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Nur A, Lai JY, Ch'ng ACW, Choong YS, Wan Isa WYH, Lim TS. A review of in vitro stochastic and non-stochastic affinity maturation strategies for phage display derived monoclonal antibodies. Int J Biol Macromol 2024; 277:134217. [PMID: 39069045 DOI: 10.1016/j.ijbiomac.2024.134217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]
Abstract
Monoclonal antibodies identified using display technologies like phage display occasionally suffers from a lack of affinity making it unsuitable for application. This drawback is circumvented with the application of affinity maturation. Affinity maturation is an essential step in the natural evolution of antibodies in the immune system. The evolution of molecular based methods has seen the development of various mutagenesis approaches. This allows for the natural evolutionary process during somatic hypermutation to be replicated in the laboratories for affinity maturation to fine-tune the affinity and selectivity of antibodies. In this review, we will discuss affinity maturation strategies for mAbs generated through phage display systems. The review will highlight various in vitro stochastic and non-stochastic affinity maturation approaches that includes but are not limited to random mutagenesis, site-directed mutagenesis, and gene synthesis.
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Affiliation(s)
- Alia Nur
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Wan Yus Haniff Wan Isa
- School of Medical Sciences, Department of Medicine, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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2
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Amor-Guéret M. Loss of cytidine deaminase expression as a potential attempt to counteract the process of carcinogenesis by reducing basal PARP-1 activity and increasing tau levels. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167213. [PMID: 38714266 DOI: 10.1016/j.bbadis.2024.167213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/01/2024] [Accepted: 05/01/2024] [Indexed: 05/09/2024]
Abstract
Cytidine deaminase (CDA) is a pyrimidine salvage pathway enzyme that catalyzes the hydrolytic deamination of free cytidine and deoxycytidine to uridine and deoxyuridine, respectively. Our team discovered that CDA deficiency is associated with several aspects of genetic instability, such as increased sister chromatid exchange and ultrafine anaphase bridge frequencies. Based on these results, we sought (1) to determine how CDA deficiency contributes to genetic instability, (2) to explore the possible relationships between CDA deficiency and carcinogenesis, and (3) to develop a new anticancer treatment targeting CDA-deficient tumors. This review summarizes our major findings indicating that CDA deficiency is associated with a genetic instability that does not confer an increased cancer risk. In light of our results and published data, I propose a novel hypothesis that loss of CDA, by reducing basal PARP-1 activity and increasing Tau levels, may reflect an attempt to prevent, slow or reverse the process of carcinogenesis.
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Affiliation(s)
- Mounira Amor-Guéret
- Institut Curie, PSL Research University, UMR 3348, 91405 Orsay, France; CNRS UMR 3348, Centre Universitaire, 91405 Orsay, France; Université Paris-Saclay, Centre Universitaire, UMR 3348, 91405 Orsay, France.
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3
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Sanchez A, Ortega P, Sakhtemani R, Manjunath L, Oh S, Bournique E, Becker A, Kim K, Durfee C, Temiz NA, Chen XS, Harris RS, Lawrence MS, Buisson R. Mesoscale DNA features impact APOBEC3A and APOBEC3B deaminase activity and shape tumor mutational landscapes. Nat Commun 2024; 15:2370. [PMID: 38499542 PMCID: PMC10948877 DOI: 10.1038/s41467-024-45909-5] [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: 07/31/2023] [Accepted: 01/09/2024] [Indexed: 03/20/2024] Open
Abstract
Antiviral DNA cytosine deaminases APOBEC3A and APOBEC3B are major sources of mutations in cancer by catalyzing cytosine-to-uracil deamination. APOBEC3A preferentially targets single-stranded DNAs, with a noted affinity for DNA regions that adopt stem-loop secondary structures. However, the detailed substrate preferences of APOBEC3A and APOBEC3B have not been fully established, and the specific influence of the DNA sequence on APOBEC3A and APOBEC3B deaminase activity remains to be investigated. Here, we find that APOBEC3B also selectively targets DNA stem-loop structures, and they are distinct from those subjected to deamination by APOBEC3A. We develop Oligo-seq, an in vitro sequencing-based method to identify specific sequence contexts promoting APOBEC3A and APOBEC3B activity. Through this approach, we demonstrate that APOBEC3A and APOBEC3B deaminase activity is strongly regulated by specific sequences surrounding the targeted cytosine. Moreover, we identify the structural features of APOBEC3B and APOBEC3A responsible for their substrate preferences. Importantly, we determine that APOBEC3B-induced mutations in hairpin-forming sequences within tumor genomes differ from the DNA stem-loop sequences mutated by APOBEC3A. Together, our study provides evidence that APOBEC3A and APOBEC3B can generate distinct mutation landscapes in cancer genomes, driven by their unique substrate selectivity.
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Affiliation(s)
- Ambrocio Sanchez
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Pedro Ortega
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Ramin Sakhtemani
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lavanya Manjunath
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Elodie Bournique
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Alexandrea Becker
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Kyumin Kim
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA.
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA.
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA.
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4
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Budzko L, Hoffa-Sobiech K, Jackowiak P, Figlerowicz M. Engineered deaminases as a key component of DNA and RNA editing tools. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102062. [PMID: 38028200 PMCID: PMC10661471 DOI: 10.1016/j.omtn.2023.102062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Over recent years, zinc-dependent deaminases have attracted increasing interest as key components of nucleic acid editing tools that can generate point mutations at specific sites in either DNA or RNA by combining a targeting module (such as a catalytically impaired CRISPR-Cas component) and an effector module (most often a deaminase). Deaminase-based molecular tools are already being utilized in a wide spectrum of therapeutic and research applications; however, their medical and biotechnological potential seems to be much greater. Recent reports indicate that the further development of nucleic acid editing systems depends largely on our ability to engineer the substrate specificity and catalytic activity of the editors themselves. In this review, we summarize the current trends and achievements in deaminase engineering. The presented data indicate that the potential of these enzymes has not yet been fully revealed or understood. Several examples show that even relatively minor changes in the structure of deaminases can give them completely new and unique properties.
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Affiliation(s)
- Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Karolina Hoffa-Sobiech
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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5
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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.
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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
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6
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Sanchez A, Ortega P, Sakhtemani R, Manjunath L, Oh S, Bournique E, Becker A, Kim K, Durfee C, Temiz NA, Chen XS, Harris RS, Lawrence MS, Buisson R. Mesoscale DNA Features Impact APOBEC3A and APOBEC3B Deaminase Activity and Shape Tumor Mutational Landscapes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551499. [PMID: 37577509 PMCID: PMC10418229 DOI: 10.1101/2023.08.02.551499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Antiviral DNA cytosine deaminases APOBEC3A and APOBEC3B are major sources of mutations in cancer by catalyzing cytosine-to-uracil deamination. APOBEC3A preferentially targets singlestranded DNAs, with a noted affinity for DNA regions that adopt stem-loop secondary structures. However, the detailed substrate preferences of APOBEC3A and APOBEC3B have been fully established, and the specific influence of the DNA sequence on APOBEC3A APOBEC3B deaminase activity remains to be investigated. Here, we find that APOBEC3B selectively targets DNA stem-loop structures, and they are distinct from those subjected deamination by APOBEC3A. We develop Oligo-seq, a novel in vitro sequencing-based to identify specific sequence contexts promoting APOBEC3A and APOBEC3B activity. Through this approach, we demonstrate that APOBEC3A an APOBEC3B deaminase activity is strongly regulated by specific sequences surrounding the targeted cytosine. Moreover, we identify structural features of APOBEC3B and APOBEC3A responsible for their substrate preferences. Importantly, we determine that APOBEC3B-induced mutations in hairpin-forming sequences within tumor genomes differ from the DNA stem-loop sequences mutated by APOBEC3A. Together, our study provides evidence that APOBEC3A and APOBEC3B can generate mutation landscapes in cancer genomes, driven by their unique substrate selectivity.
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7
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Ott JA, Mitchell C, Sheppard M, Deiss TC, Horton JMC, Haakenson JK, Huang R, Kelley AR, Davis BW, Derr JN, Smider VV, Criscitiello MF. Evolution of immunogenetic components encoding ultralong CDR H3. Immunogenetics 2023; 75:323-339. [PMID: 37084012 PMCID: PMC10119515 DOI: 10.1007/s00251-023-01305-9] [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: 01/29/2023] [Accepted: 04/03/2023] [Indexed: 04/22/2023]
Abstract
The genomes of most vertebrates contain many V, D, and J gene segments within their Ig loci to construct highly variable CDR3 sequences through combinatorial diversity. This nucleotide variability translates into an antibody population containing extensive paratope diversity. Cattle have relatively few functional VDJ gene segments, requiring innovative approaches for generating diversity like the use of ultralong-encoding IGHV and IGHD gene segments that yield dramatically elongated CDR H3. Unique knob and stalk microdomains create protracted paratopes, where the antigen-binding knob sits atop a long stalk, allowing the antibody to bind both surface and recessed antigen epitopes. We examined genomes of twelve species of Bovidae to determine when ultralong-encoding IGHV and IGHD gene segments evolved. We located the 8-bp duplication encoding the unique TTVHQ motif in ultralong IGHV segments in six Bovid species (cattle, zebu, wild yak, domestic yak, American bison, and domestic gayal), but we did not find evidence of the duplication in species beyond the Bos and Bison genera. Additionally, we analyzed mRNA from bison spleen and identified a rich repertoire of expressed ultralong CDR H3 antibody mRNA, suggesting that bison use ultralong IGHV transcripts in their host defense. We found ultralong-encoding IGHD gene segments in all the same species except domestic yak, but again not beyond the Bos and Bison clade. Thus, the duplication event leading to this ultralong-encoding IGHV gene segment and the emergence of the ultralong-encoding IGHD gene segment appears to have evolved in a common ancestor of the Bos and Bison genera 5-10 million years ago.
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Affiliation(s)
- Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Christian Mitchell
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Morgan Sheppard
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Thad C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - J M Cody Horton
- Department of Veterinary Integrative Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Jeremy K Haakenson
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Ruiqi Huang
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | | | - Brian W Davis
- Department of Veterinary Integrative Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - James N Derr
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Vaughn V Smider
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Bryan, TX, 77807, USA.
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8
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Abstract
DNA-editing enzymes perform chemical reactions on DNA nucleobases. These reactions can change the genetic identity of the modified base or modulate gene expression. Interest in DNA-editing enzymes has burgeoned in recent years due to the advent of clustered regularly interspaced short palindromic repeat-associated (CRISPR-Cas) systems, which can be used to direct their DNA-editing activity to specific genomic loci of interest. In this review, we showcase DNA-editing enzymes that have been repurposed or redesigned and developed into programmable base editors. These include deaminases, glycosylases, methyltransferases, and demethylases. We highlight the astounding degree to which these enzymes have been redesigned, evolved, and refined and present these collective engineering efforts as a paragon for future efforts to repurpose and engineer other families of enzymes. Collectively, base editors derived from these DNA-editing enzymes facilitate programmable point mutation introduction and gene expression modulation by targeted chemical modification of nucleobases.
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Affiliation(s)
- Kartik L Rallapalli
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA;
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA;
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9
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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.
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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
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10
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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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11
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Manjunath L, Oh S, Ortega P, Bouin A, Bournique E, Sanchez A, Martensen PM, Auerbach AA, Becker JT, Seldin M, Harris RS, Semler BL, Buisson R. APOBEC3B drives PKR-mediated translation shutdown and protects stress granules in response to viral infection. Nat Commun 2023; 14:820. [PMID: 36781883 PMCID: PMC9925369 DOI: 10.1038/s41467-023-36445-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
Double-stranded RNA produced during viral replication and transcription activates both protein kinase R (PKR) and ribonuclease L (RNase L), which limits viral gene expression and replication through host shutoff of translation. In this study, we find that APOBEC3B forms a complex with PABPC1 to stimulate PKR and counterbalances the PKR-suppressing activity of ADAR1 in response to infection by many types of viruses. This leads to translational blockage and the formation of stress granules. Furthermore, we show that APOBEC3B localizes to stress granules through the interaction with PABPC1. APOBEC3B facilitates the formation of protein-RNA condensates with stress granule assembly factor (G3BP1) by protecting mRNA associated with stress granules from RNAse L-induced RNA cleavage during viral infection. These results not only reveal that APOBEC3B is a key regulator of different steps of the innate immune response throughout viral infection but also highlight an alternative mechanism by which APOBEC3B can impact virus replication without editing viral genomes.
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Affiliation(s)
- Lavanya Manjunath
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Virus Research, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Virus Research, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Pedro Ortega
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Virus Research, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Alexis Bouin
- Center for Virus Research, University of California Irvine, Irvine, CA, USA
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Elodie Bournique
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Virus Research, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Ambrocio Sanchez
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Virus Research, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Pia Møller Martensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Ashley A Auerbach
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN, USA
| | - Jordan T Becker
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN, USA
| | - Marcus Seldin
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Bert L Semler
- Center for Virus Research, University of California Irvine, Irvine, CA, USA
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA.
- Center for Virus Research, University of California Irvine, Irvine, CA, USA.
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA.
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA.
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12
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Stability of APOBEC3F in the Presence of the APOBEC3 Antagonist HIV-1 Vif Increases at the Expense of Co-Expressed APOBEC3H Haplotype I. Viruses 2023; 15:v15020463. [PMID: 36851677 PMCID: PMC9960753 DOI: 10.3390/v15020463] [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: 12/29/2022] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
The seven human APOBEC3 enzymes (APOBEC3A through H, excluding E) are host restriction factors. Most of the APOBEC3 enzymes can restrict HIV-1 replication with different efficiencies. The HIV-1 Vif protein combats APOBEC3-mediated restriction by inducing ubiquitination and degradation in the proteasome. APOBEC3F and APOBEC3G can hetero-oligomerize, which increases their restriction capacity and resistance to Vif. Here we determined if APOBEC3C, APOBEC3F, or APOBEC3G could hetero-oligomerize with APOBEC3H haplotype I. APOBEC3H haplotype I has a short half-life in cells due to ubiquitination and degradation by host proteins, but is also resistant to Vif. We hypothesized that hetero-oligomerization with APOBEC3H haplotype I may result in less Vif-mediated degradation of the interacting APOBEC3 and stabilize APOBEC3H haplotype I, resulting in more efficient HIV-1 restriction. Although we found that all three APOBEC3s could interact with APOBEC3H haplotype I, only APOBEC3F affected APOBEC3H haplotype I by surprisingly accelerating its proteasomal degradation. However, this increased APOBEC3F levels in cells and virions in the absence or presence of Vif and enabled APOBEC3F-mediated restriction of HIV-1 in the presence of Vif. Altogether, the data suggest that APOBEC3 enzymes can co-regulate each other at the protein level and that they cooperate to ensure HIV-1 inactivation rather than evolution.
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13
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A Long-Running Arms Race between APOBEC1 Genes and Retroviruses in Tetrapods. J Virol 2023; 97:e0179522. [PMID: 36598198 PMCID: PMC9888297 DOI: 10.1128/jvi.01795-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Activation-induced cytidine deaminase/apolipoprotein B mRNA editing catalytic polypeptide-like (AID/APOBEC) proteins are cytosine deaminases implicated in diverse biological functions. APOBEC1 (A1) proteins have long been thought to regulate lipid metabolism, whereas the evolutionary significance of A1 proteins in antiviral defense remains largely obscure. Endogenous retroviruses (ERVs) document past retroviral infections and are ubiquitous within the vertebrate genomes. Here, we identify the A1 gene repertoire, characterize the A1-mediated mutation footprints in ERVs, and interrogate the evolutionary arms race between A1 genes and ERVs across vertebrate species. We find that A1 genes are widely present in tetrapods, recurrently amplified and lost in certain lineages, suggesting that A1 genes might have originated during the early evolution of tetrapods. A1-mediated mutation footprints can be detected in ERVs across tetrapods. Moreover, A1 genes appear to have experienced episodic positive selection in many tetrapod lineages. Taken together, we propose that a long-running arms race between A1 genes and retroviruses might have persisted throughout the evolutionary course of tetrapods. IMPORTANCE APOBEC3 (A3) genes have been thought to function in defense against retroviruses, whereas the evolutionary significance of A1 proteins in antiviral defense remains largely obscure. In this study, we identify the A1 gene repertoire, characterize the A1-mediated mutation footprints in endogenous retroviruses (ERVs), and explore the evolutionary arms race between A1 genes and ERVs across vertebrate species. We found A1 proteins originated during the early evolution of tetrapods, and detected the footprints of A1-induced hypermutations in retroviral fossils. A1 genes appear to have experienced pervasive positive selection in tetrapods. Our study indicates a long-running arms race between A1 genes and retroviruses taking place throughout the evolutionary course of tetrapods.
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14
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Roles of G4-DNA and G4-RNA in Class Switch Recombination and Additional Regulations in B-Lymphocytes. Molecules 2023; 28:molecules28031159. [PMID: 36770824 PMCID: PMC9921937 DOI: 10.3390/molecules28031159] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Mature B cells notably diversify immunoglobulin (Ig) production through class switch recombination (CSR), allowing the junction of distant "switch" (S) regions. CSR is initiated by activation-induced deaminase (AID), which targets cytosines adequately exposed within single-stranded DNA of transcribed targeted S regions, with a specific affinity for WRCY motifs. In mammals, G-rich sequences are additionally present in S regions, forming canonical G-quadruplexes (G4s) DNA structures, which favor CSR. Small molecules interacting with G4-DNA (G4 ligands), proved able to regulate CSR in B lymphocytes, either positively (such as for nucleoside diphosphate kinase isoforms) or negatively (such as for RHPS4). G4-DNA is also implicated in the control of transcription, and due to their impact on both CSR and transcriptional regulation, G4-rich sequences likely play a role in the natural history of B cell malignancies. Since G4-DNA stands at multiple locations in the genome, notably within oncogene promoters, it remains to be clarified how it can more specifically promote legitimate CSR in physiology, rather than pathogenic translocation. The specific regulatory role of G4 structures in transcribed DNA and/or in corresponding transcripts and recombination hereby appears as a major issue for understanding immune responses and lymphomagenesis.
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15
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Ghorbani A, Khataeipour SJ, Solbakken MH, Huebert DNG, Khoddami M, Eslamloo K, Collins C, Hori T, Jentoft S, Rise ML, Larijani M. Ancestral reconstruction reveals catalytic inactivation of activation-induced cytidine deaminase concomitant with cold water adaption in the Gadiformes bony fish. BMC Biol 2022; 20:293. [PMID: 36575514 PMCID: PMC9795746 DOI: 10.1186/s12915-022-01489-8] [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: 03/18/2022] [Accepted: 11/30/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Antibody affinity maturation in vertebrates requires the enzyme activation-induced cytidine deaminase (AID) which initiates secondary antibody diversification by mutating the immunoglobulin loci. AID-driven antibody diversification is conserved across jawed vertebrates since bony and cartilaginous fish. Two exceptions have recently been reported, the Pipefish and Anglerfish, in which the AID-encoding aicda gene has been lost. Both cases are associated with unusual reproductive behavior, including male pregnancy and sexual parasitism. Several cold water fish in the Atlantic cod (Gadinae) family carry an aicda gene that encodes for a full-length enzyme but lack affinity-matured antibodies and rely on antibodies of broad antigenic specificity. Hence, we examined the functionality of their AID. RESULTS By combining genomics, transcriptomics, immune responsiveness, and functional enzymology of AID from 36 extant species, we demonstrate that AID of that Atlantic cod and related fish have extremely lethargic or no catalytic activity. Through ancestral reconstruction and functional enzymology of 71 AID enzymes, we show that this enzymatic inactivation likely took place relatively recently at the emergence of the true cod family (Gadidae) from their ancestral Gadiformes order. We show that this AID inactivation is not only concordant with the previously shown loss of key adaptive immune genes and expansion of innate and cell-based immune genes in the Gadiformes but is further reflected in the genomes of these fish in the form of loss of AID-favored sequence motifs in their immunoglobulin variable region genes. CONCLUSIONS Recent demonstrations of the loss of the aicda gene in two fish species challenge the paradigm that AID-driven secondary antibody diversification is absolutely conserved in jawed vertebrates. These species have unusual reproductive behaviors forming an evolutionary pressure for a certain loss of immunity to avoid tissue rejection. We report here an instance of catalytic inactivation and functional loss of AID rather than gene loss in a conventionally reproducing vertebrate. Our data suggest that an expanded innate immunity, in addition to lower pathogenic pressures in a cold environment relieved the pressure to maintain robust secondary antibody diversification. We suggest that in this unique scenario, the AID-mediated collateral genome-wide damage would form an evolutionary pressure to lose AID function.
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Affiliation(s)
- Atefeh Ghorbani
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - S. Javad Khataeipour
- grid.25055.370000 0000 9130 6822Department of Computer Science, Faculty of Science, Memorial University of Newfoundland, St. John’s, Canada
| | - Monica H. Solbakken
- grid.5510.10000 0004 1936 8921Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David N. G. Huebert
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Minasadat Khoddami
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Khalil Eslamloo
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Cassandra Collins
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Tiago Hori
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Sissel Jentoft
- grid.5510.10000 0004 1936 8921Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Matthew L. Rise
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Mani Larijani
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
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16
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Modenini G, Abondio P, Boattini A. The coevolution between APOBEC3 and retrotransposons in primates. Mob DNA 2022; 13:27. [PMID: 36443831 PMCID: PMC9706992 DOI: 10.1186/s13100-022-00283-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/31/2022] [Indexed: 12/02/2022] Open
Abstract
Retrotransposons are genetic elements with the ability to replicate in the genome using reverse transcriptase: they have been associated with the development of different biological structures, such as the Central Nervous System (CNS), and their high mutagenic potential has been linked to various diseases, including cancer and neurological disorders. Throughout evolution and over time, Primates and Homo had to cope with infections from viruses and bacteria, and also with endogenous retroelements. Therefore, host genomes have evolved numerous methods to counteract the activity of endogenous and exogenous pathogens, and the APOBEC3 family of mutators is a prime example of a defensive mechanism in this context.In most Primates, there are seven members of the APOBEC3 family of deaminase proteins: among their functions, there is the ability to inhibit the mobilization of retrotransposons and the functionality of viruses. The evolution of the APOBEC3 proteins found in Primates is correlated with the expansion of two major families of retrotransposons, i.e. ERV and LINE-1.In this review, we will discuss how the rapid expansion of the APOBEC3 family is linked to the evolution of retrotransposons, highlighting the strong evolutionary arms race that characterized the history of APOBEC3s and endogenous retroelements in Primates. Moreover, the possible role of this relationship will be assessed in the context of embryonic development and brain-associated diseases.
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Affiliation(s)
- Giorgia Modenini
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Paolo Abondio
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy ,grid.6292.f0000 0004 1757 1758Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Alessio Boattini
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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17
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Maiti A, Hedger AK, Myint W, Balachandran V, Watts JK, Schiffer CA, Matsuo H. Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state. Nat Commun 2022; 13:7117. [PMID: 36402773 PMCID: PMC9675756 DOI: 10.1038/s41467-022-34752-1] [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: 08/15/2022] [Accepted: 11/04/2022] [Indexed: 11/21/2022] Open
Abstract
APOBEC3 proteins (A3s) are enzymes that catalyze the deamination of cytidine to uridine in single-stranded DNA (ssDNA) substrates, thus playing a key role in innate antiviral immunity. However, the APOBEC3 family has also been linked to many mutational signatures in cancer cells, which has led to an intense interest to develop inhibitors of A3's catalytic activity as therapeutics as well as tools to study A3's biochemistry, structure, and cellular function. Recent studies have shown that ssDNA containing 2'-deoxy-zebularine (dZ-ssDNA) is an inhibitor of A3s such as A3A, A3B, and A3G, although the atomic determinants of this activity have remained unknown. To fill this knowledge gap, we determined a 1.5 Å resolution structure of a dZ-ssDNA inhibitor bound to active A3G. The crystal structure revealed that the activated dZ-H2O mimics the transition state by coordinating the active site Zn2+ and engaging in additional stabilizing interactions, such as the one with the catalytic residue E259. Therefore, this structure allowed us to capture a snapshot of the A3's transition state and suggests that developing transition-state mimicking inhibitors may provide a new opportunity to design more targeted molecules for A3s in the future.
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Affiliation(s)
- Atanu Maiti
- grid.418021.e0000 0004 0535 8394Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Adam K. Hedger
- grid.168645.80000 0001 0742 0364Institute for Drug Resistance, University of Massachusetts Chan Medical School, Worcester, MA USA ,grid.168645.80000 0001 0742 0364RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA USA ,grid.168645.80000 0001 0742 0364Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Wazo Myint
- grid.418021.e0000 0004 0535 8394Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Vanivilasini Balachandran
- grid.418021.e0000 0004 0535 8394Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Jonathan K. Watts
- grid.168645.80000 0001 0742 0364RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA USA ,grid.168645.80000 0001 0742 0364Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Celia A. Schiffer
- grid.168645.80000 0001 0742 0364Institute for Drug Resistance, University of Massachusetts Chan Medical School, Worcester, MA USA ,grid.168645.80000 0001 0742 0364Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Hiroshi Matsuo
- grid.418021.e0000 0004 0535 8394Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD USA
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18
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Chen C, Sui X, Ning H, Sun Y, Du J, Chen X, Zhou X, Chen G, Shen W, Pang L, Zhou X, Shi R, Li W, Wang H, Zhao W, Zhai W, Qi Y, Wu Y, Gao Y. Identification of natural product 3, 5-diiodotyrosine as APOBEC3B inhibitor to prevent somatic mutation accumulation and cancer progression. J Immunother Cancer 2022; 10:jitc-2022-005503. [PMID: 36323433 PMCID: PMC9639148 DOI: 10.1136/jitc-2022-005503] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The development of cancer is largely dependent on the accumulation of somatic mutations, indicating the potential to develop cancer chemoprevention agents targeting mutation drivers. However, ideal cancer chemoprevention agents that can effectively inhibit the mutation drivers have not been identified yet. METHODS The somatic mutation signatures and expression analyses of APOBEC3B were performed in patient with pan-cancer. The computer-aided screening and skeleton-based searching were performed to identify natural products that can inhibit the activity of APOBEC3B. 4-nitroquinoline-1-oxide (4-NQO)-induced spontaneous esophageal squamous cell carcinoma (ESCC) and azoxymethane/dextran sulfate sodium (AOM/DSS)-induced spontaneous colon cancer mouse models were conducted to investigate the influences of APOBEC3B inhibitor on the prevention of somatic mutation accumulation and cancer progression. RESULTS Here, we discovered that the cytidine deaminase APOBEC3B correlated somatic mutations were widely observed in a variety of cancers, and its overexpression indicated poor survival. SMC247 (3, 5-diiodotyrosine), as a source of kelp iodine without side effects, could strongly bind APOBEC3B (KD=65 nM) and effectively inhibit its deaminase activity (IC50=1.69 µM). Interestingly, 3, 5-diiodotyrosine could significantly reduce the clusters of mutations, prevent the precancerous lesion progression, and prolong the survival in 4-NQO-induced spontaneous ESCC and AOM/DSS-induced spontaneous colon cancer mouse models. Furthermore, 3, 5-diiodotyrosine could reduce colitis, increase the proportion and function of T lymphocytes via IL-15 in tumor microenvironment. The synergistic cancer prevention effects were observed when 3, 5-diiodotyrosine combined with PD-1/PD-L1 blockade. CONCLUSIONS This is the first prove-of-concept study to elucidate that the natural product 3, 5-diiodotyrosine could prevent somatic mutation accumulation and cancer progression through inhibiting the enzymatic activity of APOBEC3B. In addition, 3, 5-diiodotyrosine could reduce the colitis and increase the infiltration and function of T lymphocytes via IL-15 in tumor microenvironment. 3, 5-diiodotyrosine combined with PD-1/PD-L1 blockade could elicit synergistic cancer prevention effects, indicating a novel strategy for both prevent the somatic mutation accumulation and the immune-suppressive microenvironment exacerbation.
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Affiliation(s)
- Chunxia Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xinghua Sui
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University - Shenzhen Campus, Shenzhen, Guangdong, China
| | - Haoming Ning
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yixuan Sun
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiangfeng Du
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China,Henan Key Laboratory of Bioactive Macromolecules, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaotong Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiuman Zhou
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University - Shenzhen Campus, Shenzhen, Guangdong, China
| | - Guanyu Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University - Shenzhen Campus, Shenzhen, Guangdong, China
| | - Wenhui Shen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University - Shenzhen Campus, Shenzhen, Guangdong, China
| | - Liwei Pang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaowen Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ranran Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Wanqiong Li
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University - Shenzhen Campus, Shenzhen, Guangdong, China
| | - Hongfei Wang
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan, China
| | - Wenshan Zhao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China,International Joint Laboratory for Protein and Peptide Drugs of Henan Province, Zhengzhou University, Zhengzhou, Henan, China
| | - Wenjie Zhai
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China,International Joint Laboratory for Protein and Peptide Drugs of Henan Province, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuanming Qi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China,International Joint Laboratory for Protein and Peptide Drugs of Henan Province, Zhengzhou University, Zhengzhou, Henan, China
| | - Yahong Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China,Henan Key Laboratory of Bioactive Macromolecules, Zhengzhou University, Zhengzhou, Henan, China
| | - Yanfeng Gao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University - Shenzhen Campus, Shenzhen, Guangdong, China
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19
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C-to-U RNA Editing: A Site Directed RNA Editing Tool for Restoration of Genetic Code. Genes (Basel) 2022; 13:genes13091636. [PMID: 36140804 PMCID: PMC9498875 DOI: 10.3390/genes13091636] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
The restoration of genetic code by editing mutated genes is a potential method for the treatment of genetic diseases/disorders. Genetic disorders are caused by the point mutations of thymine (T) to cytidine (C) or guanosine (G) to adenine (A), for which gene editing (editing of mutated genes) is a promising therapeutic technique. In C-to-Uridine (U) RNA editing, it converts the base C-to-U in RNA molecules and leads to nonsynonymous changes when occurring in coding regions; however, for G-to-A mutations, A-to-I editing occurs. Editing of C-to-U is not as physiologically common as that of A-to-I editing. Although hundreds to thousands of coding sites have been found to be C-to-U edited or editable in humans, the biological significance of this phenomenon remains elusive. In this review, we have tried to provide detailed information on physiological and artificial approaches for C-to-U RNA editing.
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20
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Hsueh BY, Severin GB, Elg CA, Waldron EJ, Kant A, Wessel AJ, Dover JA, Rhoades CR, Ridenhour BJ, Parent KN, Neiditch MB, Ravi J, Top EM, Waters CM. Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria. Nat Microbiol 2022; 7:1210-1220. [PMID: 35817890 PMCID: PMC9830645 DOI: 10.1038/s41564-022-01162-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/24/2022] [Indexed: 02/03/2023]
Abstract
Vibrio cholerae biotype El Tor is perpetuating the longest cholera pandemic in recorded history. The genomic islands VSP-1 and VSP-2 distinguish El Tor from previous pandemic V. cholerae strains. Using a co-occurrence analysis of VSP genes in >200,000 bacterial genomes we built gene networks to infer biological functions encoded in these islands. This revealed that dncV, a component of the cyclic-oligonucleotide-based anti-phage signalling system (CBASS) anti-phage defence system, co-occurs with an uncharacterized gene vc0175 that we rename avcD for anti-viral cytodine deaminase. We show that AvcD is a deoxycytidylate deaminase and that its activity is post-translationally inhibited by a non-coding RNA named AvcI. AvcID and bacterial homologues protect bacterial populations against phage invasion by depleting free deoxycytidine nucleotides during infection, thereby decreasing phage replication. Homologues of avcD exist in all three domains of life, and bacterial AvcID defends against phage infection by combining traits of two eukaryotic innate viral immunity proteins, APOBEC and SAMHD1.
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Affiliation(s)
- Brian Y Hsueh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Geoffrey B Severin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Clinton A Elg
- Department of Biological Sciences, Institute for Interdisciplinary Data Sciences, Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID, USA
| | - Evan J Waldron
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Abhiruchi Kant
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Alex J Wessel
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - John A Dover
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Christopher R Rhoades
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Benjamin J Ridenhour
- Department of Mathematics and Statistical Sciences, University of Idaho, Moscow, ID, USA
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Matthew B Neiditch
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Janani Ravi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, USA
| | - Eva M Top
- Department of Biological Sciences, Institute for Interdisciplinary Data Sciences, Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID, USA
| | - Christopher M Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
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21
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Majid SA, Mir JM, Bhat MA, Shalla AH, Pandey A, Hadda TB, Abdellattif MH. A pair of carbazate derivatives as novel Schiff base ligands: DFT and POM theory supported spectroscopic and biological evaluation. J Biomol Struct Dyn 2022:1-17. [PMID: 35751130 DOI: 10.1080/07391102.2022.2090437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Schiff bases are mentioned as strongly important molecular scaffolds of industrial and medicinal purposes. Due to wide range applications of carbazate derivatives herein synthesis and characterization of a new Schiff base ligand, (E)-ethyl 2-(4-methoxybenzylidene)hydrazinecarboxylate and 4-(nitrobenzaldehyde)ethylcarbazate are reported. The compound was characterized on the basis of experimental and density functional theory calculations (using the B3LYP and 6-31 G(d,p)formalism combination). Among characterization techniques elemental analysis, FT-IR, UV-Vis and NMR spectroscopic evaluations were mainly employed to carry out the formulation of the compound. In addition to computational validation of characterization other significant molecular parameters were also evaluated including geometry optimization, frontier molecular orbital analysis (FMO) and Columbic interaction of different constituent atoms of the title compound. A good agreement has been found between DFT and experimental outcomes confined to prove the structure of the compound. Moreover, molecular docking and antimicrobial studies have proven the Schiff base as an effective bioactive compound.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sheikh Abdul Majid
- Department of Chemistry, Islamic University of Science and Technology Awantipora, Pulwama, Jammu and Kashmir, India
| | - Jan Mohammad Mir
- Department of Chemistry, Islamic University of Science and Technology Awantipora, Pulwama, Jammu and Kashmir, India.,Department of Chemistry and Pharmacy, RD University, Jabalpur, Madhya Pradesh, India
| | - Muzzaffar A Bhat
- Department of Chemistry, Islamic University of Science and Technology Awantipora, Pulwama, Jammu and Kashmir, India
| | - Aabid Hussain Shalla
- Department of Chemistry, Islamic University of Science and Technology Awantipora, Pulwama, Jammu and Kashmir, India
| | - Abhishek Pandey
- Department of Chemistry and Pharmacy, RD University, Jabalpur, Madhya Pradesh, India
| | - Taibi Ben Hadda
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Magda H Abdellattif
- Department of Chemistry, College of Science, Taif University, Al-Haweiah, Taif, Saudi Arabia
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22
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Jakobsdottir GM, Brewer DS, Cooper C, Green C, Wedge DC. APOBEC3 mutational signatures are associated with extensive and diverse genomic instability across multiple tumour types. BMC Biol 2022; 20:117. [PMID: 35597990 PMCID: PMC9124393 DOI: 10.1186/s12915-022-01316-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The APOBEC3 (apolipoprotein B mRNA editing enzyme catalytic polypeptide 3) family of cytidine deaminases is responsible for two mutational signatures (SBS2 and SBS13) found in cancer genomes. APOBEC3 enzymes are activated in response to viral infection, and have been associated with increased mutation burden and TP53 mutation. In addition to this, it has been suggested that APOBEC3 activity may be responsible for mutations that do not fall into the classical APOBEC3 signatures (SBS2 and SBS13), through generation of double strand breaks.Previous work has mainly focused on the effects of APOBEC3 within individual tumour types using exome sequencing data. Here, we use whole genome sequencing data from 2451 primary tumours from 39 different tumour types in the Pan-Cancer Analysis of Whole Genomes (PCAWG) data set to investigate the relationship between APOBEC3 and genomic instability (GI). RESULTS AND CONCLUSIONS We found that the number of classical APOBEC3 signature mutations correlates with increased mutation burden across different tumour types. In addition, the number of APOBEC3 mutations is a significant predictor for six different measures of GI. Two GI measures (INDELs attributed to INDEL signatures ID6 and ID8) strongly suggest the occurrence and error prone repair of double strand breaks, and the relationship between APOBEC3 mutations and GI remains when SNVs attributed to kataegis are excluded.We provide evidence that supports a model of cancer genome evolution in which APOBEC3 acts as a causative factor in the development of diverse and widespread genomic instability through the generation of double strand breaks. This has important implications for treatment approaches for cancers that carry APOBEC3 mutations, and challenges the view that APOBECs only act opportunistically at sites of single stranded DNA.
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Affiliation(s)
- G Maria Jakobsdottir
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
- Manchester Cancer Research Centre, University of Manchester, Wilmslow Road, Manchester, M20 4GJ, UK
| | - Daniel S Brewer
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Colin Cooper
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Catherine Green
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - David C Wedge
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK.
- Manchester Cancer Research Centre, University of Manchester, Wilmslow Road, Manchester, M20 4GJ, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, OX4 2PG, UK.
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23
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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.
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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.
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24
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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.
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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,
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25
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Abstract
The AID/APOBEC polynucleotide cytidine deaminases have historically been classified as either DNA mutators or RNA editors based on their first identified nucleic acid substrate preference. DNA mutators can generate functional diversity at antibody genes but also cause genomic instability in cancer. RNA editors can generate informational diversity in the transcriptome of innate immune cells, and of cancer cells. Members of both classes can act as antiviral restriction factors. Recent structural work has illuminated differences and similarities between AID/APOBEC enzymes that can catalyse DNA mutation, RNA editing or both, suggesting that the strict functional classification of members of this family should be reconsidered. As many of these enzymes have been employed for targeted genome (or transcriptome) editing, a more holistic understanding will help improve the design of therapeutically relevant programmable base editors. In this Perspective, Pecori et al. provide an overview of the AID/APOBEC cytidine deaminase family, discussing key structural features, how they contribute to viral and tumour evolution and how they can be harnessed for (potentially therapeutic) base-editing purposes.
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26
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Dean W. Pathways of DNA Demethylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:211-238. [DOI: 10.1007/978-3-031-11454-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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The optimal pH of AID is skewed from that of its catalytic pocket by DNA-binding residues and surface charge. Biochem J 2021; 479:39-55. [PMID: 34870314 DOI: 10.1042/bcj20210529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022]
Abstract
Activation-induced cytidine deaminase (AID) is a member of the apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) family of cytidine deaminases. AID mutates immunoglobulin loci to initiate secondary antibody diversification. The APOBEC3 (A3) sub-branch mutates viral pathogens in the cytosol and acidic endosomal compartments. Accordingly, AID functions optimally near neutral pH, while most A3s are acid-adapted (optimal pH 5.5-6.5). To gain a structural understanding for this pH disparity, we constructed high-resolution maps of AID catalytic activity vs pH. We found AID's optimal pH was 7.3 but it retained most (>70%) of the activity at pH 8. Probing of ssDNA-binding residues near the catalytic pocket, key for bending ssDNA into the pocket (e.g R25) yielded mutants with altered pH preference, corroborating previous findings that the equivalent residue in APOBEC3G (H216) underlies its acidic pH preference. AID from bony fish exhibited more basic optimal pH (pH 7.5-8.1) and several R25-equivalent mutants altered pH preference. Comparison of pH optima across the AID/APOBEC3 family revealed an inverse correlation between positive surface charge and overall catalysis. The paralogue with the most robust catalytic activity (APOBEC3A) has the lowest surface charge, most acidic pH preference, while the paralogue with the most lethargic catalytic rate (AID) has the most positive surface charge and highest optimal pH. We suggest one possible mechanism is through surface charge dictating an overall optimal pH that is different from the optimal pH of the catalytic pocket microenvironment. These findings illuminate an additional structural mechanism that regulates AID/APOBEC3 mutagenesis.
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28
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Scholtes GK, Sawyer AM, Vaca CC, Clerc I, Roh M, Song C, D'Aquila RT. The von Hippel-Lindau Cullin-RING E3 ubiquitin ligase regulates APOBEC3 cytidine deaminases. Transl Res 2021; 237:1-15. [PMID: 34004371 PMCID: PMC8440357 DOI: 10.1016/j.trsl.2021.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
The 7 members of the A3 family of cytidine deaminases (A3A to A3H) share a conserved catalytic activity that converts cytidines in single-stranded (ss) DNA into uridines, thereby inducing mutations. After their initial identification as cell-intrinsic defenses against HIV and other retroviruses, A3s were also found to impair many additional viruses. Moreover, some of the A3 proteins (A3A, A3B, and A3H haplotype I) are dysregulated in cancer cells, thereby causing chromosomal mutations that can be selected to fuel progression of malignancy. Viral mechanisms that increase transcription of A3 genes or induce proteasomal degradation of A3 proteins have been characterized. However, only a few underlying biological mechanisms regulating levels of A3s in uninfected cells have been described. Here, we characterize that the von Hippel-Lindau tumor suppressor (pVHL), via its CRLpVHL, induces degradation of all 7 A3 proteins. Two independent lines of evidence supported the conclusion that the multiprotein CRLpVHL complex is necessary for A3 degradation. CRLpVHL more effectively induced degradation of nuclear, procancer A3 (A3B) than the cytoplasmic, antiretroviral A3 (A3G). These results identify specific cellular factors that regulate A3s post-translationally.
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Affiliation(s)
- Gael K Scholtes
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Aubrey M Sawyer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Cristina C Vaca
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Isabelle Clerc
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Meejeon Roh
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Chisu Song
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Richard T D'Aquila
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
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29
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Hou S, Lee JM, Myint W, Matsuo H, Kurt Yilmaz N, Schiffer CA. Structural basis of substrate specificity in human cytidine deaminase family APOBEC3s. J Biol Chem 2021; 297:100909. [PMID: 34171358 PMCID: PMC8313598 DOI: 10.1016/j.jbc.2021.100909] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 06/21/2021] [Accepted: 06/21/2021] [Indexed: 01/22/2023] Open
Abstract
The human cytidine deaminase family of APOBEC3s (A3s) plays critical roles in both innate immunity and the development of cancers. A3s comprise seven functionally overlapping but distinct members that can be exploited as nucleotide base editors for treating genetic diseases. Although overall structurally similar, A3s have vastly varying deamination activity and substrate preferences. Recent crystal structures of ssDNA-bound A3s together with experimental studies have provided some insights into distinct substrate specificities among the family members. However, the molecular interactions responsible for their distinct biological functions and how structure regulates substrate specificity are not clear. In this study, we identified the structural basis of substrate specificities in three catalytically active A3 domains whose crystal structures have been previously characterized: A3A, A3B- CTD, and A3G-CTD. Through molecular modeling and dynamic simulations, we found an interdependency between ssDNA substrate binding conformation and nucleotide sequence specificity. In addition to the U-shaped conformation seen in the crystal structure with the CTC0 motif, A3A can accommodate the CCC0 motif when ssDNA is in a more linear (L) conformation. A3B can also bind both U- and L-shaped ssDNA, unlike A3G, which can stably recognize only linear ssDNA. These varied conformations are stabilized by sequence-specific interactions with active site loops 1 and 7, which are highly variable among A3s. Our results explain the molecular basis of previously observed substrate specificities in A3s and have implications for designing A3-specific inhibitors for cancer therapy as well as engineering base-editing systems for gene therapy.
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Affiliation(s)
- Shurong Hou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jeong Min Lee
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Wazo Myint
- Basic Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Hiroshi Matsuo
- Basic Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
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30
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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 DOI: 10.1177/15353702211031247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 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.
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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
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31
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Gaba A, Flath B, Chelico L. Examination of the APOBEC3 Barrier to Cross Species Transmission of Primate Lentiviruses. Viruses 2021; 13:1084. [PMID: 34200141 PMCID: PMC8228377 DOI: 10.3390/v13061084] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
The transmission of viruses from animal hosts into humans have led to the emergence of several diseases. Usually these cross-species transmissions are blocked by host restriction factors, which are proteins that can block virus replication at a specific step. In the natural virus host, the restriction factor activity is usually suppressed by a viral antagonist protein, but this is not the case for restriction factors from an unnatural host. However, due to ongoing viral evolution, sometimes the viral antagonist can evolve to suppress restriction factors in a new host, enabling cross-species transmission. Here we examine the classical case of this paradigm by reviewing research on APOBEC3 restriction factors and how they can suppress human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). APOBEC3 enzymes are single-stranded DNA cytidine deaminases that can induce mutagenesis of proviral DNA by catalyzing the conversion of cytidine to promutagenic uridine on single-stranded viral (-)DNA if they escape the HIV/SIV antagonist protein, Vif. APOBEC3 degradation is induced by Vif through the proteasome pathway. SIV has been transmitted between Old World Monkeys and to hominids. Here we examine the adaptations that enabled such events and the ongoing impact of the APOBEC3-Vif interface on HIV in humans.
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Affiliation(s)
| | | | - Linda Chelico
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SA S7H 0E5, Canada; (A.G.); (B.F.)
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32
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Hu Y, Knecht KM, Shen Q, Xiong Y. Multifaceted HIV-1 Vif interactions with human E3 ubiquitin ligase and APOBEC3s. FEBS J 2021; 288:3407-3417. [PMID: 32893454 PMCID: PMC8172064 DOI: 10.1111/febs.15550] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/01/2020] [Indexed: 12/31/2022]
Abstract
APOBEC3 (A3) proteins are a family of host antiviral restriction factors that potently inhibit various retroviral infections, including human immunodeficiency virus (HIV)-1. To overcome this restriction, HIV-1 virion infectivity factor (Vif) recruits the cellular cofactor CBFβ to assist in targeting A3 proteins to a host E3 ligase complex for polyubiquitination and subsequent proteasomal degradation. Intervention of the Vif-A3 interactions could be a promising therapeutic strategy to facilitate A3-mediated suppression of HIV-1 in patients. In this structural snapshot, we review the structural features of the recently determined structure of human A3F in complex with HIV-1 Vif and its cofactor CBFβ, discuss insights into the molecular principles of Vif-A3 interplay during the arms race between the virus and host, and highlight the therapeutic implications.
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Affiliation(s)
- Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Kirsten M. Knecht
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Qi Shen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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33
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Ghorbani A, Quinlan EM, Larijani M. Evolutionary Comparative Analyses of DNA-Editing Enzymes of the Immune System: From 5-Dimensional Description of Protein Structures to Immunological Insights and Applications to Protein Engineering. Front Immunol 2021; 12:642343. [PMID: 34135887 PMCID: PMC8201067 DOI: 10.3389/fimmu.2021.642343] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/06/2021] [Indexed: 01/02/2023] Open
Abstract
The immune system is unique among all biological sub-systems in its usage of DNA-editing enzymes to introduce targeted gene mutations and double-strand DNA breaks to diversify antigen receptor genes and combat viral infections. These processes, initiated by specific DNA-editing enzymes, often result in mistargeted induction of genome lesions that initiate and drive cancers. Like other molecules involved in human health and disease, the DNA-editing enzymes of the immune system have been intensively studied in humans and mice, with little attention paid (< 1% of published studies) to the same enzymes in evolutionarily distant species. Here, we present a systematic review of the literature on the characterization of one such DNA-editing enzyme, activation-induced cytidine deaminase (AID), from an evolutionary comparative perspective. The central thesis of this review is that although the evolutionary comparative approach represents a minuscule fraction of published works on this and other DNA-editing enzymes, this approach has made significant impacts across the fields of structural biology, immunology, and cancer research. Using AID as an example, we highlight the value of the evolutionary comparative approach in discoveries already made, and in the context of emerging directions in immunology and protein engineering. We introduce the concept of 5-dimensional (5D) description of protein structures, a more nuanced view of a structure that is made possible by evolutionary comparative studies. In this higher dimensional view of a protein's structure, the classical 3-dimensional (3D) structure is integrated in the context of real-time conformations and evolutionary time shifts (4th dimension) and the relevance of these dynamics to its biological function (5th dimension).
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Affiliation(s)
- Atefeh Ghorbani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Emma M Quinlan
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Mani Larijani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
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Kottke T, Tonne J, Evgin L, Driscoll CB, van Vloten J, Jennings VA, Huff AL, Zell B, Thompson JM, Wongthida P, Pulido J, Schuelke MR, Samson A, Selby P, Ilett E, McNiven M, Roberts LR, Borad MJ, Pandha H, Harrington K, Melcher A, Vile RG. Oncolytic virotherapy induced CSDE1 neo-antigenesis restricts VSV replication but can be targeted by immunotherapy. Nat Commun 2021; 12:1930. [PMID: 33772027 PMCID: PMC7997928 DOI: 10.1038/s41467-021-22115-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/25/2021] [Indexed: 01/06/2023] Open
Abstract
In our clinical trials of oncolytic vesicular stomatitis virus expressing interferon beta (VSV-IFNβ), several patients achieved initial responses followed by aggressive relapse. We show here that VSV-IFNβ-escape tumors predictably express a point-mutated CSDE1P5S form of the RNA-binding Cold Shock Domain-containing E1 protein, which promotes escape as an inhibitor of VSV replication by disrupting viral transcription. Given time, VSV-IFNβ evolves a compensatory mutation in the P/M Inter-Genic Region which rescues replication in CSDE1P5S cells. These data show that CSDE1 is a major cellular co-factor for VSV replication. However, CSDE1P5S also generates a neo-epitope recognized by non-tolerized T cells. We exploit this predictable neo-antigenesis to drive, and trap, tumors into an escape phenotype, which can be ambushed by vaccination against CSDE1P5S, preventing tumor escape. Combining frontline therapy with escape-targeting immunotherapy will be applicable across multiple therapies which drive tumor mutation/evolution and simultaneously generate novel, targetable immunopeptidomes associated with acquired treatment resistance.
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Affiliation(s)
- Timothy Kottke
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jason Tonne
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Laura Evgin
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Jacob van Vloten
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Victoria A Jennings
- Chester Beatty Laboratories, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Amanda L Huff
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Brady Zell
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jill M Thompson
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Jose Pulido
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Adel Samson
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Peter Selby
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Elizabeth Ilett
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Mark McNiven
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Mitesh J Borad
- Division of Hematology/Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Hardev Pandha
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Kevin Harrington
- Chester Beatty Laboratories, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Alan Melcher
- Chester Beatty Laboratories, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Richard G Vile
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA.
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK.
- Department of Immunology, Mayo Clinic, Rochester, MN, USA.
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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: 6] [Impact Index Per Article: 2.0] [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.
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Roufas C, Georgakopoulos-Soares I, Zaravinos A. Molecular correlates of immune cytolytic subgroups in colorectal cancer by integrated genomics analysis. NAR Cancer 2021; 3:zcab005. [PMID: 34316699 PMCID: PMC8210146 DOI: 10.1093/narcan/zcab005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 12/17/2022] Open
Abstract
Although immune checkpoint inhibition (ICI) has shown promising results in metastatic dMMR/MSI-H colorectal cancer (CRC), the majority of pMMR/MSS patients do not respond to such therapies. To systematically evaluate the determinants of immune response in CRC, we explored whether patients with diverse levels of immune cytolytic activity (CYT) have different patterns of chromothripsis and kataegis. Analysis of CRC genomic data from the TCGA, indicated an excess of chromothriptic clusters among CYT-low colon adenocarcinomas, affecting known cancer drivers (APC, KRAS, BRAF, TP53 and FBXW7), immune checkpoints (CD274, PDCD1LG2, IDO1/2 and LAG3) and immune-related genes (ENTPD1, PRF1, NKG7, FAS, GZMA/B/H/K and CD73). CYT-high tumors were characterized by hypermutation, enrichment in APOBEC-associated mutations and kataegis events, as well as APOBEC activation. We also assessed differences in the most prevalent mutational signatures (SBS15, SBS20, SBS54 and DBS2) across cytolytic subgroups. Regarding the composition of immune cells in the tumor milieu, we found enrichment of M1 macrophages, CD8+ T cells and Tregs, as well as higher CD8+ T-cells/Tregs ratio among CYT-high tumors. CYT-high patients had higher immunophenoscores, which is predictive of their responsiveness if they were to be treated with anti-PD-1 alone or in combination with anti-CTLA-4 drugs. These results could have implications for patient responsiveness to immune checkpoint inhibitors.
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Affiliation(s)
- Constantinos Roufas
- Department of Life Sciences, School of Sciences, European University Cyprus, 1516 Nicosia, Cyprus
| | - Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Apostolos Zaravinos
- Department of Basic Medical Sciences, College of Medicine, Member of QU Health, Qatar University, 2713 Doha, Qatar
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Barzak FM, Ryan TM, Kvach MV, Kurup HM, Aihara H, Harris RS, Filichev VV, Harjes E, Jameson GB. Small-Angle X-ray Scattering Models of APOBEC3B Catalytic Domain in a Complex with a Single-Stranded DNA Inhibitor. Viruses 2021; 13:290. [PMID: 33673243 PMCID: PMC7918907 DOI: 10.3390/v13020290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open
Abstract
In normal cells APOBEC3 (A3A-A3H) enzymes as part of the innate immune system deaminate cytosine to uracil on single-stranded DNA (ssDNA) to scramble DNA in order to give protection against a range of exogenous retroviruses, DNA-based parasites, and endogenous retroelements. However, some viruses and cancer cells use these enzymes, especially A3A and A3B, to escape the adaptive immune response and thereby lead to the evolution of drug resistance. We have synthesized first-in-class inhibitors featuring modified ssDNA. We present models based on small-angle X-ray scattering (SAXS) data that (1) confirm that the mode of binding of inhibitor to an active A3B C-terminal domain construct in the solution state is the same as the mode of binding substrate to inactive mutants of A3A and A3B revealed in X-ray crystal structures and (2) give insight into the disulfide-linked inactive dimer formed under the oxidizing conditions of purification.
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Affiliation(s)
- Fareeda M. Barzak
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
| | - Timothy M. Ryan
- SAXS/WAXS, Australian Synchrotron/ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia;
| | - Maksim V. Kvach
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
| | - Harikrishnan M. Kurup
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.); (R.S.H.)
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.); (R.S.H.)
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Vyacheslav V. Filichev
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Geoffrey B. Jameson
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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Oreste U, Ametrano A, Coscia MR. On Origin and Evolution of the Antibody Molecule. BIOLOGY 2021; 10:biology10020140. [PMID: 33578914 PMCID: PMC7916673 DOI: 10.3390/biology10020140] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/29/2022]
Abstract
Simple Summary Like many other molecules playing vital functions in animals, the antibody molecule possesses a complex structure with distinctive features. The structure of the basic unit, i.e., the immunoglobulin domain of very ancient origin is substantially simple. However, high complexity resides in the types and numbers of the domains composing the whole molecule. The emergence of the antibody molecule during evolution overturned the effectiveness of the organisms’ defense system. The particular organization of the coding genes, the mechanisms generating antibody diversity, and the plasticity of the overall protein structure, attest to an extraordinary successful evolutionary history. Here, we attempt to trace, across the evolutionary scale, the very early origins of the most significant features characterizing the structure of the antibody molecule and of the molecular mechanisms underlying its major role in recognizing an almost unlimited number of pathogens. Abstract The vertebrate immune system provides a powerful defense because of the ability to potentially recognize an unlimited number of pathogens. The antibody molecule, also termed immunoglobulin (Ig) is one of the major mediators of the immune response. It is built up from two types of Ig domains: the variable domain, which provides the capability to recognize and bind a potentially infinite range of foreign substances, and the constant domains, which exert the effector functions. In the last 20 years, advances in our understanding of the molecular mechanisms and structural features of antibody in mammals and in a variety of other organisms have uncovered the underlying principles and complexity of this fundamental molecule. One notable evolutionary topic is the origin and evolution of antibody. Many aspects have been clearly stated, but some others remain limited or obscure. By considering a wide range of prokaryotic and eukaryotic organisms through a literature survey about the topic, we have provided an integrated view of the emergence of antibodies in evolution and underlined the very ancient origins.
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Affiliation(s)
- Umberto Oreste
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino, 111, 80131 Naples, Italy; (U.O.); (A.A.)
| | - Alessia Ametrano
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino, 111, 80131 Naples, Italy; (U.O.); (A.A.)
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy
| | - Maria Rosaria Coscia
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino, 111, 80131 Naples, Italy; (U.O.); (A.A.)
- Correspondence: ; Tel.: +39-081-6132556
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IgH 3' regulatory region increases ectopic class switch recombination. PLoS Genet 2021; 17:e1009288. [PMID: 33556079 PMCID: PMC7869978 DOI: 10.1371/journal.pgen.1009288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/24/2020] [Indexed: 11/19/2022] Open
Abstract
DNA lesions inflicted by activation-induced deaminase (AID) instrumentally initiate the processes reshaping immunoglobulin genes in mature B-cells, from local somatic hypermutation (SHM) to junctions of distant breaks during class switch recombination (CSR). It remains incompletely understood how these divergent outcomes of AID attacks are differentially and temporally focused, with CSR strictly occurring in the Ig heavy chain (IgH) locus while SHM concentrates on rearranged V(D)J regions in the IgH and Ig light chain loci. In the IgH locus, disruption of either the 3’Regulatory Region (3’RR) super-enhancer or of switch (S) regions preceding constant genes, profoundly affects CSR. Reciprocally, we now examined if these elements are sufficient to induce CSR in a synthetic locus based on the Igκ locus backbone. Addition of a surrogate “core 3’RR” (c3’RR) and of a pair of transcribed and spliced Switch regions, together with a reporter system for “κ-CSR” yielded a switchable Igκ locus. While the c3’RR stimulated SHM at S regions, it also lowered the local SHM threshold necessary for switch recombination to occur. The 3’RR thus both helps recruit AID to initiate DNA lesions, but then also promotes their resolution through long-distance synapses and recombination following double-strand breaks. Class switching allows B lymphocytes to replace expression of immunoglobin M with that of immunoglobulins G, A or E. The genetic support of class switching, is a unique and large deletion uniquely occuring within the immunoglobulin heavy chain (IgH) locus. This recombination is triggered after DNA lesions inflicted by the activation-induced deaminase (AID) enzyme. In immunoglobulin light chain loci, AID only stimulates somatic hypermutation. In such a non-IgH locus, we now show that the IgH 3’ superenhancer can promote junctions between distant DNA breaks and ectopic class switch recombination. This study identifies the minimal elements necessary for class-switch recombination to occur instead of hypermutation in a locus targeted by AID, i.e. transcribed (and spliced) target sites for AID in so-called S regions, and the 3’IgH superenhancer which both helps recruit AID for DNA lesions, and helps repair these lesions through distant gene synapsis and recombination.
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40
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Matz H, Munir D, Logue J, Dooley H. The immunoglobulins of cartilaginous fishes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 115:103873. [PMID: 32979434 PMCID: PMC7708420 DOI: 10.1016/j.dci.2020.103873] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/12/2020] [Accepted: 09/16/2020] [Indexed: 05/12/2023]
Abstract
Cartilaginous fishes, comprising the chimeras, sharks, skates, and rays, split from the common ancestor with other jawed vertebrates approx. 450 million years ago. Being the oldest extant taxonomic group to possess an immunoglobulin (Ig)-based adaptive immune system, examination of this group has taught us much about the evolution of adaptive immunity, as well as the conserved and taxon-specific characteristics of Igs. Significant progress has been made analyzing sequences from numerous genomic and transcriptomic data sets. These findings have been supported by additional functional studies characterizing the Igs and humoral response of sharks and their relatives. This review will summarize what we have learned about the genomic organization, protein structure, and in vivo function of these Ig isotypes in cartilaginous fishes and highlight the areas where our knowledge is still lacking.
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Affiliation(s)
- Hanover Matz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA; Institute of Marine and Environmental Technology, Baltimore, MD, USA
| | - Danish Munir
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - James Logue
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Helen Dooley
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA; Institute of Marine and Environmental Technology, Baltimore, MD, USA.
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41
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Ott JA, Ohta Y, Flajnik MF, Criscitiello MF. Lost structural and functional inter-relationships between Ig and TCR loci in mammals revealed in sharks. Immunogenetics 2021; 73:17-33. [PMID: 33449123 PMCID: PMC7909615 DOI: 10.1007/s00251-020-01183-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022]
Abstract
Immunoglobulins and T cell receptors (TCR) have obvious structural similarities as well as similar immunogenetic diversification and selection mechanisms. Nevertheless, the two receptor systems and the loci that encode them are distinct in humans and classical murine models, and the gene segments comprising each repertoire are mutually exclusive. Additionally, while both B and T cells employ recombination-activating genes (RAG) for primary diversification, immunoglobulins are afforded a supplementary set of activation-induced cytidine deaminase (AID)-mediated diversification tools. As the oldest-emerging vertebrates sharing the same adaptive B and T cell receptor systems as humans, extant cartilaginous fishes allow a potential view of the ancestral immune system. In this review, we discuss breakthroughs we have made in studies of nurse shark (Ginglymostoma cirratum) T cell receptors demonstrating substantial integration of loci and diversification mechanisms in primordial B and T cell repertoires. We survey these findings in this shark model where they were first described, while noting corroborating examples in other vertebrate groups. We also consider other examples where the gnathostome common ancestry of the B and T cell receptor systems have allowed dovetailing of genomic elements and AID-based diversification approaches for the TCR. The cartilaginous fish seem to have retained this T/B cell plasticity to a greater extent than more derived vertebrate groups, but representatives in all vertebrate taxa except bony fish and placental mammals show such plasticity.
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Affiliation(s)
- Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, USA
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, USA
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX, 77843, USA.
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42
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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.
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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.
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Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution. Virology 2021; 556:62-72. [PMID: 33545556 PMCID: PMC7831814 DOI: 10.1016/j.virol.2020.12.018] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022]
Abstract
Members of the APOBEC family of cytidine deaminases show antiviral activities in mammalian cells through lethal editing in the genomes of small DNA viruses, herpesviruses and retroviruses, and potentially those of RNA viruses such as coronaviruses. Consistent with the latter, APOBEC-like directional C→U transitions of genomic plus-strand RNA are greatly overrepresented in SARS-CoV-2 genome sequences of variants emerging during the COVID-19 pandemic. A C→U mutational process may leave evolutionary imprints on coronavirus genomes, including extensive homoplasy from editing and reversion at targeted sites and the occurrence of driven amino acid sequence changes in viral proteins. If sustained over longer periods, this process may account for the previously reported marked global depletion of C and excess of U bases in human seasonal coronavirus genomes. This review synthesizes the current knowledge on APOBEC evolution and function and the evidence of their role in APOBEC-mediated genome editing of SARS-CoV-2 and other coronaviruses. SARS-CoV-2 sequence variants contain an overabundance of C- > U transitions C- > U transitions are the hallmark of the activity of APOBEC cytosine deaminases Further work is needed to determine APOBEC's role in coronavirus evolution
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44
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Jacquet S, Pontier D, Etienne L. Rapid Evolution of HERC6 and Duplication of a Chimeric HERC5/6 Gene in Rodents and Bats Suggest an Overlooked Role of HERCs in Mammalian Immunity. Front Immunol 2021; 11:605270. [PMID: 33391270 PMCID: PMC7775381 DOI: 10.3389/fimmu.2020.605270] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
Studying the evolutionary diversification of mammalian antiviral defenses is of main importance to better understand our innate immune repertoire. The small HERC proteins are part of a multigene family, including HERC5 and HERC6, which have probably diversified through complex evolutionary history in mammals. Here, we performed mammalian-wide phylogenetic and genomic analyses of HERC5 and HERC6, using 83 orthologous sequences from bats, rodents, primates, artiodactyls, and carnivores—the top five representative groups of mammalian evolution. We found that HERC5 has been under weak and differential positive selection in mammals, with only primate HERC5 showing evidences of pathogen-driven selection. In contrast, HERC6 has been under strong and recurrent adaptive evolution in mammals, suggesting past and widespread genetic arms-races with viral pathogens. Importantly, the rapid evolution of mammalian HERC6 spacer domain suggests that it might be a host-pathogen interface, targeting viral proteins and/or being the target of virus antagonists. Finally, we identified a HERC5/6 chimeric gene that arose from independent duplication in rodent and bat lineages and encodes for a conserved HERC5 N-terminal domain and divergent HERC6 spacer and HECT domains. This duplicated chimeric gene highlights adaptations that potentially contribute to rodent and bat immunity. Our findings open new research avenues on the functions of HERC6 and HERC5/6 in mammals, and on their implication in antiviral innate immunity.
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Affiliation(s)
- Stéphanie Jacquet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Villeurbanne, France.,CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France.,LabEx Ecofect, Université de Lyon, Lyon, France
| | - Dominique Pontier
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Villeurbanne, France.,LabEx Ecofect, Université de Lyon, Lyon, France
| | - Lucie Etienne
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France.,LabEx Ecofect, Université de Lyon, Lyon, France
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45
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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.
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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
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46
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The Role of APOBECs in Viral Replication. Microorganisms 2020; 8:microorganisms8121899. [PMID: 33266042 PMCID: PMC7760323 DOI: 10.3390/microorganisms8121899] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/14/2022] Open
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) proteins are a diverse and evolutionarily conserved family of cytidine deaminases that provide a variety of functions from tissue-specific gene expression and immunoglobulin diversity to control of viruses and retrotransposons. APOBEC family expansion has been documented among mammalian species, suggesting a powerful selection for their activity. Enzymes with a duplicated zinc-binding domain often have catalytically active and inactive domains, yet both have antiviral function. Although APOBEC antiviral function was discovered through hypermutation of HIV-1 genomes lacking an active Vif protein, much evidence indicates that APOBECs also inhibit virus replication through mechanisms other than mutagenesis. Multiple steps of the viral replication cycle may be affected, although nucleic acid replication is a primary target. Packaging of APOBECs into virions was first noted with HIV-1, yet is not a prerequisite for viral inhibition. APOBEC antagonism may occur in viral producer and recipient cells. Signatures of APOBEC activity include G-to-A and C-to-T mutations in a particular sequence context. The importance of APOBEC activity for viral inhibition is reflected in the identification of numerous viral factors, including HIV-1 Vif, which are dedicated to antagonism of these deaminases. Such viral antagonists often are only partially successful, leading to APOBEC selection for viral variants that enhance replication or avoid immune elimination.
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47
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Maroufi F, Maali A, Abdollahpour-Alitappeh M, Ahmadi MH, Azad M. CRISPR-mediated modification of DNA methylation pattern in the new era of cancer therapy. Epigenomics 2020; 12:1845-1859. [PMID: 33185489 DOI: 10.2217/epi-2020-0110] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In the last 2 decades, a wide variety of studies have been conducted on epigenetics and its role in various cancers. A major mechanism of epigenetic regulation is DNA methylation, including aberrant DNA methylation variations such as hypermethylation and hypomethylation in the promoters of critical genes, which are commonly detected in tumors and mark the early stages of cancer development. Therefore, epigenetic therapy has been of special importance in the last decade for cancer treatment. In epigenetic therapy, all efforts are made to modulate gene expression to the normal status. Importantly, recent studies have shown that epigenetic therapy is focusing on the new gene editing technology, CRISPR-Cas9. This tool was found to be able to effectively modulate gene expression and alter almost any sequence in the genome of cells, resulting in events such as a change in acetylation, methylation, or histone modifications. Of note, the CRISPR-Cas9 system can be used for the treatment of cancers caused by epigenetic alterations. The CRISPR-Cas9 system has greater advantages than other available methods, including potent activity, easy design and high velocity as well as the ability to target any DNA or RNA site. In this review, we described epigenetic modulators, which can be used in the CRISPR-Cas9 system, as well as their functions in gene expression alterations that lead to cancer initiation and progression. In addition, we surveyed various species of CRISPR-dead Cas9 (dCas9) systems, a mutant version of Cas9 with no endonuclease activity. Such systems are applicable in epigenetic therapy for gene expression modulation through chemical group editing on nucleosomes and chromatin remodeling, which finally return the cell to the normal status and prevent cancer progression.
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Affiliation(s)
- Faezeh Maroufi
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Amirhosein Maali
- Student Research Committee, Pasteur institute of Iran, Tehran, Iran.,Department of Medical Biotechnology, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - Mohammad Hossein Ahmadi
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mehdi Azad
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
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48
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Maiti A, Myint W, Delviks-Frankenberry KA, Hou S, Kanai T, Balachandran V, Sierra Rodriguez C, Tripathi R, Kurt Yilmaz N, Pathak VK, Schiffer CA, Matsuo H. Crystal Structure of a Soluble APOBEC3G Variant Suggests ssDNA to Bind in a Channel that Extends between the Two Domains. J Mol Biol 2020; 432:6042-6060. [PMID: 33098858 DOI: 10.1016/j.jmb.2020.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 11/16/2022]
Abstract
APOBEC3G (A3G) is a single-stranded DNA (ssDNA) cytosine deaminase that can restrict HIV-1 infection by mutating the viral genome. A3G consists of a non-catalytic N-terminal domain (NTD) and a catalytic C-terminal domain (CTD) connected by a short linker. While the CTD catalyzes cytosine deamination, the NTD is believed to provide additional affinity for ssDNA. Structures of both A3G domains have been solved individually; however, a full-length A3G structure has been challenging. Recently, crystal structures of full-length rhesus macaque A3G variants were solved which suggested dimerization mechanisms and RNA binding surfaces, whereas the dimerization appeared to compromise catalytic activity. We determined the crystal structure of a soluble variant of human A3G (sA3G) at 2.5 Å and from these data generated a model structure of wild-type A3G. This model demonstrated that the NTD was rotated 90° relative to the CTD along the major axis of the molecule, an orientation that forms a positively charged channel connected to the CTD catalytic site, consisting of NTD loop-1 and CTD loop-3. Structure-based mutations, in vitro deamination and DNA binding assays, and HIV-1 restriction assays identify R24, located in the NTD loop-1, as essential to a critical interaction with ssDNA. Furthermore, sA3G was shown to bind a deoxy-cytidine dinucleotide near the catalytic Zn2+, yet not in the catalytic position, where the interactions between deoxy-cytidines and CTD loop-1 and loop-7 residues were different from those formed with substrate. These new interactions suggest a mechanism explaining why A3G exhibits a 3' to 5' directional preference in processive deamination.
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Affiliation(s)
- Atanu Maiti
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Wazo Myint
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Krista A Delviks-Frankenberry
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Shurong Hou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Tapan Kanai
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Department of Chemistry, Banasthali University, Banasthali 304022, Rajasthan, India
| | | | | | - Rashmi Tripathi
- Department of Bioscience and Biotechnology, Banasthali University, Banasthali 304022, Rajasthan, India
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, 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.
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Tamalet C, Devaux C, Dubourg G, Colson P. Resistance to human immunodeficiency virus infection: a rare but neglected state. Ann N Y Acad Sci 2020; 1485:22-42. [PMID: 33009659 DOI: 10.1111/nyas.14452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/25/2020] [Accepted: 07/07/2020] [Indexed: 11/29/2022]
Abstract
The natural history of human immunodeficiency virus (HIV) infection is well understood. In most individuals sexually exposed to HIV, the risk of becoming infected depends on the viral load and on sexual practices and gender. However, a low percentage of individuals who practice frequent unprotected sexual intercourse with HIV-infected partners remain uninfected. Although the systematic study of these individuals has made it possible to identify HIV resistance factors including protective genetic patterns, such epidemiological situations remain paradoxical and not fully understood. In vitro experiments have demonstrated that peripheral blood mononuclear cells (PBMCs) from HIV-free, unexposed blood donors are not equally susceptible to HIV infection; in addition, PBMCs from highly exposed seronegative individuals are generally resistant to infection by primary HIV clinical isolates. We review the literature on permissiveness of PBMCs from healthy blood donors and uninfected hyperexposed individuals to sustained infection and replication of HIV-1 in vitro. In addition, we focus on recent evidence indicating that the gut microbiota may either contribute to natural resistance to or delay replication of HIV infected individuals.
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Affiliation(s)
- Catherine Tamalet
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Gregory Dubourg
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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50
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Swiatczak B. Genomic Stress Responses Drive Lymphocyte Evolvability: An Ancient and Ubiquitous Mechanism. Bioessays 2020; 42:e2000032. [PMID: 32767393 DOI: 10.1002/bies.202000032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/03/2020] [Indexed: 12/15/2022]
Abstract
Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which can already be found in bacteria and archaea. These ancient systems of mutagenesis and repair act to increase phenotypic diversity of microbial cell populations and operate to enhance their ability to produce fit variants during stress. Coopted by lymphocytes, the ancient mutagenic processing systems retained their diversification functions instilling the adaptive immune cells with enhanced evolvability and defensive capacity to resist infection and damage. As reviewed here, the ubiquity and conserved character of specialized variation-generating mechanisms from bacteria to lymphocytes highlight the importance of these mechanisms for evolution of life in general.
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Affiliation(s)
- Bartlomiej Swiatczak
- Department of History of Science and Scientific Archeology, University of Science and Technology of China, 96 Jinzhai Rd., Hefei, 230026, China
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