triggering a range of cellular responses. Thus, A3A/B have emerged as key drivers of genome evolution during cancer development, contributing to tumorigenesis, tumor heterogeneity, and therapeutic resistance. Yet, the expression of A3A/B in cancer cells presents a cancer vulnerability that can be exploited therapeutically. In this review, we discuss the recent studies that shed light on the mechanisms regulating A3A expression and the impact of A3A in cancer. We also review recent advances in the development of A3A inhibitors and provide perspectives on the future directions of A3A research.
Collapse
Affiliation(s)
- Ajinkya S Kawale
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
| |
Collapse
|
2
|
Fingerman DF, O'Leary DR, Hansen AR, Tran T, Harris BR, DeWeerd RA, Hayer KE, Fan J, Chen E, Tennakoon M, Meroni A, Szeto JH, Devenport J, LaVigne D, Weitzman MD, Shalem O, Bednarski J, Vindigni A, Zhao X, Green AM. The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress. EMBO J 2024; 43:3240-3255. [PMID: 38886582 PMCID: PMC11294446 DOI: 10.1038/s44318-024-00137-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/09/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
Mutational patterns caused by APOBEC3 cytidine deaminase activity are evident throughout human cancer genomes. In particular, the APOBEC3A family member is a potent genotoxin that causes substantial DNA damage in experimental systems and human tumors. However, the mechanisms that ensure genome stability in cells with active APOBEC3A are unknown. Through an unbiased genome-wide screen, we define the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex as essential for cell viability when APOBEC3A is active. We observe an absence of APOBEC3A mutagenesis in human tumors with SMC5/6 dysfunction, consistent with synthetic lethality. Cancer cells depleted of SMC5/6 incur substantial genome damage from APOBEC3A activity during DNA replication. Further, APOBEC3A activity results in replication tract lengthening which is dependent on PrimPol, consistent with re-initiation of DNA synthesis downstream of APOBEC3A-induced lesions. Loss of SMC5/6 abrogates elongated replication tracts and increases DNA breaks upon APOBEC3A activity. Our findings indicate that replication fork lengthening reflects a DNA damage response to APOBEC3A activity that promotes genome stability in an SMC5/6-dependent manner. Therefore, SMC5/6 presents a potential therapeutic vulnerability in tumors with active APOBEC3A.
Collapse
Affiliation(s)
- Dylan F Fingerman
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - David R O'Leary
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Ava R Hansen
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Drexel University College of Medicine, Philadelphia, PA, USA
| | - Thi Tran
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Brooke R Harris
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Katharina E Hayer
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jiayi Fan
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Emily Chen
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- School of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Mithila Tennakoon
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Alice Meroni
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Julia H Szeto
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jessica Devenport
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Danielle LaVigne
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew D Weitzman
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ophir Shalem
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeffrey Bednarski
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Alessandro Vindigni
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
3
|
McCool MA, Bryant CJ, Abriola L, Surovtseva YV, Baserga SJ. The cytidine deaminase APOBEC3A regulates nucleolar function to promote cell growth and ribosome biogenesis. PLoS Biol 2024; 22:e3002718. [PMID: 38976757 PMCID: PMC11257408 DOI: 10.1371/journal.pbio.3002718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 07/18/2024] [Accepted: 06/20/2024] [Indexed: 07/10/2024] Open
Abstract
Cancer initiates as a consequence of genomic mutations and its subsequent progression relies in part on increased production of ribosomes to maintain high levels of protein synthesis for unchecked cell growth. Recently, cytidine deaminases have been uncovered as sources of mutagenesis in cancer. In an attempt to form a connection between these 2 cancer driving processes, we interrogated the cytidine deaminase family of proteins for potential roles in human ribosome biogenesis. We identified and validated APOBEC3A and APOBEC4 as novel ribosome biogenesis factors through our laboratory's established screening platform for the discovery of regulators of nucleolar function in MCF10A cells. Through siRNA depletion experiments, we highlight APOBEC3A's requirement in making ribosomes and specific role within the processing and maturation steps that form the large subunit 5.8S and 28S ribosomal (r)RNAs. We demonstrate that a subset of APOBEC3A resides within the nucleolus and associates with critical ribosome biogenesis factors. Mechanistic insight was revealed by transient overexpression of both wild-type and a catalytically dead mutated APOBEC3A, which both increase cell growth and protein synthesis. Through an innovative nuclear RNA sequencing methodology, we identify only modest predicted APOBEC3A C-to-U target sites on the pre-rRNA and pre-mRNAs. Our work reveals a potential direct role for APOBEC3A in ribosome biogenesis likely independent of its editing function. More broadly, we found an additional function of APOBEC3A in cancer pathology through its function in ribosome biogenesis, expanding its relevance as a target for cancer therapeutics.
Collapse
Affiliation(s)
- Mason A. McCool
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Carson J. Bryant
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, Connecticut, United States of America
| | - Yulia V. Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, Connecticut, United States of America
| | - Susan J. Baserga
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| |
Collapse
|
4
|
Chattopadhyay P, Mehta P, Kanika, Mishra P, Chen Liu CS, Tarai B, Budhiraja S, Pandey R. RNA editing in host lncRNAs as potential modulator in SARS-CoV-2 variants-host immune response dynamics. iScience 2024; 27:109846. [PMID: 38770134 PMCID: PMC11103575 DOI: 10.1016/j.isci.2024.109846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/18/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
Both host and viral RNA editing plays a crucial role in host's response to infection, yet our understanding of host RNA editing remains limited. In this study of in-house generated RNA sequencing (RNA-seq) data of 211 hospitalized COVID-19 patients with PreVOC, Delta, and Omicron variants, we observed a significant differential editing frequency and patterns in long non-coding RNAs (lncRNAs), with Delta group displaying lower RNA editing compared to PreVOC/Omicron patients. Notably, multiple transcripts of UGDH-AS1 and NEAT1 exhibited high editing frequencies. Expression of ADAR1/APOBEC3A/APOBEC3G and differential abundance of repeats were possible modulators of differential editing across patient groups. We observed a shift in crucial infection-related pathways wherein the pathways were downregulated in Delta compared to PreVOC and Omicron. Our genomics-based evidence suggests that lncRNA editing influences stability, miRNA binding, and expression of both lncRNA and target genes. Overall, the study highlights the role of lncRNAs and how editing within host lncRNAs modulates the disease severity.
Collapse
Affiliation(s)
- Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kanika
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Pallavi Mishra
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Chinky Shiu Chen Liu
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 110017, India
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 110017, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| |
Collapse
|
5
|
Ren CY, Liu YS, He YS, Zhang LP, Rao JH, Rao Y, Chen JH. Engineered CBEs based on Macaca fascicularis A3A with improved properties for precise genome editing. Cell Rep 2024; 43:113878. [PMID: 38431844 DOI: 10.1016/j.celrep.2024.113878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/20/2023] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
Cytidine deaminase defines the properties of cytosine base editors (CBEs) for C-to-T conversion. Replacing the cytidine deaminase rat APOBEC1 (rA1) in CBEs with a human APOBEC3A (hA3A) improves CBE properties. However, the potential CBE application of macaque A3A orthologs remains undetermined. Our current study develops and evaluates engineered CBEs based on Macaca fascicularis A3A (mA3A). Here, we demonstrate that BE4-mA3A and its RNA-editing-derived variants exhibit improved CBE properties, except for DNA off-target activity, compared to BE3-rA1 and BE4-rA1. Unexpectedly, deleting Ser-Val-Arg (SVR) in BE4-mA3A dramatically reduces DNA and RNA off-target activities and improves editing accuracy, with on-target efficiency unaffected. In contrast, a chimeric BE4-hA3A-SVR+ shows editing efficiency increased by about 50%, with other properties unaffected. Our findings demonstrate that mA3A-based CBEs could provide prototype options with advantages over rA1- and hA3A-based CBEs for further optimization, highlighting the importance of the SVR motif in defining CBE intrinsic properties.
Collapse
Affiliation(s)
- Chun-Yan Ren
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan-Shan Liu
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China
| | - Yu-Shan He
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Lin-Pei Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jun-Hua Rao
- Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Jiangnan University-Xinshijie Eye Hospital Joint Ophthalmic Research Center, Xinshijie Eye Hospital, Wuxi, China.
| |
Collapse
|
6
|
O'Leary DR, Hansen AR, Fingerman DF, Tran T, Harris BR, Hayer KE, Fan J, Chen E, Tennakoon M, DeWeerd RA, Meroni A, Szeto JH, Weitzman MD, Shalem O, Bednarski J, Vindigni A, Zhao X, Green AM. The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.28.568952. [PMID: 38077016 PMCID: PMC10705431 DOI: 10.1101/2023.11.28.568952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Mutational patterns caused by APOBEC3 cytidine deaminase activity are evident throughout human cancer genomes. In particular, the APOBEC3A family member is a potent genotoxin that causes substantial DNA damage in experimental systems and human tumors. However, the mechanisms that ensure genome stability in cells with active APOBEC3A are unknown. Through an unbiased genome-wide screen, we define the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex as essential for cell viability when APOBEC3A is active. We observe an absence of APOBEC3A mutagenesis in human tumors with SMC5/6 dysfunction, consistent with synthetic lethality. Cancer cells depleted of SMC5/6 incur substantial genome damage from APOBEC3A activity during DNA replication. Further, APOBEC3A activity results in replication tract lengthening which is dependent on PrimPol, consistent with re-initiation of DNA synthesis downstream of APOBEC3A-induced lesions. Loss of SMC5/6 abrogates elongated replication tracts and increases DNA breaks upon APOBEC3A activity. Our findings indicate that replication fork lengthening reflects a DNA damage response to APOBEC3A activity that promotes genome stability in an SMC5/6-dependent manner. Therefore, SMC5/6 presents a potential therapeutic vulnerability in tumors with active APOBEC3A.
Collapse
|
7
|
O’Toole Á, Neher RA, Ndodo N, Borges V, Gannon B, Gomes JP, Groves N, King DJ, Maloney D, Lemey P, Lewandowski K, Loman N, Myers R, Omah IF, Suchard MA, Worobey M, Chand M, Ihekweazu C, Ulaeto D, Adetifa I, Rambaut A. APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016. Science 2023; 382:595-600. [PMID: 37917680 PMCID: PMC10880385 DOI: 10.1126/science.adg8116] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 09/21/2023] [Indexed: 11/04/2023]
Abstract
Historically, mpox has been characterized as an endemic zoonotic disease that transmits through contact with the reservoir rodent host in West and Central Africa. However, in May 2022, human cases of mpox were detected spreading internationally beyond countries with known endemic reservoirs. When the first cases from 2022 were sequenced, they shared 42 nucleotide differences from the closest mpox virus (MPXV) previously sampled. Nearly all these mutations are characteristic of the action of APOBEC3 deaminases, host enzymes with antiviral function. Assuming APOBEC3 editing is characteristic of human MPXV infection, we developed a dual-process phylogenetic molecular clock that-inferring a rate of ~6 APOBEC3 mutations per year-estimates that MPXV has been circulating in humans since 2016. These observations of sustained MPXV transmission present a fundamental shift to the perceived paradigm of MPXV epidemiology as a zoonosis and highlight the need for revising public health messaging around MPXV as well as outbreak management and control.
Collapse
Affiliation(s)
- Áine O’Toole
- Institute of Ecology & Evolution, University of Edinburgh; Edinburgh, EH9 3FL, United Kingdom
| | - Richard A. Neher
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics; Basel, Switzerland
| | - Nnaemeka Ndodo
- Nigeria Centers for Disease Control and Prevention; Abuja, Nigeria
| | - Vitor Borges
- National Institute of Health Doutor Ricardo Jorge (INSA); Lisbon, Portugal
| | - Ben Gannon
- UK Health Security Agency, Porton Down; Salisbury, United Kingdom
| | - João Paulo Gomes
- National Institute of Health Doutor Ricardo Jorge (INSA); Lisbon, Portugal
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Natalie Groves
- UK Health Security Agency; London, E14 5EA, United Kingdom
| | - David J King
- CBR Division, Defence Science and Technology Laboratory; Salisbury SP4 0JQ, United Kingdom
| | - Daniel Maloney
- Institute of Ecology & Evolution, University of Edinburgh; Edinburgh, EH9 3FL, United Kingdom
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven; Leuven, Belgium
| | | | - Nicholas Loman
- UK Health Security Agency; London, E14 5EA, United Kingdom
- University of Birmingham; Birmingham, United Kingdom
| | - Richard Myers
- UK Health Security Agency; London, E14 5EA, United Kingdom
| | - Ifeanyi F. Omah
- Institute of Ecology & Evolution, University of Edinburgh; Edinburgh, EH9 3FL, United Kingdom
- Department of Parasitology and Entomology, Nnamdi Azikiwe University, Awka, Anambra State, Nigeria
| | - Marc A. Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California; Los Angeles, California, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona; Tucson, Arizona, USA
| | - Meera Chand
- UK Health Security Agency; London, E14 5EA, United Kingdom
| | - Chikwe Ihekweazu
- Nigeria Centers for Disease Control and Prevention; Abuja, Nigeria
| | - David Ulaeto
- UK Health Security Agency; London, E14 5EA, United Kingdom
| | - Ifedayo Adetifa
- Nigeria Centers for Disease Control and Prevention; Abuja, Nigeria
| | - Andrew Rambaut
- Institute of Ecology & Evolution, University of Edinburgh; Edinburgh, EH9 3FL, United Kingdom
| |
Collapse
|
8
|
Carpenter MA, Temiz NA, Ibrahim MA, Jarvis MC, Brown MR, Argyris PP, Brown WL, Starrett GJ, Yee D, Harris RS. Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer. PLoS Genet 2023; 19:e1011043. [PMID: 38033156 PMCID: PMC10715669 DOI: 10.1371/journal.pgen.1011043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/12/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
A prominent source of mutation in cancer is single-stranded DNA cytosine deamination by cellular APOBEC3 enzymes, which results in signature C-to-T and C-to-G mutations in TCA and TCT motifs. Although multiple enzymes have been implicated, reports conflict and it is unclear which protein(s) are responsible. Here we report the development of a selectable system to quantify genome mutation and demonstrate its utility by comparing the mutagenic activities of three leading candidates-APOBEC3A, APOBEC3B, and APOBEC3H. The human cell line, HAP1, is engineered to express the thymidine kinase (TK) gene of HSV-1, which confers sensitivity to ganciclovir. Expression of APOBEC3A and APOBEC3B, but not catalytic mutant controls or APOBEC3H, triggers increased frequencies of TK mutation and similar TC-biased cytosine mutation profiles in the selectable TK reporter gene. Whole genome sequences from independent clones enabled an analysis of thousands of single base substitution mutations and extraction of local sequence preferences with APOBEC3A preferring YTCW motifs 70% of the time and APOBEC3B 50% of the time (Y = C/T; W = A/T). Signature comparisons with breast tumor whole genome sequences indicate that most malignancies manifest intermediate percentages of APOBEC3 signature mutations in YTCW motifs, mostly between 50 and 70%, suggesting that both enzymes contribute in a combinatorial manner to the overall mutation landscape. Although the vast majority of APOBEC3A- and APOBEC3B-induced single base substitution mutations occur outside of predicted chromosomal DNA hairpin structures, whole genome sequence analyses and supporting biochemical studies also indicate that both enzymes are capable of deaminating the single-stranded loop regions of DNA hairpins at elevated rates. These studies combine to help resolve a long-standing etiologic debate on the source of APOBEC3 signature mutations in cancer and indicate that future diagnostic and therapeutic efforts should focus on both APOBEC3A and APOBEC3B.
Collapse
Affiliation(s)
- Michael A. Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, United States of America
| | - Nuri A. Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Mahmoud A. Ibrahim
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States of America
| | - Matthew C. Jarvis
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Margaret R. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Prokopios P. Argyris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - William L. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Gabriel J. Starrett
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Douglas Yee
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, United States of America
| |
Collapse
|
9
|
Ding J, Wang S, Liu Q, Duan Y, Cheng T, Ye Z, Cui Z, Zhang A, Liu Q, Zhang Z, Zhang N, Liu Q, An N, Zhao J, Yi D, Li Q, Wang J, Zhang Y, Ma L, Guo S, Wang J, Liang C, Zhou J, Cen S, Li X. Schlafen-5 inhibits LINE-1 retrotransposition. iScience 2023; 26:107968. [PMID: 37810251 PMCID: PMC10551903 DOI: 10.1016/j.isci.2023.107968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 07/20/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023] Open
Abstract
Long interspersed element 1 (LINE-1) is the only currently known active autonomous transposon in humans, and its retrotransposition may cause deleterious effects on the structure and function of host cell genomes and result in sporadic genetic diseases. Host cells therefore developed defense strategies to restrict LINE-1 mobilization. In this study, we demonstrated that IFN-inducible Schlafen5 (SLFN5) inhibits LINE-1 retrotransposition. Mechanistic studies revealed that SLFN5 interrupts LINE-1 ribonucleoprotein particle (RNP) formation, thus diminishing nuclear entry of the LINE-1 RNA template and subsequent LINE-1 cDNA production. The ability of SLFN5 to bind to LINE-1 RNA and the involvement of the helicase domain of SLFN5 in its inhibitory activity suggest a mechanism that SLFN5 binds to LINE-1 RNA followed by dissociation of ORF1p through its helicase activity, resulting in impaired RNP formation. These data highlight a new mechanism of host cells to restrict LINE-1 mobilization.
Collapse
Affiliation(s)
- Jiwei Ding
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shujie Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qipeng Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yuqing Duan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tingting Cheng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhongjie Ye
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhanding Cui
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qiuyu Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zixiong Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qian Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ni An
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianyuan Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dongrong Yi
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Quanjie Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jing Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yongxin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Saisai Guo
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jinhui Wang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chen Liang
- The Lady Davis Institute-Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| |
Collapse
|
10
|
Luqman-Fatah A, Miyoshi T. Human LINE-1 retrotransposons: impacts on the genome and regulation by host factors. Genes Genet Syst 2023; 98:121-154. [PMID: 36436935 DOI: 10.1266/ggs.22-00038] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Genome sequencing revealed that nearly half of the human genome is comprised of transposable elements. Although most of these elements have been rendered inactive due to mutations, full-length intact long interspersed element-1 (LINE-1 or L1) copies retain the ability to mobilize through RNA intermediates by a so-called "copy-and-paste" mechanism, termed retrotransposition. L1 is the only known autonomous mobile genetic element in the genome, and its retrotransposition contributes to inter- or intra-individual genetic variation within the human population. However, L1 retrotransposition also poses a threat to genome integrity due to gene disruption and chromosomal instability. Moreover, recent studies suggest that aberrant L1 expression can impact human health by causing diseases such as cancer and chronic inflammation that might lead to autoimmune disorders. To counteract these adverse effects, the host cells have evolved multiple layers of defense mechanisms at the epigenetic, RNA and protein levels. Intriguingly, several host factors have also been reported to facilitate L1 retrotransposition, suggesting that there is competition between negative and positive regulation of L1 by host factors. Here, we summarize the known host proteins that regulate L1 activity at different stages of the replication cycle and discuss how these factors modulate disease-associated phenotypes caused by L1.
Collapse
Affiliation(s)
- Ahmad Luqman-Fatah
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University
- Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University
| | - Tomoichiro Miyoshi
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University
- Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University
| |
Collapse
|
11
|
Liu Q, Yi D, Ding J, Mao Y, Wang S, Ma L, Li Q, Wang J, Zhang Y, Zhao J, Guo S, Liu Z, Guo F, Zhao D, Liang C, Li X, Peng X, Cen S. MOV10 recruits DCP2 to decap human LINE-1 RNA by forming large cytoplasmic granules with phase separation properties. EMBO Rep 2023; 24:e56512. [PMID: 37437058 PMCID: PMC10481665 DOI: 10.15252/embr.202256512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
Long interspersed element 1 (LINE-1) is the only active autonomous mobile element in the human genome. Its transposition can exert deleterious effects on the structure and function of the host genome and cause sporadic genetic diseases. Tight control of LINE-1 mobilization by the host is crucial for genetic stability. In this study, we report that MOV10 recruits the main decapping enzyme DCP2 to LINE-1 RNA and forms a complex of MOV10, DCP2, and LINE-1 RNP, exhibiting liquid-liquid phase separation (LLPS) properties. DCP2 cooperates with MOV10 to decap LINE-1 RNA, which causes degradation of LINE-1 RNA and thus reduces LINE-1 retrotransposition. We here identify DCP2 as one of the key effector proteins determining LINE-1 replication, and elucidate an LLPS mechanism that facilitates the anti-LINE-1 action of MOV10 and DCP2.
Collapse
Affiliation(s)
- Qian Liu
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Dongrong Yi
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Jiwei Ding
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Yang Mao
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Shujie Wang
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Ling Ma
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Quanjie Li
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Jing Wang
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Yongxin Zhang
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Jianyuan Zhao
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Saisai Guo
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Zhenlong Liu
- Lady Davis Institute, Jewish General HospitalMcGill UniversityMontrealQCCanada
| | - Fei Guo
- Institute of Pathogen BiologyChinese Academy of Medical ScienceBeijingChina
| | - Dongbing Zhao
- National Cancer CenterChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Chen Liang
- Lady Davis Institute, Jewish General HospitalMcGill UniversityMontrealQCCanada
| | - Xiaoyu Li
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| | - Xiaozhong Peng
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Shan Cen
- Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical SchoolBeijingChina
| |
Collapse
|
12
|
Kim K, Shi AB, Kelley K, Chen XS. Unraveling the Enzyme-Substrate Properties for APOBEC3A-Mediated RNA Editing. J Mol Biol 2023; 435:168198. [PMID: 37442413 PMCID: PMC10528890 DOI: 10.1016/j.jmb.2023.168198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
The APOBEC3 family of human cytidine deaminases is involved in various cellular processes, including the innate and acquired immune system, mostly through inducing C-to-U in single-stranded DNA and/or RNA mutations. Although recent studies have examined RNA editing by APOBEC3A (A3A), its intracellular target specificity are not fully characterized. To address this gap, we performed in-depth analysis of cellular RNA editing using our recently developed sensitive cell-based fluorescence assay. Our findings demonstrate that A3A and an A3A-loop1-containing APOBEC3B (A3B) chimera are capable of RNA editing. We observed that A3A prefers to edit specific RNA substrates which are not efficiently deaminated by other APOBEC members. The editing efficiency of A3A is influenced by the RNA sequence contexts and distinct stem-loop secondary structures. Based on the identified RNA specificity features, we predicted potential A3A-editing targets in the encoding region of cellular mRNAs and discovered novel RNA transcripts that are extensively edited by A3A. Furthermore, we found a trend of increased synonymous mutations at the sites for more efficient A3A-editing, indicating evolutionary adaptation to the higher editing rate by A3A. Our results shed light on the intracellular RNA editing properties of A3A and provide insights into new RNA targets and potential impact of A3A-mediated RNA editing.
Collapse
Affiliation(s)
- Kyumin Kim
- Molecular and Computational Biology Program, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA. https://twitter.com/KYUMINK1324
| | - Alan B Shi
- Molecular and Computational Biology Program, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Kori Kelley
- Molecular and Computational Biology Program, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology Program, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA; Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA.
| |
Collapse
|
13
|
Zhang D, Irving AT. Antiviral effects of interferon-stimulated genes in bats. Front Cell Infect Microbiol 2023; 13:1224532. [PMID: 37661999 PMCID: PMC10472940 DOI: 10.3389/fcimb.2023.1224532] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/10/2023] [Indexed: 09/05/2023] Open
Abstract
The interferon pathway is the first line of defense in viral infection in all mammals, and its induction stimulates broad expression of interferon-stimulated genes (ISGs). In mice and also humans, the antiviral function of ISGs has been extensively studied. As an important viral reservoir in nature, bats can coexist with a variety of pathogenic viruses without overt signs of disease, yet only limited data are available for the role of ISGs in bats. There are multiple species of bats and work has begun deciphering the differences and similarities between ISG function of human/mouse and different bat species. This review summarizes the current knowledge of conserved and bat-specific-ISGs and their known antiviral effector functions.
Collapse
Affiliation(s)
- Dan Zhang
- Zhejiang University-University of Edinburgh Institute, Haining, China
| | - Aaron T. Irving
- Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Centre for Infection, Immunity & Cancer, Zhejiang University-University of Edinburgh Institute, Haining, China
- BIMET - Biomedical and Health Translational Research Centre of Zhejiang Province, China
- College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
14
|
Moon S, Namkoong S. Ribonucleoprotein Granules: Between Stress and Transposable Elements. Biomolecules 2023; 13:1027. [PMID: 37509063 PMCID: PMC10377603 DOI: 10.3390/biom13071027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Transposable elements (TEs) are DNA sequences that can transpose and replicate within the genome, leading to genetic changes that affect various aspects of host biology. Evolutionarily, hosts have also developed molecular mechanisms to suppress TEs at the transcriptional and post-transcriptional levels. Recent studies suggest that stress-induced formation of ribonucleoprotein (RNP) granules, including stress granule (SG) and processing body (P-body), can play a role in the sequestration of TEs to prevent transposition, suggesting an additional layer of the regulatory mechanism for TEs. RNP granules have been shown to contain factors involved in RNA regulation, including mRNA decay enzymes, RNA-binding proteins, and noncoding RNAs, which could potentially contribute to the regulation of TEs. Therefore, understanding the interplay between TEs and RNP granules is crucial for elucidating the mechanisms for maintaining genomic stability and controlling gene expression. In this review, we provide a brief overview of the current knowledge regarding the interplay between TEs and RNP granules, proposing RNP granules as a novel layer of the regulatory mechanism for TEs during stress.
Collapse
Affiliation(s)
- Sungjin Moon
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Sim Namkoong
- Department of Biochemistry, Kangwon National University, Chuncheon 24341, Republic of Korea
| |
Collapse
|
15
|
Granadillo Rodríguez M, Wong L, Chelico L. Similar deamination activities but different phenotypic outcomes induced by APOBEC3 enzymes in breast epithelial cells. Front Genome Ed 2023; 5:1196697. [PMID: 37324648 PMCID: PMC10267419 DOI: 10.3389/fgeed.2023.1196697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
APOBEC3 (A3) enzymes deaminate cytosine to uracil in viral single-stranded DNA as a mutagenic barrier for some viruses. A3-induced deaminations can also occur in human genomes resulting in an endogenous source of somatic mutations in multiple cancers. However, the roles of each A3 are unclear since few studies have assessed these enzymes in parallel. Thus, we developed stable cell lines expressing A3A, A3B, or A3H Hap I using non-tumorigenic MCF10A and tumorigenic MCF7 breast epithelial cells to assess their mutagenic potential and cancer phenotypes in breast cells. The activity of these enzymes was characterized by γH2AX foci formation and in vitro deamination. Cell migration and soft agar colony formation assays assessed cellular transformation potential. We found that all three A3 enzymes had similar γH2AX foci formation, despite different deamination activities in vitro. Notably, in nuclear lysates, the in vitro deaminase activity of A3A, A3B, and A3H did not require digestion of cellular RNA, in contrast to that of A3B and A3H in whole-cell lysates. Their similar activities in cells, nonetheless, resulted in distinct phenotypes where A3A decreased colony formation in soft agar, A3B decreased colony formation in soft agar after hydroxyurea treatment, and A3H Hap I promoted cell migration. Overall, we show that in vitro deamination data do not always reflect cell DNA damage, all three A3s induce DNA damage, and the impact of each is different.
Collapse
|
16
|
Göttig L, Weiß C, Stubbe M, Hanrieder L, Hofmann S, Grodziecki A, Stadler D, Carpentier A, Protzer U, Schreiner S. Apobec3A Deamination Functions Are Involved in Antagonizing Efficient Human Adenovirus Replication and Gene Expression. mBio 2023:e0347822. [PMID: 37154747 DOI: 10.1128/mbio.03478-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Apobec3A is involved in the antiviral host defense, targeting nuclear DNA, introducing point mutations, and thereby activating DNA damage response (DDR). Here, we found a significant upregulation of Apobec3A during HAdV infection, including Apobec3A protein stabilization mediated by the viral proteins E1B-55K and E4orf6, which subsequently limited HAdV replication and most likely involved a deaminase-dependent mechanism. The transient silencing of Apobec3A enhanced adenoviral replication. HAdV triggered Apobec3A dimer formation and enhanced activity to repress the virus. Apobec3A decreased E2A SUMOylation and interfered with viral replication centers. A comparative sequence analysis revealed that HAdV types A, C, and F may have evolved a strategy to escape Apobec3A-mediated deamination via reduced frequencies of TC dinucleotides within the viral genome. Although viral components induce major changes within infected cells to support lytic life cycles, our findings demonstrate that host Apobec3A-mediated restriction limits virus replication, albeit that HAdV may have evolved to escape this restriction. This allows for novel insights into the HAdV/host-cell interplay, which broaden the current view of how a host cell can limit HAdV infection. IMPORTANCE Our data provide a novel conceptual insight into the virus/host-cell interplay, changing the current view of how a host-cell can defeat a virus infection. Thus, our study reveals a novel and general impact of cellular Apobec3A on the intervention of human adenovirus (HAdV) gene expression and replication by improving the host antiviral defense mechanisms, thereby providing a novel basis for innovative antiviral strategies in future therapeutic settings. Ongoing investigations of the cellular pathways that are modulated by HAdV are of great interest, particularly since adenovirus-based vectors actually serve as COVID vaccine vectors and also frequently serve as tools in human gene therapy and oncolytic treatment options. HAdV constitute an ideal model system by which to analyze the transforming capabilities of DNA tumor viruses as well as the underlying molecular principles of virus-induced and cellular tumorigenesis.
Collapse
Affiliation(s)
- Lilian Göttig
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christina Weiß
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Miona Stubbe
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Lisa Hanrieder
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Samuel Hofmann
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (Resolving Infection Susceptibility; EXC 2155), Hannover Medical School, Hannover, Germany
| | - Alessandro Grodziecki
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (Resolving Infection Susceptibility; EXC 2155), Hannover Medical School, Hannover, Germany
| | - Daniela Stadler
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | | | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Sabrina Schreiner
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Munich, Germany
- Cluster of Excellence RESIST (Resolving Infection Susceptibility; EXC 2155), Hannover Medical School, Hannover, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| |
Collapse
|
17
|
Britan-Rosich Y, Ma J, Kotler E, Hassan F, Botvinnik A, Smith Y, Moshel O, Nasereddin A, Sharma G, Pikarsky E, Ross S, Kotler M. APOBEC3G protects the genome of human cultured cells and mice from radiation-induced damage. FEBS J 2023; 290:1822-1839. [PMID: 36325681 PMCID: PMC10079569 DOI: 10.1111/febs.16673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/14/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
Abstract
Cytosine deaminases AID/APOBEC proteins act as potent nucleic acid editors, playing important roles in innate and adaptive immunity. However, the mutagenic effects of some of these proteins compromise genomic integrity and may promote tumorigenesis. Here, we demonstrate that human APOBEC3G (A3G), in addition to its role in innate immunity, promotes repair of double-strand breaks (DSBs) in vitro and in vivo. Transgenic mice expressing A3G successfully survived lethal irradiation, whereas wild-type controls quickly succumbed to radiation syndrome. Mass spectrometric analyses identified the differential upregulation of a plethora of proteins involved in DSB repair pathways in A3G-expressing cells early following irradiation to facilitate repair. Importantly, we find that A3G not only accelerates DSB repair but also promotes deamination-dependent error-free rejoining. These findings have two implications: (a) strategies aimed at inhibiting A3G may improve the efficacy of genotoxic therapies used to cure malignant tumours; and (b) enhancing A3G activity may reduce acute radiation syndrome in individuals exposed to ionizing radiation.
Collapse
Affiliation(s)
- Yelena Britan-Rosich
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Jing Ma
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, USA
| | - Eran Kotler
- Department of Genetics, Stanford University School of Medicine, Ca, USA
| | - Faizan Hassan
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Alexander Botvinnik
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Yoav Smith
- Genomic Data Analysis, Hadassah Medical School, Hebrew University, Jerusalem, Israel
| | - Ofra Moshel
- Core Research Facility, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Abed Nasereddin
- Core Research Facility of the Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Gunjan Sharma
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Eli Pikarsky
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Susan Ross
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, USA
| | - Moshe Kotler
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| |
Collapse
|
18
|
Jones KM, Shehata M, Carpenter MA, Amaro RE, Harki DA. APOBEC3A Catalytic Inactivity Mutation Induces Tertiary Structure Destabilization. ACS Med Chem Lett 2023; 14:338-343. [PMID: 36923917 PMCID: PMC10009786 DOI: 10.1021/acsmedchemlett.2c00517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/03/2023] [Indexed: 02/16/2023] Open
Abstract
APOBEC3A (A3A)-catalyzed DNA cytosine deamination is implicated in virus and cancer mutagenesis, and A3A is a target for small molecule drug discovery. The catalytic glutamic acid (E72) is frequently mutated in biochemical studies to characterize deamination-dependent versus deamination-independent A3A functions. Additionally, catalytically active A3A is toxic in bacterial expression systems, which adversely affects yield during recombinant A3A expression. Here, we demonstrate that mutating the catalytic glutamic acid to an isosteric glutamine (E72Q) significantly decreases the thermal stability of the protein, compared to the alanine-inactivating mutation (E72A). Differential scanning fluorimetry and mass spectrometry reveal that A3A E72Q is less thermally stable than A3A E72A or wild-type A3A. Strikingly, A3A E72Q is partially denatured at 37 °C and binds single-stranded DNA with significantly poorer affinity compared to A3A E72A. This study constitutes an important cautionary note on A3A protein design and informs that A3A E72A is the preferred catalytic inactivation mutation for most applications.
Collapse
Affiliation(s)
- Katherine
F. M. Jones
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mohamed Shehata
- Department
of Chemistry and Biochemistry, University
of California − San Diego, La Jolla, California 92093, United States
| | - Michael A. Carpenter
- Department
of Biochemistry & Structural Biology, University of Texas Health Science Center San Antonio, San Antonio, Texas 78229, United States
| | - Rommie E. Amaro
- Department
of Chemistry and Biochemistry, University
of California − San Diego, La Jolla, California 92093, United States
| | - Daniel A. Harki
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
19
|
Warkocki Z. An update on post-transcriptional regulation of retrotransposons. FEBS Lett 2023; 597:380-406. [PMID: 36460901 DOI: 10.1002/1873-3468.14551] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/09/2022] [Accepted: 11/18/2022] [Indexed: 12/04/2022]
Abstract
Retrotransposons, including LINE-1, Alu, SVA, and endogenous retroviruses, are one of the major constituents of human genomic repetitive sequences. Through the process of retrotransposition, some of them occasionally insert into new genomic locations by a copy-paste mechanism involving RNA intermediates. Irrespective of de novo genomic insertions, retrotransposon expression can lead to DNA double-strand breaks and stimulate cellular innate immunity through endogenous patterns. As a result, retrotransposons are tightly regulated by multi-layered regulatory processes to prevent the dangerous effects of their expression. In recent years, significant progress was made in revealing how retrotransposon biology intertwines with general post-transcriptional RNA metabolism. Here, I summarize current knowledge on the involvement of post-transcriptional factors in the biology of retrotransposons, focusing on LINE-1. I emphasize general RNA metabolisms such as methylation of adenine (m6 A), RNA 3'-end polyadenylation and uridylation, RNA decay and translation regulation. I discuss the effects of retrotransposon RNP sequestration in cytoplasmic bodies and autophagy. Finally, I summarize how innate immunity restricts retrotransposons and how retrotransposons make use of cellular enzymes, including the DNA repair machinery, to complete their replication cycles.
Collapse
Affiliation(s)
- Zbigniew Warkocki
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| |
Collapse
|
20
|
Li Y, Tang M, Zhang FJ, Huang Y, Zhang J, Li J, Wang Y, Yang J, Zhu S. Screening of ulcerative colitis biomarkers and potential pathways based on weighted gene co-expression network, machine learning and ceRNA hypothesis. Hereditas 2022; 159:42. [PMID: 36419192 PMCID: PMC9685902 DOI: 10.1186/s41065-022-00259-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/12/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Ulcerative colitis (UC) refers to an intractable intestinal inflammatory disease. Its increasing incidence rate imposes a huge burden on patients and society. The UC etiology has not been determined, so screening potential biomarkers is critical to preventing disease progression and selecting optimal therapeutic strategies more effectively. METHODS The microarray datasets of intestinal mucosal biopsy of UC patients were selected from the GEO database, and integrated with R language to screen differentially expressed genes and draw proteins interaction network diagrams. GO, KEGG, DO and GSEA enrichment analyses were performed to explore their biological functions. Through machine learning and WGCNA analysis, targets that can be used as UC potential biomarkers are screened out. ROC curves were drawn to verify the reliability of the results and predicted the mechanism of marker genes from the aspects of immune cell infiltration, co-expression analysis, and competitive endogenous network (ceRNA). RESULTS Two datasets GSE75214 and GSE87466 were integrated for screening, and a total of 107 differentially expressed genes were obtained. They were mainly related to biological functions such as humoral immune response and inflammatory response. Further screened out five marker genes, and found that they were associated with M0 macrophages, quiescent mast cells, M2 macrophages, and activated NK cells in terms of immune cell infiltration. The co-expression network found significant co-expression relationships between 54 miRNAs and 5 marker genes. According to the ceRNA hypothesis, NEAT1-miR-342-3p/miR-650-SLC6A14, NEAT1-miR-650-IRAK3, and XIST-miR-342-3p-IRAK3 axes were found as potential regulatory pathways in UC. CONCLUSION This study screened out five biomarkers that can be used for the diagnosis and treatment of UC, namely SLC6A14, TIMP1, IRAK3, HMGCS2, and APOBEC3B. Confirmed that they play a role in the occurrence and development of UC at the level of immune infiltration, and proposed a potential RNA regulatory pathway that controls the progression of UC.
Collapse
Affiliation(s)
- Ying Li
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China ,grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, The First College for Clinical Medicine, Jinan, China
| | - Mengyao Tang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Innovation and Research of Traditional Chinese Medicine, Jinan, 250000 China
| | - Feng Jun Zhang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China ,grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, The First College for Clinical Medicine, Jinan, China
| | - Yihan Huang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China
| | - Jing Zhang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China
| | - Junqi Li
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China
| | - Yunpeng Wang
- grid.479672.9Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Department of Gastroenterology, Jinan, China
| | - Jinguang Yang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, The First College for Clinical Medicine, Jinan, China
| | - Shu Zhu
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Innovation and Research of Traditional Chinese Medicine, Jinan, 250000 China
| |
Collapse
|
21
|
Tikhonov AS, Mintaev RR, Glazkova DV, Bogoslovskaya EV, Shipulin GA. HIV Restriction Factor APOBEC3G and Prospects for Its Use in Gene Therapy for HIV. Mol Biol 2022. [DOI: 10.1134/s0026893322040112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
22
|
Stenglein MD. The Case for Studying New Viruses of New Hosts. Annu Rev Virol 2022; 9:157-172. [PMID: 35671564 DOI: 10.1146/annurev-virology-100220-112915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Virology has largely focused on viruses that are pathogenic to humans or to the other species that we care most about. There is no doubt that this has been a worthwhile investment. But many transformative advances have been made through the in-depth study of relatively obscure viruses that do not appear on lists of prioritized pathogens. In this review, I highlight the benefits that can accrue from the study of viruses and hosts off the beaten track. I take stock of viral sequence diversity across host taxa as an estimate of the bias that exists in our understanding of host-virus interactions. I describe the gains that have been made through the metagenomic discovery of thousands of new viruses in previously unsampled hosts as well as the limitations of metagenomic surveys. I conclude by suggesting that the study of viruses that naturally infect existing and emerging model organisms represents an opportunity to push virology forward in useful and hard to predict ways.Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Mark D Stenglein
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA;
| |
Collapse
|
23
|
Taura M, Frank JA, Takahashi T, Kong Y, Kudo E, Song E, Tokuyama M, Iwasaki A. APOBEC3A regulates transcription from interferon-stimulated response elements. Proc Natl Acad Sci U S A 2022; 119:e2011665119. [PMID: 35549556 PMCID: PMC9171812 DOI: 10.1073/pnas.2011665119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 04/11/2022] [Indexed: 01/04/2023] Open
Abstract
APOBEC3A (A3A) is a cytidine deaminase that inactivates a variety of viruses through introduction of lethal mutations to the viral genome. Additionally, A3A can suppress HIV-1 transcription in a deaminase-independent manner by binding to the long terminal repeat of proviral HIV-1. However, it is unknown whether A3A targets additional host genomic loci for repression. In this study, we found that A3A suppresses gene expression by binding TTTC doublets that are in close proximity to each other. However, one TTTC motif is sufficient for A3A binding. Because TTTC doublets are present in interferon (IFN)-stimulated response elements (ISRE), we hypothesized that A3A may impact IFN-stimulated gene (ISG) expression. After scanning the human genome for TTTC doublet occurrences, we discovered that these motifs are enriched in the proximal promoters of genes associated with antiviral responses and type I IFN (IFN-I) signaling. As a proof of principle, we examined whether A3A can impact ISG15 expression. We found that A3A binding to the ISRE inhibits phosphorylated STAT-1 binding and suppresses ISG15 induction in response to IFN-I treatment. Consistent with these data, our RNA-sequencing analyses indicate that A3A loss results in increased IFN-I–dependent induction of several ISGs. This study revealed that A3A plays an unexpected role in ISG regulation and suggests that A3A contributes to a negative feedback loop during IFN signaling.
Collapse
Affiliation(s)
- Manabu Taura
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
- Laboratory of Bioresponse Regulation, Graduate School of Pharmaceutical Sciences, Osaka University, 565-0871 Suita, Japan
| | - John A. Frank
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Takehiro Takahashi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Yong Kong
- Department of Molecular Biophysics and Biochemistry, W. M. Keck Foundation Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, CT 06520
| | - Eriko Kudo
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Maria Tokuyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
- HHMI, Chevy Chase, MD 20815
| |
Collapse
|
24
|
Rheinemann L, Downhour DM, Davenport KA, McKeown AN, Sundquist WI, Elde NC. Recurrent evolution of an inhibitor of ESCRT-dependent virus budding and LINE-1 retrotransposition in primates. Curr Biol 2022; 32:1511-1522.e6. [PMID: 35245459 PMCID: PMC9007875 DOI: 10.1016/j.cub.2022.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 12/20/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022]
Abstract
Most antiviral proteins recognize specific features of viruses. In contrast, the recently described antiviral factor retroCHMP3 interferes with the "host endosomal complexes required for transport" (ESCRT) pathway to inhibit the budding of enveloped viruses. RetroCHMP3 arose independently on multiple occasions via duplication and truncation of the gene encoding the ESCRT-III factor CHMP3. However, since the ESCRT pathway is essential for cellular membrane fission reactions, ESCRT inhibition is potentially cytotoxic. This raises fundamental questions about how hosts can repurpose core cellular functions into antiviral functions without incurring a fitness cost due to excess cellular toxicity. We reveal the evolutionary process of detoxification for retroCHMP3 in New World monkeys using a combination of ancestral reconstructions, cytotoxicity, and virus release assays. A duplicated, full-length copy of retroCHMP3 in the ancestors of New World monkeys provides modest inhibition of virus budding while exhibiting subtle cytotoxicity. Ancient retroCHMP3 then accumulated mutations that reduced cytotoxicity but preserved virus inhibition before a truncating stop codon arose in the more recent ancestors of squirrel monkeys, resulting in potent inhibition. In species where full-length copies of retroCHMP3 still exist, their artificial truncation generated potent virus-budding inhibitors with little cytotoxicity, revealing the potential for future antiviral defenses in modern species. In addition, we discovered that retroCHMP3 restricts LINE-1 retrotransposition, revealing how different challenges to genome integrity might explain multiple independent origins of retroCHMP3 in different species to converge on new immune functions.
Collapse
Affiliation(s)
- Lara Rheinemann
- Department of Biochemistry, University of Utah School of Medicine, 15 N Medical Drive East, Salt Lake City, UT 84112, USA
| | - Diane Miller Downhour
- Department of Human Genetics, University of Utah School of Medicine, 15 N 2030 E, Salt Lake City, UT 84112, USA
| | - Kristen A Davenport
- Department of Biochemistry, University of Utah School of Medicine, 15 N Medical Drive East, Salt Lake City, UT 84112, USA; Department of Human Genetics, University of Utah School of Medicine, 15 N 2030 E, Salt Lake City, UT 84112, USA
| | - Alesia N McKeown
- Department of Human Genetics, University of Utah School of Medicine, 15 N 2030 E, Salt Lake City, UT 84112, USA
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah School of Medicine, 15 N Medical Drive East, Salt Lake City, UT 84112, USA
| | - Nels C Elde
- Department of Human Genetics, University of Utah School of Medicine, 15 N 2030 E, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA.
| |
Collapse
|
25
|
DeWeerd RA, Németh E, Póti Á, Petryk N, Chen CL, Hyrien O, Szüts D, Green AM. Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers. Cell Rep 2022; 38:110555. [PMID: 35320711 PMCID: PMC9283007 DOI: 10.1016/j.celrep.2022.110555] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 12/15/2021] [Accepted: 03/02/2022] [Indexed: 12/14/2022] Open
Abstract
Mutational signatures defined by single base substitution (SBS) patterns in cancer have elucidated potential mutagenic processes that contribute to malignancy. Two prevalent mutational patterns in human cancers are attributed to the APOBEC3 cytidine deaminase enzymes. Among the seven human APOBEC3 proteins, APOBEC3A is a potent deaminase and proposed driver of cancer mutagenesis. In this study, we prospectively examine genome-wide aberrations by expressing human APOBEC3A in avian DT40 cells. From whole-genome sequencing, we detect hundreds to thousands of base substitutions per genome. The APOBEC3A signature includes widespread cytidine mutations and a unique insertion-deletion (indel) signature consisting largely of cytidine deletions. This multi-dimensional APOBEC3A signature is prevalent in human cancer genomes. Our data further reveal replication-associated mutations, the rate of stem-loop and clustered mutations, and deamination of methylated cytidines. This comprehensive signature of APOBEC3A mutagenesis is a tool for future studies and a potential biomarker for APOBEC3 activity in cancer.
Collapse
Affiliation(s)
- Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nataliya Petryk
- Epigenetics & Cell Fate UMR7216, CNRS, University of Paris, 35 rue Hélène Brion, 75013 Paris, France
| | - Chun-Long Chen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, France
| | - Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d'Ulm, 75005 Paris, France
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
26
|
Chen Y, Luo L, Deng L, Tian X, Chen S, Xu A, Yuan S. New Insights Into the Lineage-Specific Expansion and Functional Diversification of Lamprey AID/APOBEC Family. Front Immunol 2022; 13:822616. [PMID: 35359986 PMCID: PMC8962628 DOI: 10.3389/fimmu.2022.822616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
The AID/APOBEC family which converts cytidine to uridine on RNA or DNA experienced dynamic expansion in primates in order to resist exogenous viruses and endogenous retrotransposons. Recently, expansion of AID/APOBEC-like homologs has also been observed in the extant jawless vertebrate lamprey. To reveal what causes such expansion and leads to the functional diversification of lamprey cytosine deaminases (CDAs), we reassessed the CDA genes in Lethenteron japonicum (Lj). We first confirmed the expansion of LjCDA1L1 (CDA1-like 1) genes and found the expression correlation of LjCDA2 and LjCDA1L2 with LjVLRs (variable lymphocyte receptors). Among up to 14 LjCDA1L1 proteins, LjCDA1L1_4a has an extremely high deamination activity on ssDNA and buDNA and, unexpectedly, on dsDNA. LjCDA1L1s can also restrict the infection of HSV-1 particles. Thus, the arms race between the host and pathogens along with the recruitment by VLR assembly may participate together to form a driving force in the expansion and diversification of the lamprey AID/APOBEC family.
Collapse
Affiliation(s)
- Yan Chen
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Laboratory of Ocean Science and Engineering (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lingjie Luo
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Laboratory of Ocean Science and Engineering (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lisi Deng
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Laboratory of Ocean Science and Engineering (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaoxue Tian
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Laboratory of Ocean Science and Engineering (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shangwu Chen
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Laboratory of Ocean Science and Engineering (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Anlong Xu
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Laboratory of Ocean Science and Engineering (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Shaochun Yuan, ; Anlong Xu,
| | - Shaochun Yuan
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Laboratory of Ocean Science and Engineering (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Shaochun Yuan, ; Anlong Xu,
| |
Collapse
|
27
|
The current toolbox for APOBEC drug discovery. Trends Pharmacol Sci 2022; 43:362-377. [PMID: 35272863 PMCID: PMC9018551 DOI: 10.1016/j.tips.2022.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/03/2022] [Accepted: 02/09/2022] [Indexed: 12/14/2022]
Abstract
Mutational processes driving genome evolution and heterogeneity contribute to immune evasion and therapy resistance in viral infections and cancer. APOBEC3 (A3) enzymes promote such mutations by catalyzing the deamination of cytosines to uracils in single-stranded DNA. Chemical inhibition of A3 enzymes may yield an antimutation therapeutic strategy to improve the durability of current drug therapies that are prone to resistance mutations. A3 small-molecule drug discovery efforts to date have been restricted to a single high-throughput biochemical activity assay; however, the arsenal of discovery assays has significantly expanded in recent years. The assays used to study A3 enzymes are reviewed here with an eye towards their potential for small-molecule discovery efforts.
Collapse
|
28
|
Shilova ON, Tsyba DL, Shilov ES. Mutagenic Activity of AID/APOBEC Deaminases in Antiviral Defense and Carcinogenesis. Mol Biol 2022; 56:46-58. [PMID: 35194245 PMCID: PMC8852905 DOI: 10.1134/s002689332201006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/23/2021] [Accepted: 06/01/2021] [Indexed: 01/02/2023]
Abstract
Proteins of the AID/APOBEC family are capable of cytidine deamination in nucleic acids forming uracil. These enzymes are involved in mRNA editing, protection against viruses, the introduction of point mutations into DNA during somatic hypermutation, and antibody isotype switching. Since these deaminases, especially AID, are potent mutagens, their expression, activity, and specificity are regulated by several intracellular mechanisms. In this review, we discuss the mechanisms of impaired expression and activation of AID/APOBEC proteins in human tumors and their role in carcinogenesis and tumor progression. Also, the diagnostic and potential therapeutic value of increased expression of AID/APOBEC in different types of tumors is analyzed. We assume that in the case of solid tumors, increased expression of endogenous deaminases can serve as a marker of response to immunotherapy since multiple point mutations in host DNA could lead to amino acid substitutions in tumor proteins and thereby increase the frequency of neoepitopes.
Collapse
Affiliation(s)
- O. N. Shilova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - D. L. Tsyba
- Pavlov First State Medical University, 197022 St. Petersburg, Russia
- Sirius University of Science and Technology, 354340 Sochi, Russia
| | - E. S. Shilov
- Faculty of Biology, Moscow State University, 119234 Moscow, Russia
| |
Collapse
|
29
|
Bergstrom EN, Luebeck J, Petljak M, Khandekar A, Barnes M, Zhang T, Steele CD, Pillay N, Landi MT, Bafna V, Mischel PS, Harris RS, Alexandrov LB. Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA. Nature 2022; 602:510-517. [PMID: 35140399 PMCID: PMC8850194 DOI: 10.1038/s41586-022-04398-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 01/04/2022] [Indexed: 12/28/2022]
Abstract
Clustered somatic mutations are common in cancer genomes and previous analyses reveal several types of clustered single-base substitutions, which include doublet- and multi-base substitutions1-5, diffuse hypermutation termed omikli6, and longer strand-coordinated events termed kataegis3,7-9. Here we provide a comprehensive characterization of clustered substitutions and clustered small insertions and deletions (indels) across 2,583 whole-genome-sequenced cancers from 30 types of cancer10. Clustered mutations were highly enriched in driver genes and associated with differential gene expression and changes in overall survival. Several distinct mutational processes gave rise to clustered indels, including signatures that were enriched in tobacco smokers and homologous-recombination-deficient cancers. Doublet-base substitutions were caused by at least 12 mutational processes, whereas most multi-base substitutions were generated by either tobacco smoking or exposure to ultraviolet light. Omikli events, which have previously been attributed to APOBEC3 activity6, accounted for a large proportion of clustered substitutions; however, only 16.2% of omikli matched APOBEC3 patterns. Kataegis was generated by multiple mutational processes, and 76.1% of all kataegic events exhibited mutational patterns that are associated with the activation-induced deaminase (AID) and APOBEC3 family of deaminases. Co-occurrence of APOBEC3 kataegis and extrachromosomal DNA (ecDNA), termed kyklonas (Greek for cyclone), was found in 31% of samples with ecDNA. Multiple distinct kyklonic events were observed on most mutated ecDNA. ecDNA containing known cancer genes exhibited both positive selection and kyklonic hypermutation. Our results reveal the diversity of clustered mutational processes in human cancer and the role of APOBEC3 in recurrently mutating and fuelling the evolution of ecDNA.
Collapse
Affiliation(s)
- Erik N Bergstrom
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Mia Petljak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher D Steele
- Research Department of Pathology, Cancer Institute, University College London, London, UK
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
| | - Reuben S Harris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
30
|
DeWeerd R, Green AM. Qualitative and Quantitative Analysis of DNA Cytidine Deaminase Activity. Methods Mol Biol 2022; 2444:161-169. [PMID: 35290637 DOI: 10.1007/978-1-0716-2063-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The human genome encodes eleven DNA cytidine deaminases in the AID/APOBEC family, which encompass endogenous roles ranging from genetic diversification of the immunoglobulin locus to virus restriction. All AID/APOBEC functions are enabled by their catalyzation of cytidine deamination resulting in mutations and DNA damage. When acting aberrantly, deaminases can cause off-target mutations in the cellular genome resulting in somatic mutations, DNA damage, and genome instability. An association between cytidine deaminase-induced mutations and human cancers has been recognized over the last decade, necessitating assays for investigation of intracellular deaminase activity. Here we present two assays for deamination activity which enable in vitro evaluation of in vivo events. We define both a qualitative assay to confirm deaminase activity within cells as well as a quantitative assay for granular evaluation and comparisons of deamination activity across different cell populations or experimental conditions. The two procedures are customizable assays which can easily be adapted to individual labs and experiments.
Collapse
Affiliation(s)
- Rachel DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
31
|
Wörmann SM, Zhang A, Thege FI, Cowan RW, Rupani DN, Wang R, Manning SL, Gates C, Wu W, Levin-Klein R, Rajapakshe KI, Yu M, Multani AS, Kang Y, Taniguchi CM, Schlacher K, Bellin MD, Katz MHG, Kim MP, Fleming JB, Gallinger S, Maddipati R, Harris RS, Notta F, Ross SR, Maitra A, Rhim AD. APOBEC3A drives deaminase domain-independent chromosomal instability to promote pancreatic cancer metastasis. NATURE CANCER 2021; 2:1338-1356. [PMID: 35121902 DOI: 10.1038/s43018-021-00268-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023]
Abstract
Despite efforts in understanding its underlying mechanisms, the etiology of chromosomal instability (CIN) remains unclear for many tumor types. Here, we identify CIN initiation as a previously undescribed function for APOBEC3A (A3A), a cytidine deaminase upregulated across cancer types. Using genetic mouse models of pancreatic ductal adenocarcinoma (PDA) and genomics analyses in human tumor cells we show that A3A-induced CIN leads to aggressive tumors characterized by enhanced early dissemination and metastasis in a STING-dependent manner and independently of the canonical deaminase functions of A3A. We show that A3A upregulation recapitulates numerous copy number alterations commonly observed in patients with PDA, including co-deletions in DNA repair pathway genes, which in turn render these tumors susceptible to poly (ADP-ribose) polymerase inhibition. Overall, our results demonstrate that A3A plays an unexpected role in PDA as a specific driver of CIN, with significant effects on disease progression and treatment.
Collapse
Affiliation(s)
- Sonja M Wörmann
- Ahmed Cancer Center for Pancreatic Cancer Research, MD Anderson Cancer Center, University of Texas, Houston, TX, USA.
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, University of Texas, Houston, TX, USA.
| | - Amy Zhang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fredrik I Thege
- Ahmed Cancer Center for Pancreatic Cancer Research, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Robert W Cowan
- Ahmed Cancer Center for Pancreatic Cancer Research, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
- Department of Gastroenterology, Hepatology & Nutrition, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Dhwani N Rupani
- Ahmed Cancer Center for Pancreatic Cancer Research, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
- Department of Gastroenterology, Hepatology & Nutrition, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Runsheng Wang
- Ahmed Cancer Center for Pancreatic Cancer Research, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
- Department of Gastroenterology, Hepatology & Nutrition, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Sara L Manning
- Ahmed Cancer Center for Pancreatic Cancer Research, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
- Department of Gastroenterology, Hepatology & Nutrition, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Chris Gates
- BRCF Bioinformatics Core, University of Michigan, School of Medicine, Ann Arbor, MI, USA
| | - Weisheng Wu
- BRCF Bioinformatics Core, University of Michigan, School of Medicine, Ann Arbor, MI, USA
| | - Rena Levin-Klein
- 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
| | - Kimal I Rajapakshe
- Ahmed Cancer Center for Pancreatic Cancer Research, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Meifang Yu
- Department of Experimental Radiation Oncology, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Asha S Multani
- Department of Genetics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Ya'an Kang
- Department of Surgical Oncology, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Cullen M Taniguchi
- Department of Experimental Radiation Oncology, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Katharina Schlacher
- Department of Cancer Biology, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melena D Bellin
- University of Minnesota Medical Center, Schulze Diabetes Institute, Minneapolis, MN, USA
| | - Matthew H G Katz
- Department of Surgical Oncology, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Michael P Kim
- Department of Surgical Oncology, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Jason B Fleming
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | | | - Ravikanth Maddipati
- Department of Internal Medicine and Hamon Center for Therapeutic Oncology Research and Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - 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
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Susan R Ross
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Anirban Maitra
- Ahmed Cancer Center for Pancreatic Cancer Research, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Andrew D Rhim
- Ahmed Cancer Center for Pancreatic Cancer Research, MD Anderson Cancer Center, University of Texas, Houston, TX, USA.
- Department of Gastroenterology, Hepatology & Nutrition, MD Anderson Cancer Center, University of Texas, Houston, TX, USA.
| |
Collapse
|
32
|
Rapti K, Grimm D. Adeno-Associated Viruses (AAV) and Host Immunity - A Race Between the Hare and the Hedgehog. Front Immunol 2021; 12:753467. [PMID: 34777364 PMCID: PMC8586419 DOI: 10.3389/fimmu.2021.753467] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022] Open
Abstract
Adeno-associated viruses (AAV) have emerged as the lead vector in clinical trials and form the basis for several approved gene therapies for human diseases, mainly owing to their ability to sustain robust and long-term in vivo transgene expression, their amenability to genetic engineering of cargo and capsid, as well as their moderate toxicity and immunogenicity. Still, recent reports of fatalities in a clinical trial for a neuromuscular disease, although linked to an exceptionally high vector dose, have raised new caution about the safety of recombinant AAVs. Moreover, concerns linger about the presence of pre-existing anti-AAV antibodies in the human population, which precludes a significant percentage of patients from receiving, and benefitting from, AAV gene therapies. These concerns are exacerbated by observations of cellular immune responses and other adverse events, including detrimental off-target transgene expression in dorsal root ganglia. Here, we provide an update on our knowledge of the immunological and molecular race between AAV (the “hedgehog”) and its human host (the “hare”), together with a compendium of state-of-the-art technologies which provide an advantage to AAV and which, thus, promise safer and more broadly applicable AAV gene therapies in the future.
Collapse
Affiliation(s)
- Kleopatra Rapti
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, Heidelberg, Germany.,BioQuant Center, BQ0030, University of Heidelberg, Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, Heidelberg, Germany.,BioQuant Center, BQ0030, University of Heidelberg, Heidelberg, Germany.,German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF) and German Center for Cardiovascular Research Deutsches Zentrum für Herz-Kreislauf-Erkrankungen (DZHK), Partner Site Heidelberg, Heidelberg, Germany
| |
Collapse
|
33
|
Ramos KS, Bojang P, Bowers E. Role of long interspersed nuclear element-1 in the regulation of chromatin landscapes and genome dynamics. Exp Biol Med (Maywood) 2021; 246:2082-2097. [PMID: 34304633 PMCID: PMC8524765 DOI: 10.1177/15353702211031247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 12/27/2022] Open
Abstract
LINE-1 retrotransposon, the most active mobile element of the human genome, is subject to tight regulatory control. Stressful environments and disease modify the recruitment of regulatory proteins leading to unregulated activation of LINE-1. The activation of LINE-1 influences genome dynamics through altered chromatin landscapes, insertion mutations, deletions, and modulation of cellular plasticity. To date, LINE-1 retrotransposition has been linked to various cancer types and may in fact underwrite the genetic basis of various other forms of chronic human illness. The occurrence of LINE-1 polymorphisms in the human population may define inter-individual differences in susceptibility to disease. This review is written in honor of Dr Peter Stambrook, a friend and colleague who carried out highly impactful cancer research over many years of professional practice. Dr Stambrook devoted considerable energy to helping others live up to their full potential and to navigate the complexities of professional life. He was an inspirational leader, a strong advocate, a kind mentor, a vocal supporter and cheerleader, and yes, a hard critic and tough friend when needed. His passionate stand on issues, his witty sense of humor, and his love for humanity have left a huge mark in our lives. We hope that that the knowledge summarized here will advance our understanding of the role of LINE-1 in cancer biology and expedite the development of innovative cancer diagnostics and treatments in the ways that Dr Stambrook himself had so passionately envisioned.
Collapse
Affiliation(s)
- Kenneth S Ramos
- Institute of Biosciences and Technology, Texas A&M Health, Houston, TX 77030, USA
| | - Pasano Bojang
- University of Kentucky College of Medicine, Lexington, KY 40506, USA
| | - Emma Bowers
- Institute of Biosciences and Technology, Texas A&M Health, Houston, TX 77030, USA
| |
Collapse
|
34
|
Caval V, Suspène R, Khalfi P, Gaillard J, Caignard G, Vitour D, Roingeard P, Vartanian JP, Wain-Hobson S. Frame-shifted APOBEC3A encodes two alternative proapoptotic proteins that target the mitochondrial network. J Biol Chem 2021; 297:101081. [PMID: 34403699 PMCID: PMC8424220 DOI: 10.1016/j.jbc.2021.101081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/02/2022] Open
Abstract
The human APOBEC3A (A3A) cytidine deaminase is a powerful DNA mutator enzyme recognized as a major source of somatic mutations in tumor cell genomes. However, there is a discrepancy between APOBEC3A mRNA levels after interferon stimulation in myeloid cells and A3A detection at the protein level. To understand this difference, we investigated the expression of two novel alternative “A3Alt” proteins encoded in the +1-shifted reading frame of the APOBEC3A gene. A3Alt-L and its shorter isoform A3Alt-S appear to be transmembrane proteins targeted to the mitochondrial compartment that induce membrane depolarization and apoptosis. Thus, the APOBEC3A gene represents a new example wherein a single gene encodes two proapoptotic proteins, A3A cytidine deaminases that target the genome and A3Alt proteins that target mitochondria.
Collapse
Affiliation(s)
- Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France.
| | | | - Pierre Khalfi
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France; Sorbonne Université, Complexité du Vivant, ED515, Paris, France
| | - Julien Gaillard
- Morphogenèse et Antigénicité du VIH et des Virus des Hépatites, Inserm-U1259 MAVIVH, Université de Tours and CHRU de Tours, Tours, France; Plate-Forme IBiSA des Microscopies, PPF ASB, Université de Tours and CHRU de Tours, Tours, France
| | - Grégory Caignard
- UMR Virologie, INRAE, Ecole Nationale Vétérinaire d'Alfort, Laboratoire de santé animale d'Alfort, Anses, Université Paris-Est, Maisons-Alfort, France
| | - Damien Vitour
- UMR Virologie, INRAE, Ecole Nationale Vétérinaire d'Alfort, Laboratoire de santé animale d'Alfort, Anses, Université Paris-Est, Maisons-Alfort, France
| | - Philippe Roingeard
- Morphogenèse et Antigénicité du VIH et des Virus des Hépatites, Inserm-U1259 MAVIVH, Université de Tours and CHRU de Tours, Tours, France; Plate-Forme IBiSA des Microscopies, PPF ASB, Université de Tours and CHRU de Tours, Tours, France
| | | | | |
Collapse
|
35
|
Green AM, DeWeerd RA, O'Leary DR, Hansen AR, Hayer KE, Kulej K, Dineen AS, Szeto JH, Garcia BA, Weitzman MD. Interaction with the CCT chaperonin complex limits APOBEC3A cytidine deaminase cytotoxicity. EMBO Rep 2021; 22:e52145. [PMID: 34347354 DOI: 10.15252/embr.202052145] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 11/09/2022] Open
Abstract
The APOBEC3 cytidine deaminases are implicated as the cause of a prevalent somatic mutation pattern found in cancer genomes. The APOBEC3 enzymes act as viral restriction factors by mutating viral genomes. Mutation of the cellular genome is presumed to be an off-target activity of the enzymes, although the regulatory measures for APOBEC3 expression and activity remain undefined. It is therefore difficult to predict circumstances that enable APOBEC3 interaction with cellular DNA that leads to mutagenesis. The APOBEC3A (A3A) enzyme is the most potent deaminase of the family. Using proteomics, we evaluate protein interactors of A3A to identify potential regulators. We find that A3A interacts with the chaperonin-containing TCP-1 (CCT) complex, a cellular machine that assists in protein folding and function. Importantly, depletion of CCT results in A3A-induced DNA damage and cytotoxicity. Evaluation of cancer genomes demonstrates an enrichment of A3A mutational signatures in cancers with silencing mutations in CCT subunit genes. Together, these data suggest that the CCT complex interacts with A3A, and that disruption of CCT function results in increased A3A mutational activity.
Collapse
Affiliation(s)
- Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - David R O'Leary
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ava R Hansen
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Katharina E Hayer
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katarzyna Kulej
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ariel S Dineen
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Julia H Szeto
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| |
Collapse
|
36
|
Sadeghpour S, Khodaee S, Rahnama M, Rahimi H, Ebrahimi D. Human APOBEC3 Variations and Viral Infection. Viruses 2021; 13:1366. [PMID: 34372572 PMCID: PMC8310219 DOI: 10.3390/v13071366] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
Human APOBEC3 (apolipoprotein B mRNA-editing catalytic polypeptide-like 3) enzymes are capable of inhibiting a wide range of endogenous and exogenous viruses using deaminase and deaminase-independent mechanisms. These enzymes are essential components of our innate immune system, as evidenced by (a) their strong positive selection and expansion in primates, (b) the evolution of viral counter-defense mechanisms, such as proteasomal degradation mediated by HIV Vif, and (c) hypermutation and inactivation of a large number of integrated HIV-1 proviruses. Numerous APOBEC3 single nucleotide polymorphisms, haplotypes, and splice variants have been identified in humans. Several of these variants have been reported to be associated with differential antiviral immunity. This review focuses on the current knowledge in the field about these natural variations and their roles in infectious diseases.
Collapse
Affiliation(s)
- Shiva Sadeghpour
- Department of Biological Science, University of California Irvine, Irvine, CA 92697, USA;
| | - Saeideh Khodaee
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran;
| | - Mostafa Rahnama
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA;
| | - Hamzeh Rahimi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran;
| | - Diako Ebrahimi
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| |
Collapse
|
37
|
Infection of Bronchial Epithelial Cells by the Human Adenoviruses A12, B3, and C2 Differently Regulates the Innate Antiviral Effector APOBEC3B. J Virol 2021; 95:e0241320. [PMID: 33853956 DOI: 10.1128/jvi.02413-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Human adenoviruses (HAdVs) are a large family of DNA viruses that include more than 100 genotypes divided into seven species (A to G) and induce respiratory tract infections, gastroenteritis, and conjunctivitis. Genetically modified adenoviruses are also used as vaccines, gene therapies, and anticancer treatments. The APOBEC3s are a family of cytidine deaminases that restrict viruses by introducing mutations in their genomes. Viruses developed different strategies to cope with the APOBEC3 selection pressure, but nothing is known on the interplay between the APOBEC3s and the HAdVs. In this study, we focused on three HAdV strains: the B3 and C2 strains, as they are very frequent, and the A12 strain, which is less common but is oncogenic in animal models. We demonstrated that the three HAdV strains induce a similar APOBEC3B upregulation at the transcriptional level. At the protein level, however, APOBEC3B is abundantly expressed during HAdV-A12 and -C2 infection and shows a nuclear distribution. On the contrary, APOBEC3B is barely detectable in HAdV-B3-infected cells. APOBEC3B deaminase activity is detected in total protein extracts upon HAdV-A12 and -C2 infection. Bioinformatic analysis demonstrates that the HAdV-A12 genome bears a stronger APOBEC3 evolutionary footprint than that of the HAdV-C2 and HAdV-B3 genomes. Our results show that HAdV infection triggers the transcriptional upregulation of the antiviral innate effector APOBEC3B. The discrepancies between the APOBEC3B mRNA and protein levels might reflect the ability of some HAdV strains to antagonize the APOBEC3B protein. These findings point toward an involvement of APOBEC3B in HAdV restriction and evolution. IMPORTANCE The APOBEC3 family of cytosine deaminases has important roles in antiviral innate immunity and cancer. Notably, APOBEC3A and APOBEC3B are actively upregulated by several DNA tumor viruses and contribute to transformation by introducing mutations in the cellular genome. Human adenoviruses (HAdVs) are a large family of DNA viruses that cause generally asymptomatic infections in immunocompetent adults. HAdVs encode several oncogenes, and some HAdV strains, like HAdV-A12, induce tumors in hamsters and mice. Here, we show that HAdV infection specifically promotes the expression of the APOBEC3B gene. We report that infection with the A12 strain induces a strong expression of an enzymatically active APOBEC3B protein in bronchial epithelial cells. We provide bioinformatic evidence that HAdVs' genomes and notably the A12 genome are under APOBEC3 selection pressure. Thus, APOBEC3B might contribute to adenoviral restriction, diversification, and oncogenic potential of particular strains.
Collapse
|
38
|
Tang G, Xie B, Hong X, Qin H, Wang J, Huang H, Hao P, Li X. Creating RNA Specific C-to-U Editase from APOBEC3A by Separation of Its Activities on DNA and RNA Substrates. ACS Synth Biol 2021; 10:1106-1115. [PMID: 33938211 DOI: 10.1021/acssynbio.0c00627] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
APOBEC3A (A3A) is a cytidine deaminase involved in innate immune response and is able to catalyze deamination on both DNA and RNA substrates. It was used in creating the CRISPR-mediated base editor, but has since been held back due to its dual activities. On the other hand, it has been a challenge to separate A3A's dual activities in order to enable it for single-base RNA editors. Here we developed the reporter system for C-to-U RNA editing and employed rational design for mutagenesis to differentiate deaminase activities on RNA and DNA substrates to obtain an RNA-specific editase. Generation and examination of 23 previous A3A mutants showed their deamination activity on RNA was mostly abolished when their activity on DNA was impaired, with the exception of mutant N57Q that displayed an inverse change. We designed new mutations on Loops 1 and 7 based on A3A's crystal structure and found mutants H29R and Y132G had differential effects on catalytic activity on RNA and DNA substrates. In order to engineer an A3A with RNA-specific deaminase activity, we combined Y132G with mutations in Loop 1 or helix 6 by rational design. Two multipoint mutants, Y132G/K30R and Y132G/G188A/R189A/L190A, were successful in retaining high deaminase activity on RNA substrate while eliminating deaminase activity on DNA. We, for the first time, created novel human A3A variants with RNA-specific cytidine deaminase activity, providing insight into A3A's mechanism on substrate recognition and a new addition of a toolset to the creation of a RNA-specific C-to-U base editor.
Collapse
Affiliation(s)
- Guiyue Tang
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Bingran Xie
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiangna Hong
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Hang Qin
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jingfang Wang
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hai Huang
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Pei Hao
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| |
Collapse
|
39
|
Insights into the Structures and Multimeric Status of APOBEC Proteins Involved in Viral Restriction and Other Cellular Functions. Viruses 2021; 13:v13030497. [PMID: 33802945 PMCID: PMC8002816 DOI: 10.3390/v13030497] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 12/16/2022] Open
Abstract
Apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) proteins belong to a family of deaminase proteins that can catalyze the deamination of cytosine to uracil on single-stranded DNA or/and RNA. APOBEC proteins are involved in diverse biological functions, including adaptive and innate immunity, which are critical for restricting viral infection and endogenous retroelements. Dysregulation of their functions can cause undesired genomic mutations and RNA modification, leading to various associated diseases, such as hyper-IgM syndrome and cancer. This review focuses on the structural and biochemical data on the multimerization status of individual APOBECs and the associated functional implications. Many APOBECs form various multimeric complexes, and multimerization is an important way to regulate functions for some of these proteins at several levels, such as deaminase activity, protein stability, subcellular localization, protein storage and activation, virion packaging, and antiviral activity. The multimerization of some APOBECs is more complicated than others, due to the associated complex RNA binding modes.
Collapse
|
40
|
Law EK, Levin-Klein R, Jarvis MC, Kim H, Argyris PP, Carpenter MA, Starrett GJ, Temiz NA, Larson LK, Durfee C, Burns MB, Vogel RI, Stavrou S, Aguilera AN, Wagner S, Largaespada DA, Starr TK, Ross SR, Harris RS. APOBEC3A catalyzes mutation and drives carcinogenesis in vivo. J Exp Med 2021; 217:152061. [PMID: 32870257 PMCID: PMC7953736 DOI: 10.1084/jem.20200261] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/08/2020] [Accepted: 07/22/2020] [Indexed: 12/24/2022] Open
Abstract
The APOBEC3 family of antiviral DNA cytosine deaminases is implicated as the second largest source of mutation in cancer. This mutational process may be a causal driver or inconsequential passenger to the overall tumor phenotype. We show that human APOBEC3A expression in murine colon and liver tissues increases tumorigenesis. All other APOBEC3 family members, including APOBEC3B, fail to promote liver tumor formation. Tumor DNA sequences from APOBEC3A-expressing animals display hallmark APOBEC signature mutations in TCA/T motifs. Bioinformatic comparisons of the observed APOBEC3A mutation signature in murine tumors, previously reported APOBEC3A and APOBEC3B mutation signatures in yeast, and reanalyzed APOBEC mutation signatures in human tumor datasets support cause-and-effect relationships for APOBEC3A-catalyzed deamination and mutagenesis in driving multiple human cancers.
Collapse
Affiliation(s)
- Emily K Law
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Rena Levin-Klein
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Matthew C Jarvis
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Hyoung Kim
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Prokopios P Argyris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN.,Division of Oral and Maxillofacial Pathology, School of Dentistry, University of Minnesota, Minneapolis, MN
| | - Michael A Carpenter
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Gabriel J Starrett
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN.,Laboratory of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Nuri A Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Health Informatics, University of Minnesota, Minneapolis, MN
| | - Lindsay K Larson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Cameron Durfee
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Michael B Burns
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN.,Department of Biology, Loyola University, Chicago, IL
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN
| | - Spyridon Stavrou
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Alexya N Aguilera
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Sandra Wagner
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - David A Largaespada
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Timothy K Starr
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN
| | - Susan R Ross
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Reuben S Harris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| |
Collapse
|
41
|
Langenbucher A, Bowen D, Sakhtemani R, Bournique E, Wise JF, Zou L, Bhagwat AS, Buisson R, Lawrence MS. An extended APOBEC3A mutation signature in cancer. Nat Commun 2021; 12:1602. [PMID: 33707442 PMCID: PMC7952602 DOI: 10.1038/s41467-021-21891-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 02/17/2021] [Indexed: 12/11/2022] Open
Abstract
APOBEC mutagenesis, a major driver of cancer evolution, is known for targeting TpC sites in DNA. Recently, we showed that APOBEC3A (A3A) targets DNA hairpin loops. Here, we show that DNA secondary structure is in fact an orthogonal influence on A3A substrate optimality and, surprisingly, can override the TpC sequence preference. VpC (non-TpC) sites in optimal hairpins can outperform TpC sites as mutational hotspots. This expanded understanding of APOBEC mutagenesis illuminates the genomic Twin Paradox, a puzzling pattern of closely spaced mutation hotspots in cancer genomes, in which one is a canonical TpC site but the other is a VpC site, and double mutants are seen only in trans, suggesting a two-hit driver event. Our results clarify this paradox, revealing that both hotspots in these twins are optimal A3A substrates. Our findings reshape the notion of a mutation signature, highlighting the additive roles played by DNA sequence and DNA structure.
Collapse
Affiliation(s)
- 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, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Ramin Sakhtemani
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - Elodie Bournique
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Jillian F Wise
- 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
- Department of Cancer Immunology, Institute for Cancer Research, University of Oslo, Oslo, Norway
| | - 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.
| | - Ashok S Bhagwat
- Department of Chemistry, Wayne State University, Detroit, MI, USA.
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, USA.
| | - Rémi Buisson
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, CA, USA.
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California Irvine, Irvine, CA, 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.
| |
Collapse
|
42
|
Jaguva Vasudevan AA, Balakrishnan K, Franken A, Krikoni A, Häussinger D, Luedde T, Münk C. Murine leukemia virus resists producer cell APOBEC3A by its Glycosylated Gag but not target cell APOBEC3A. Virology 2021; 557:1-14. [PMID: 33581610 DOI: 10.1016/j.virol.2021.01.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/22/2021] [Accepted: 01/29/2021] [Indexed: 12/14/2022]
Abstract
The human APOBEC3A (A3A) polynucleotide cytidine deaminase has been shown to have antiviral activity against HTLV-1 but not HIV-1, when expressed in the virus producer cell. In viral target cells, high levels of endogenous A3A activity have been associated with the restriction of HIV-1 during infection. Here we demonstrate that A3A derived from both target cells and producer cells can block the infection of Moloney-MLV (MLV) and related AKV-derived strains of MLV in a deaminase-dependent mode. Furthermore, glycosylated Gag (glycoGag) of MLV inhibits the encapsidation of human A3A, but target cell A3A was not affected by glycoGag and exerted deamination of viral DNA. Importantly, our results clearly indicate that poor glycoGag expression in MLV gag-pol packaging constructs as compared to abundant levels in full-length amphotropic MLV makes these viral vectors sensitive to A3A-mediated restriction. This raises the possibility of acquiring A3A-induced mutations in retroviral gene therapy applications.
Collapse
Affiliation(s)
- Ananda Ayyappan Jaguva Vasudevan
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany.
| | - Kannan Balakrishnan
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany; Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
| | - André Franken
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Aikaterini Krikoni
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Tom Luedde
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany.
| |
Collapse
|
43
|
Maiti A, Hou S, Schiffer CA, Matsuo H. Interactions of APOBEC3s with DNA and RNA. Curr Opin Struct Biol 2021; 67:195-204. [PMID: 33486429 DOI: 10.1016/j.sbi.2020.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/25/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
APOBEC3 enzymes are key enzymes in our innate immune system regulating antiviral response in HIV and unfortunately adding diversity in cancer as they deaminate cytosine. Seven unique single and double domain APOBEC3s provide them with unique activity and specificity profiles for this deamination. Recent crystal and NMR structures of APOBEC3 complexes are unraveling the variety of epitopes involved in binding nucleic acids, including at the catalytic site, elsewhere on the catalytic domain and in the inactive N-terminal domain. The interplay between these diverse interactions is critical to uncovering the mechanisms by which APOBEC3s recognize and process their substrates.
Collapse
Affiliation(s)
- Atanu Maiti
- Basic Science Program, 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
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.
| | - Hiroshi Matsuo
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
| |
Collapse
|
44
|
Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution. Virology 2021; 556:62-72. [PMID: 33545556 PMCID: PMC7831814 DOI: 10.1016/j.virol.2020.12.018] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022]
Abstract
Members of the APOBEC family of cytidine deaminases show antiviral activities in mammalian cells through lethal editing in the genomes of small DNA viruses, herpesviruses and retroviruses, and potentially those of RNA viruses such as coronaviruses. Consistent with the latter, APOBEC-like directional C→U transitions of genomic plus-strand RNA are greatly overrepresented in SARS-CoV-2 genome sequences of variants emerging during the COVID-19 pandemic. A C→U mutational process may leave evolutionary imprints on coronavirus genomes, including extensive homoplasy from editing and reversion at targeted sites and the occurrence of driven amino acid sequence changes in viral proteins. If sustained over longer periods, this process may account for the previously reported marked global depletion of C and excess of U bases in human seasonal coronavirus genomes. This review synthesizes the current knowledge on APOBEC evolution and function and the evidence of their role in APOBEC-mediated genome editing of SARS-CoV-2 and other coronaviruses. SARS-CoV-2 sequence variants contain an overabundance of C- > U transitions C- > U transitions are the hallmark of the activity of APOBEC cytosine deaminases Further work is needed to determine APOBEC's role in coronavirus evolution
Collapse
|
45
|
Expression of APOBEC family members as regulators of endogenous retroelements and malignant transformation in systemic autoimmunity. Clin Immunol 2020; 223:108649. [PMID: 33326823 DOI: 10.1016/j.clim.2020.108649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To explore whether APOBEC family members are involved in the response to inappropriate expression of L1 retroelements in primary Sjögren's syndrome (SS) and systemic lupus erythematosus (SLE), as well as in SS related lymphomagenesis. METHODS Minor salivary glands (MSG) and kidney biopsy (KB) specimens were obtained from 41 SS patients (10 with lymphoma) and 23 patients with SLE, respectively. PBMC and sera were also collected from 73 SLE patients. Full-length L1 transcripts, members of the APOBEC and IFN family were quantitated by real time PCR. Type I IFN activity was assessed in lupus plasma by a cell assay. RESULTS APOBEC3A was increased in SS MSG, SLE KB and PBMC and correlated with L1. AID and APOBEC3G were particularly overexpressed in MSG tissues derived from SS lymphoma patients. CONCLUSION These data reveal a previously unappreciated role of APOBEC family proteins in the pathogenesis of systemic autoimmunity and SS related lymphomagenesis.
Collapse
|
46
|
Hakata Y, Miyazawa M. Deaminase-Independent Mode of Antiretroviral Action in Human and Mouse APOBEC3 Proteins. Microorganisms 2020; 8:microorganisms8121976. [PMID: 33322756 PMCID: PMC7764128 DOI: 10.3390/microorganisms8121976] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023] Open
Abstract
Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3) proteins (APOBEC3s) are deaminases that convert cytosines to uracils predominantly on a single-stranded DNA, and function as intrinsic restriction factors in the innate immune system to suppress replication of viruses (including retroviruses) and movement of retrotransposons. Enzymatic activity is supposed to be essential for the APOBEC3 antiviral function. However, it is not the only way that APOBEC3s exert their biological function. Since the discovery of human APOBEC3G as a restriction factor for HIV-1, the deaminase-independent mode of action has been observed. At present, it is apparent that both the deaminase-dependent and -independent pathways are tightly involved not only in combating viruses but also in human tumorigenesis. Although the deaminase-dependent pathway has been extensively characterized so far, understanding of the deaminase-independent pathway remains immature. Here, we review existing knowledge regarding the deaminase-independent antiretroviral functions of APOBEC3s and their molecular mechanisms. We also discuss the possible unidentified molecular mechanism for the deaminase-independent antiretroviral function mediated by mouse APOBEC3.
Collapse
Affiliation(s)
- Yoshiyuki Hakata
- Department of Immunology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan;
- Correspondence: ; Tel.: +81-72-367-7660
| | - Masaaki Miyazawa
- Department of Immunology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan;
- Kindai University Anti-Aging Center, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| |
Collapse
|
47
|
The Role of APOBECs in Viral Replication. Microorganisms 2020; 8:microorganisms8121899. [PMID: 33266042 PMCID: PMC7760323 DOI: 10.3390/microorganisms8121899] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/14/2022] Open
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) proteins are a diverse and evolutionarily conserved family of cytidine deaminases that provide a variety of functions from tissue-specific gene expression and immunoglobulin diversity to control of viruses and retrotransposons. APOBEC family expansion has been documented among mammalian species, suggesting a powerful selection for their activity. Enzymes with a duplicated zinc-binding domain often have catalytically active and inactive domains, yet both have antiviral function. Although APOBEC antiviral function was discovered through hypermutation of HIV-1 genomes lacking an active Vif protein, much evidence indicates that APOBECs also inhibit virus replication through mechanisms other than mutagenesis. Multiple steps of the viral replication cycle may be affected, although nucleic acid replication is a primary target. Packaging of APOBECs into virions was first noted with HIV-1, yet is not a prerequisite for viral inhibition. APOBEC antagonism may occur in viral producer and recipient cells. Signatures of APOBEC activity include G-to-A and C-to-T mutations in a particular sequence context. The importance of APOBEC activity for viral inhibition is reflected in the identification of numerous viral factors, including HIV-1 Vif, which are dedicated to antagonism of these deaminases. Such viral antagonists often are only partially successful, leading to APOBEC selection for viral variants that enhance replication or avoid immune elimination.
Collapse
|
48
|
Breaking the sound barrier: Towards next-generation AAV vectors for gene therapy of hearing disorders. Hear Res 2020; 413:108092. [PMID: 33268240 DOI: 10.1016/j.heares.2020.108092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 09/14/2020] [Accepted: 10/08/2020] [Indexed: 12/20/2022]
Abstract
Owing to the advances in transgenic animal technology and the advent of the next-generation sequencing era, over 120 genes causing hereditary hearing loss have been identified by now. In parallel, the field of human gene therapy continues to make exciting and rapid progress, culminating in the recent approval of several ex vivo and in vivo applications. Despite these encouraging developments and the growing interest in causative treatments for hearing disorders, gene therapeutic interventions in the inner ear remain in their infancy and await clinical translation. This review focuses on the adeno-associated virus (AAV), which nowadays represents one of the safest and most promising vectors in gene therapy. We first provide an overview of AAV biology and outline the principles of therapeutic gene transfer with recombinant AAV vectors, before pointing out major challenges and solutions for clinical translation including vector manufacturing and species translatability. Finally, we highlight seminal technologies for engineering and selection of next-generation "designer" AAV capsids, and illustrate their power and potential with recent examples of their application for inner ear gene transfer in animals.
Collapse
|
49
|
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.
Collapse
|
50
|
Poulain F, Lejeune N, Willemart K, Gillet NA. Footprint of the host restriction factors APOBEC3 on the genome of human viruses. PLoS Pathog 2020; 16:e1008718. [PMID: 32797103 PMCID: PMC7449416 DOI: 10.1371/journal.ppat.1008718] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 08/26/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
APOBEC3 enzymes are innate immune effectors that introduce mutations into viral genomes. These enzymes are cytidine deaminases which transform cytosine into uracil. They preferentially mutate cytidine preceded by thymidine making the 5'TC motif their favored target. Viruses have evolved different strategies to evade APOBEC3 restriction. Certain viruses actively encode viral proteins antagonizing the APOBEC3s, others passively face the APOBEC3 selection pressure thanks to a depleted genome for APOBEC3-targeted motifs. Hence, the APOBEC3s left on the genome of certain viruses an evolutionary footprint. The aim of our study is the identification of these viruses having a genome shaped by the APOBEC3s. We analyzed the genome of 33,400 human viruses for the depletion of APOBEC3-favored motifs. We demonstrate that the APOBEC3 selection pressure impacts at least 22% of all currently annotated human viral species. The papillomaviridae and polyomaviridae are the most intensively footprinted families; evidencing a selection pressure acting genome-wide and on both strands. Members of the parvoviridae family are differentially targeted in term of both magnitude and localization of the footprint. Interestingly, a massive APOBEC3 footprint is present on both strands of the B19 erythroparvovirus; making this viral genome one of the most cleaned sequences for APOBEC3-favored motifs. We also identified the endemic coronaviridae as significantly footprinted. Interestingly, no such footprint has been detected on the zoonotic MERS-CoV, SARS-CoV-1 and SARS-CoV-2 coronaviruses. In addition to viruses that are footprinted genome-wide, certain viruses are footprinted only on very short sections of their genome. That is the case for the gamma-herpesviridae and adenoviridae where the footprint is localized on the lytic origins of replication. A mild footprint can also be detected on the negative strand of the reverse transcribing HIV-1, HIV-2, HTLV-1 and HBV viruses. Together, our data illustrate the extent of the APOBEC3 selection pressure on the human viruses and identify new putatively APOBEC3-targeted viruses.
Collapse
Affiliation(s)
- Florian Poulain
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
| | - Noémie Lejeune
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
| | - Kévin Willemart
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
| | - Nicolas A. Gillet
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
| |
Collapse
|