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Colson P, Fantini J, Delerce J, Bader W, Levasseur A, Pontarotti P, Devaux C, Raoult D. "Outlaw" mutations in quasispecies of SARS-CoV-2 inhibit replication. Emerg Microbes Infect 2024; 13:2368211. [PMID: 38916498 PMCID: PMC11207925 DOI: 10.1080/22221751.2024.2368211] [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: 11/09/2023] [Accepted: 06/10/2024] [Indexed: 06/26/2024]
Abstract
The evolution of SARS-CoV-2, the agent of COVID-19, has been remarkable for its high mutation potential, leading to the appearance of variants. Some mutations have never appeared in the published genomes, which represent consensus, or bona fide genomes. Here we tested the hypothesis that mutations that did not appear in consensus genomes were, in fact, as frequent as the mutations that appeared during the various epidemic episodes, but were not expressed because lethal. To identify these mutations, we analysed the genomes of 90 nasopharyngeal samples and the quasispecies determined by next-generation sequencing. Mutations observed in the quasispecies and not in the consensus genomes were considered to be lethal, what we called "outlaw" mutations. Among these mutations, we analysed the 21 most frequent. Eight of these "outlaws" were in the RNA polymerase and we were able to use a structural biology model and molecular dynamics simulations to demonstrate the functional incapacity of these mutated RNA polymerases. Three other mutations affected the spike, a major protein involved in the pathogenesis of COVID-19. Overall, by analysing the SARS-CoV-2 quasispecies obtained during sequencing, this method made it possible to identify "outlaws," showing areas that could potentially become the target of treatments.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Jacques Fantini
- INSERM UMR UA 16, Aix-Marseille Université, Marseille, France
| | | | - Wahiba Bader
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS), Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS), Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, Marseille, France
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2
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Mao XL, Eriani G, Zhou XL. ADATs: roles in tRNA editing and relevance to disease. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39034823 DOI: 10.3724/abbs.2024125] [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: 07/23/2024] Open
Abstract
Transfer RNAs (tRNAs) play central roles in protein biosynthesis. Post-transcriptional RNA modifications affect tRNA function and stability. Among these modifications, RNA editing is a widespread RNA modification in three domains of life. Proteins of the adenosine deaminase acting on tRNA (ADAT) family were discovered more than 20 years ago. They catalyze the deamination of adenosine to inosine (A-to-I) or cytidine to uridine (C-to-U) during tRNA maturation. The most studied example is the TadA- or ADAT2/3-mediated A-to-I conversion of the tRNA wobble position in the anticodon of prokaryotic or eukaryotic tRNAs, respectively. This review provides detailed information on A-to-I and C-to-U editing of tRNAs in different domains of life, presents recent new findings on ADATs for DNA editing, and finally comments on the association of mutations in the ADAT3 gene with intellectual disability.
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Affiliation(s)
- Xue-Ling Mao
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Xiao-Long Zhou
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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3
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Kawale AS, Zou L. Regulation, functional impact, and therapeutic targeting of APOBEC3A in cancer. DNA Repair (Amst) 2024; 141:103734. [PMID: 39047499 DOI: 10.1016/j.dnarep.2024.103734] [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: 05/02/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Enzymes of the apolipoprotein B mRNA editing catalytic polypeptide like (APOBEC) family are cytosine deaminases that convert cytosine to uracil in DNA and RNA. Among these proteins, APOBEC3 sub-family members, APOBEC3A (A3A) and APOBEC3B (A3B), are prominent sources of mutagenesis in cancer cells. The aberrant expression of A3A and A3B in cancer cells leads to accumulation of mutations with specific single-base substitution (SBS) signatures, characterized by C→T and C→G changes, in a number of tumor types. In addition to fueling mutagenesis, A3A and A3B, particularly A3A, induce DNA replication stress, DNA damage, and chromosomal instability through their catalytic activities, triggering a range of cellular responses. Thus, A3A/B have emerged as key drivers of genome evolution during cancer development, contributing to tumorigenesis, tumor heterogeneity, and therapeutic resistance. Yet, the expression of A3A/B in cancer cells presents a cancer vulnerability that can be exploited therapeutically. In this review, we discuss the recent studies that shed light on the mechanisms regulating A3A expression and the impact of A3A in cancer. We also review recent advances in the development of A3A inhibitors and provide perspectives on the future directions of A3A research.
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Affiliation(s)
- Ajinkya S Kawale
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
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Bernal YA, Durán E, Solar I, Sagredo EA, Armisén R. ADAR-Mediated A>I(G) RNA Editing in the Genotoxic Drug Response of Breast Cancer. Int J Mol Sci 2024; 25:7424. [PMID: 39000531 PMCID: PMC11242177 DOI: 10.3390/ijms25137424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 06/13/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Epitranscriptomics is a field that delves into post-transcriptional changes. Among these modifications, the conversion of adenosine to inosine, traduced as guanosine (A>I(G)), is one of the known RNA-editing mechanisms, catalyzed by ADARs. This type of RNA editing is the most common type of editing in mammals and contributes to biological diversity. Disruption in the A>I(G) RNA-editing balance has been linked to diseases, including several types of cancer. Drug resistance in patients with cancer represents a significant public health concern, contributing to increased mortality rates resulting from therapy non-responsiveness and disease progression, representing the greatest challenge for researchers in this field. The A>I(G) RNA editing is involved in several mechanisms over the immunotherapy and genotoxic drug response and drug resistance. This review investigates the relationship between ADAR1 and specific A>I(G) RNA-edited sites, focusing particularly on breast cancer, and the impact of these sites on DNA damage repair and the immune response over anti-cancer therapy. We address the underlying mechanisms, bioinformatics, and in vitro strategies for the identification and validation of A>I(G) RNA-edited sites. We gathered databases related to A>I(G) RNA editing and cancer and discussed the potential clinical and research implications of understanding A>I(G) RNA-editing patterns. Understanding the intricate role of ADAR1-mediated A>I(G) RNA editing in breast cancer holds significant promise for the development of personalized treatment approaches tailored to individual patients' A>I(G) RNA-editing profiles.
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Affiliation(s)
- Yanara A Bernal
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| | - Eduardo Durán
- Subdepartamento de Genómica y Genética Molecular, Sección Genética Humana, Instituto de Salud Pública de Chile, Avenida Marathon 1000, Ñuñoa, Santiago 7780050, Chile
| | - Isidora Solar
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| | - Eduardo A Sagredo
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-171 77 Stockholm, Sweden
| | - Ricardo Armisén
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
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5
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Brown GW. The cytidine deaminase APOBEC3C has unique sequence and genome feature preferences. Genetics 2024:iyae092. [PMID: 38946641 DOI: 10.1093/genetics/iyae092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/22/2024] [Indexed: 07/02/2024] Open
Abstract
APOBEC proteins are cytidine deaminases that restrict the replication of viruses and transposable elements. Several members of the APOBEC3 family, APOBEC3A, APOBEC3B, and APOBEC3H-I, can access the nucleus and cause what is thought to be indiscriminate deamination of the genome, resulting in mutagenesis and genome instability. Although APOBEC3C is also present in the nucleus, the full scope of its deamination target preferences is unknown. By expressing human APOBEC3C in a yeast model system, I have defined the APOBEC3C mutation signature, as well as the preferred genome features of APOBEC3C targets. The APOBEC3C mutation signature is distinct from those of the known cancer genome mutators APOBEC3A and APOBEC3B. APOBEC3C produces DNA strand-coordinated mutation clusters, and APOBEC3C mutations are enriched near the transcription start sites of active genes. Surprisingly, APOBEC3C lacks the bias for the lagging strand of DNA replication that is seen for APOBEC3A and APOBEC3B. The unique preferences of APOBEC3C constitute a mutation profile that will be useful in defining sites of APOBEC3C mutagenesis in human genomes.
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Affiliation(s)
- Grant W Brown
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, Canada M5S 1A8
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 3E1
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6
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Li Y, Zhu R, Jin J, Guo H, Zhang J, He Z, Liang T, Guo L. Exploring the Role of Clustered Mutations in Carcinogenesis and Their Potential Clinical Implications in Cancer. Int J Mol Sci 2024; 25:6744. [PMID: 38928450 PMCID: PMC11203652 DOI: 10.3390/ijms25126744] [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: 04/23/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Abnormal cell proliferation and growth leading to cancer primarily result from cumulative genome mutations. Single gene mutations alone do not fully explain cancer onset and progression; instead, clustered mutations-simultaneous occurrences of multiple mutations-are considered to be pivotal in cancer development and advancement. These mutations can affect different genes and pathways, resulting in cells undergoing malignant transformation with multiple functional abnormalities. Clustered mutations influence cancer growth rates, metastatic potential, and drug treatment sensitivity. This summary highlights the various types and characteristics of clustered mutations to understand their associations with carcinogenesis and discusses their potential clinical significance in cancer. As a unique mutation type, clustered mutations may involve genomic instability, DNA repair mechanism defects, and environmental exposures, potentially correlating with responsiveness to immunotherapy. Understanding the characteristics and underlying processes of clustered mutations enhances our comprehension of carcinogenesis and cancer progression, providing new diagnostic and therapeutic approaches for cancer.
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Affiliation(s)
- Yi Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Rui Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaming Jin
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Haochuan Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaxi Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Zhiheng He
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Li Guo
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
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7
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Villiger L, Joung J, Koblan L, Weissman J, Abudayyeh OO, Gootenberg JS. CRISPR technologies for genome, epigenome and transcriptome editing. Nat Rev Mol Cell Biol 2024; 25:464-487. [PMID: 38308006 DOI: 10.1038/s41580-023-00697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 02/04/2024]
Abstract
Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health.
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Affiliation(s)
- Lukas Villiger
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA
| | - Julia Joung
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
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8
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Ubhi T, Zaslaver O, Quaile AT, Plenker D, Cao P, Pham NA, Békési A, Jang GH, O'Kane GM, Notta F, Moffat J, Wilson JM, Gallinger S, Vértessy BG, Tuveson DA, Röst HL, Brown GW. Cytidine deaminases APOBEC3C and APOBEC3D promote DNA replication stress resistance in pancreatic cancer cells. NATURE CANCER 2024; 5:895-915. [PMID: 38448522 DOI: 10.1038/s43018-024-00742-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/09/2024] [Indexed: 03/08/2024]
Abstract
Gemcitabine is a potent inhibitor of DNA replication and is a mainstay therapeutic for diverse cancers, particularly pancreatic ductal adenocarcinoma (PDAC). However, most tumors remain refractory to gemcitabine therapies. Here, to define the cancer cell response to gemcitabine, we performed genome-scale CRISPR-Cas9 chemical-genetic screens in PDAC cells and found selective loss of cell fitness upon disruption of the cytidine deaminases APOBEC3C and APOBEC3D. Following gemcitabine treatment, APOBEC3C and APOBEC3D promote DNA replication stress resistance and cell survival by deaminating cytidines in the nuclear genome to ensure DNA replication fork restart and repair in PDAC cells. We provide evidence that the chemical-genetic interaction between APOBEC3C or APOBEC3D and gemcitabine is absent in nontransformed cells but is recapitulated across different PDAC cell lines, in PDAC organoids and in PDAC xenografts. Thus, we uncover roles for APOBEC3C and APOBEC3D in DNA replication stress resistance and offer plausible targets for improving gemcitabine-based therapies for PDAC.
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Affiliation(s)
- Tajinder Ubhi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Olga Zaslaver
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Andrew T Quaile
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Dennis Plenker
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Xilis Inc., Durham, NC, USA
| | - Pinjiang Cao
- Living Biobank, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Living Biobank, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Angéla Békési
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Budapest, Hungary
- Genome Metabolism Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Research Network, Budapest, Hungary
| | - Gun-Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Grainne M O'Kane
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Division of Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Julie M Wilson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Beáta G Vértessy
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Budapest, Hungary
- Genome Metabolism Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Research Network, Budapest, Hungary
| | - David A Tuveson
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Hannes L Röst
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Grant W Brown
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
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Crane AB, Jetti SK, Littleton JT. A stochastic RNA editing process targets a limited number of sites in individual Drosophila glutamatergic motoneurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594696. [PMID: 38798345 PMCID: PMC11118563 DOI: 10.1101/2024.05.17.594696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
RNA editing is a post-transcriptional source of protein diversity and occurs across the animal kingdom. Given the complete profile of mRNA targets and their editing rate in individual cells is unclear, we analyzed single cell RNA transcriptomes from Drosophila larval tonic and phasic glutamatergic motoneuron subtypes to determine the most highly edited targets and identify cell-type specific editing. From ∼15,000 genes encoded in the genome, 316 high confidence A-to-I canonical RNA edit sites were identified, with 102 causing missense amino acid changes in proteins regulating membrane excitability, synaptic transmission, and cellular function. Some sites showed 100% editing in single neurons as observed with mRNAs encoding mammalian AMPA receptors. However, most sites were edited at lower levels and generated variable expression of edited and unedited mRNAs within individual neurons. Together, these data provide insights into how the RNA editing landscape alters protein function to modulate the properties of two well-characterized neuronal populations in Drosophila .
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Hewel C, Schmidt H, Runkel S, Kohnen W, Schweiger-Seemann S, Michel A, Bikar SE, Lieb B, Plachter B, Hankeln T, Linke M, Gerber S. Nanopore adaptive sampling of a metagenomic sample derived from a human monkeypox case. J Med Virol 2024; 96:e29610. [PMID: 38654702 DOI: 10.1002/jmv.29610] [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: 11/06/2023] [Revised: 03/18/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
In 2022, a series of human monkeypox cases in multiple countries led to the largest and most widespread outbreak outside the known endemic areas. Setup of proper genomic surveillance is of utmost importance to control such outbreaks. To this end, we performed Nanopore (PromethION P24) and Illumina (NextSeq. 2000) Whole Genome Sequencing (WGS) of a monkeypox sample. Adaptive sampling was applied for in silico depletion of the human host genome, allowing for the enrichment of low abundance viral DNA without a priori knowledge of sample composition. Nanopore sequencing allowed for high viral genome coverage, tracking of sample composition during sequencing, strain determination, and preliminary assessment of mutational pattern. In addition to that, only Nanopore data allowed us to resolve the entire monkeypox virus genome, with respect to two structural variants belonging to the genes OPG015 and OPG208. These SVs in important host range genes seem stable throughout the outbreak and are frequently misassembled and/or misannotated due to the prevalence of short read sequencing or short read first assembly. Ideally, standalone standard Illumina sequencing should not be used for Monkeypox WGS and de novo assembly, since it will obfuscate the structure of the genome, which has an impact on the quality and completeness of the genomes deposited in public databases and thus possibly on the ability to evaluate the complete genetic reason for the host range change of monkeypox in the current pandemic.
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Affiliation(s)
- Charlotte Hewel
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Hanno Schmidt
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Institute for Virology and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Stefan Runkel
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Transfusion Unit & Test Center, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Wolfgang Kohnen
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Department of Hygiene and Infection Prevention, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Susann Schweiger-Seemann
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - André Michel
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Medical Management Department, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sven-Ernö Bikar
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- StarSEQ GmbH, Mainz, Germany
| | | | - Bodo Plachter
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Institute for Virology and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Thomas Hankeln
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Molecular Genetics & Genome Analysis, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Matthias Linke
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- SARS-CoV-2 Sequencing Consortium Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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11
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Lorenzo JP, Molla L, Amro EM, Ibarra IL, Ruf S, Neber C, Gkougkousis C, Ridani J, Subramani PG, Boulais J, Harjanto D, Vonica A, Di Noia JM, Dieterich C, Zaugg JB, Papavasiliou FN. APOBEC2 safeguards skeletal muscle cell fate through binding chromatin and regulating transcription of non-muscle genes during myoblast differentiation. Proc Natl Acad Sci U S A 2024; 121:e2312330121. [PMID: 38625936 PMCID: PMC11047093 DOI: 10.1073/pnas.2312330121] [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: 07/25/2023] [Accepted: 03/07/2024] [Indexed: 04/18/2024] Open
Abstract
The apolipoprotein B messenger RNA editing enzyme, catalytic polypeptide (APOBEC) family is composed of nucleic acid editors with roles ranging from antibody diversification to RNA editing. APOBEC2, a member of this family with an evolutionarily conserved nucleic acid-binding cytidine deaminase domain, has neither an established substrate nor function. Using a cellular model of muscle differentiation where APOBEC2 is inducibly expressed, we confirmed that APOBEC2 does not have the attributed molecular functions of the APOBEC family, such as RNA editing, DNA demethylation, and DNA mutation. Instead, we found that during muscle differentiation APOBEC2 occupied a specific motif within promoter regions; its removal from those regions resulted in transcriptional changes. Mechanistically, these changes reflect the direct interaction of APOBEC2 with histone deacetylase (HDAC) transcriptional corepressor complexes. We also found that APOBEC2 could bind DNA directly, in a sequence-specific fashion, suggesting that it functions as a recruiter of HDAC to specific genes whose promoters it occupies. These genes are normally suppressed during muscle cell differentiation, and their suppression may contribute to the safeguarding of muscle cell fate. Altogether, our results reveal a unique role for APOBEC2 within the APOBEC family.
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Affiliation(s)
- J. Paulo Lorenzo
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg69120, Germany
| | - Linda Molla
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY10065
| | - Elias Moris Amro
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
| | - Ignacio L. Ibarra
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Sandra Ruf
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
| | - Cedrik Neber
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
| | - Christos Gkougkousis
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
| | - Jana Ridani
- Institut de Recherches Cliniques de Montréal, Montréal, QCH2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QCH4A 3J1, Canada
| | - Poorani Ganesh Subramani
- Institut de Recherches Cliniques de Montréal, Montréal, QCH2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QCH4A 3J1, Canada
| | - Jonathan Boulais
- Institut de Recherches Cliniques de Montréal, Montréal, QCH2W 1R7, Canada
| | - Dewi Harjanto
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY10065
| | - Alin Vonica
- Department of Biology, Nazareth University, Rochester, NY14618
| | - Javier M. Di Noia
- Institut de Recherches Cliniques de Montréal, Montréal, QCH2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QCH4A 3J1, Canada
- Department of Medicine, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg69120, Germany
- German Center for Cardiovascular Research (DZHK) - Partner site Heidelberg/Mannheim, Heidelberg69120, Germany
| | - Judith B. Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
| | - F. Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg69120, Germany
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY10065
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12
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De Rosa C, Iommelli F, De Rosa V, Ercolano G, Sodano F, Tuccillo C, Amato L, Tirino V, Ariano A, Cimmino F, di Guida G, Filosa G, di Liello A, Ciardiello D, Martinelli E, Troiani T, Napolitano S, Martini G, Ciardiello F, Papaccio F, Morgillo F, Della Corte CM. PBMCs as Tool for Identification of Novel Immunotherapy Biomarkers in Lung Cancer. Biomedicines 2024; 12:809. [PMID: 38672164 PMCID: PMC11048624 DOI: 10.3390/biomedicines12040809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Lung cancer (LC), including both non-small (NSCLC) and small (SCLC) subtypes, is currently treated with a combination of chemo- and immunotherapy. However, predictive biomarkers to identify high-risk patients are needed. Here, we explore the role of peripheral blood mononuclear cells (PBMCs) as a tool for novel biomarkers searching. METHODS We analyzed the expression of the cGAS-STING pathway, a key DNA sensor that activates during chemotherapy, in PBMCs from LC patients divided into best responders (BR), responders (R) and non-responders (NR). The PBMCs were whole exome sequenced (WES). RESULTS PBMCs from BR and R patients of LC cohorts showed the highest levels of STING (p < 0.0001) and CXCL10 (p < 0.0001). From WES, each subject had at least 1 germline/somatic alteration in a DDR gene and the presence of more DDR gene mutations correlated with clinical responses, suggesting novel biomarker implications. Thus, we tested the effect of the pharmacological DDR inhibitor (DDRi) in PBMCs and in three-dimensional spheroid co-culture of PBMCs and LC cell lines; we found that DDRi strongly increased cGAS-STING expression and tumor infiltration ability of immune cells in NR and R patients. Furthermore, we performed FACS analysis of PBMCs derived from LC patients from the BR, R and NR cohorts and we found that cytotoxic T cell subpopulations displayed the highest STING expression. CONCLUSIONS cGAS-STING signaling activation in PBMCs may be a novel potential predictive biomarker for the response to immunotherapy and high levels are correlated with a better response to treatment along with an overall increased antitumor immune injury.
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Affiliation(s)
- Caterina De Rosa
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (C.D.R.); (C.T.); (L.A.); (A.A.); (G.d.G.); (G.F.); (A.d.L.); (E.M.); (T.T.); (S.N.); (G.M.); (F.C.); (F.M.)
| | - Francesca Iommelli
- Institute of Biostructures and Bioimaging, National Research Council, 80145 Naples, Italy;
| | - Viviana De Rosa
- Institute of Biostructures and Bioimaging, National Research Council, 80145 Naples, Italy;
| | - Giuseppe Ercolano
- Department of Pharmacy, School of Medicine, University of Naples Federico II, 80138 Naples, Italy; (G.E.); (F.S.)
| | - Federica Sodano
- Department of Pharmacy, School of Medicine, University of Naples Federico II, 80138 Naples, Italy; (G.E.); (F.S.)
| | - Concetta Tuccillo
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (C.D.R.); (C.T.); (L.A.); (A.A.); (G.d.G.); (G.F.); (A.d.L.); (E.M.); (T.T.); (S.N.); (G.M.); (F.C.); (F.M.)
| | - Luisa Amato
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (C.D.R.); (C.T.); (L.A.); (A.A.); (G.d.G.); (G.F.); (A.d.L.); (E.M.); (T.T.); (S.N.); (G.M.); (F.C.); (F.M.)
| | - Virginia Tirino
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy;
- U.P. Diagnostica Citometrica e Mutazionale, A.O.U. Vanvitelli, Università degli Studi della Campania, 80138 Naples, Italy
| | - Annalisa Ariano
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (C.D.R.); (C.T.); (L.A.); (A.A.); (G.d.G.); (G.F.); (A.d.L.); (E.M.); (T.T.); (S.N.); (G.M.); (F.C.); (F.M.)
| | - Flora Cimmino
- Hospital “Martiri Di Villa Malta”, 84087 Sarno, Italy;
| | - Gaetano di Guida
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (C.D.R.); (C.T.); (L.A.); (A.A.); (G.d.G.); (G.F.); (A.d.L.); (E.M.); (T.T.); (S.N.); (G.M.); (F.C.); (F.M.)
| | - Gennaro Filosa
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (C.D.R.); (C.T.); (L.A.); (A.A.); (G.d.G.); (G.F.); (A.d.L.); (E.M.); (T.T.); (S.N.); (G.M.); (F.C.); (F.M.)
| | - Alessandra di Liello
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (C.D.R.); (C.T.); (L.A.); (A.A.); (G.d.G.); (G.F.); (A.d.L.); (E.M.); (T.T.); (S.N.); (G.M.); (F.C.); (F.M.)
| | - Davide Ciardiello
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology (IEO), IRCCS, 20141 Milan, Italy;
| | - Erika Martinelli
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (C.D.R.); (C.T.); (L.A.); (A.A.); (G.d.G.); (G.F.); (A.d.L.); (E.M.); (T.T.); (S.N.); (G.M.); (F.C.); (F.M.)
| | - Teresa Troiani
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (C.D.R.); (C.T.); (L.A.); (A.A.); (G.d.G.); (G.F.); (A.d.L.); (E.M.); (T.T.); (S.N.); (G.M.); (F.C.); (F.M.)
| | - Stefania Napolitano
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (C.D.R.); (C.T.); (L.A.); (A.A.); (G.d.G.); (G.F.); (A.d.L.); (E.M.); (T.T.); (S.N.); (G.M.); (F.C.); (F.M.)
| | - Giulia Martini
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (C.D.R.); (C.T.); (L.A.); (A.A.); (G.d.G.); (G.F.); (A.d.L.); (E.M.); (T.T.); (S.N.); (G.M.); (F.C.); (F.M.)
| | - Fortunato Ciardiello
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (C.D.R.); (C.T.); (L.A.); (A.A.); (G.d.G.); (G.F.); (A.d.L.); (E.M.); (T.T.); (S.N.); (G.M.); (F.C.); (F.M.)
| | - Federica Papaccio
- Department of Medicine, Surgery and Dentistry, “Scuola Medica Salernitana”, University of Salerno, 84084 Baronissi, Italy;
| | - Floriana Morgillo
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (C.D.R.); (C.T.); (L.A.); (A.A.); (G.d.G.); (G.F.); (A.d.L.); (E.M.); (T.T.); (S.N.); (G.M.); (F.C.); (F.M.)
| | - Carminia Maria Della Corte
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (C.D.R.); (C.T.); (L.A.); (A.A.); (G.d.G.); (G.F.); (A.d.L.); (E.M.); (T.T.); (S.N.); (G.M.); (F.C.); (F.M.)
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13
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Zhang T, Sang J, Hoang PH, Zhao W, Rosenbaum J, Johnson KE, Klimczak LJ, McElderry J, Klein A, Wirth C, Bergstrom EN, Díaz-Gay M, Vangara R, Colon-Matos F, Hutchinson A, Lawrence SM, Cole N, Zhu B, Przytycka TM, Shi J, Caporaso NE, Homer R, Pesatori AC, Consonni D, Imielinski M, Chanock SJ, Wedge DC, Gordenin DA, Alexandrov LB, Harris RS, Landi MT. APOBEC shapes tumor evolution and age at onset of lung cancer in smokers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587805. [PMID: 38617360 PMCID: PMC11014539 DOI: 10.1101/2024.04.02.587805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
APOBEC enzymes are part of the innate immunity and are responsible for restricting viruses and retroelements by deaminating cytosine residues1,2. Most solid tumors harbor different levels of somatic mutations attributed to the off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B)3-6. However, how APOBEC3A/B enzymes shape the tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, by combining deep whole-genome sequencing with multi-omics profiling of 309 lung cancers from smokers with detailed tobacco smoking information, we identify two subtypes defined by low (LAS) and high (HAS) APOBEC mutagenesis. LAS are enriched for A3B-like mutagenesis and KRAS mutations, whereas HAS for A3A-like mutagenesis and TP53 mutations. Unlike APOBEC3A, APOBEC3B expression is strongly associated with an upregulation of the base excision repair pathway. Hypermutation by unrepaired A3A and tobacco smoking mutagenesis combined with TP53-induced genomic instability can trigger senescence7, apoptosis8, and cell regeneration9, as indicated by high expression of pulmonary healing signaling pathway, stemness markers and distal cell-of-origin in HAS. The expected association of tobacco smoking variables (e.g., time to first cigarette) with genomic/epigenomic changes are not observed in HAS, a plausible consequence of frequent cell senescence or apoptosis. HAS have more neoantigens, slower clonal expansion, and older age at onset compared to LAS, particularly in heavy smokers, consistent with high proportions of newly generated, unmutated cells and frequent immuno-editing. These findings show how heterogeneity in mutational burden across co-occurring mutational processes and cell types contributes to tumor development, with important clinical implications.
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Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H. Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - John McElderry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alyssa Klein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher Wirth
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Frank Colon-Matos
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Scott M. Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nathan Cole
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Robert Homer
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Angela C. Pesatori
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Dario Consonni
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C. Wedge
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, 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
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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14
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Jiang L, Zhang L, Shu Y, Zhang Y, Gao L, Qiu S, Zhang W, Dai W, Chen S, Huang Y, Liu Y. Deciphering the role of Enterococcus faecium cytidine deaminase in gemcitabine resistance of gallbladder cancer. J Biol Chem 2024; 300:107171. [PMID: 38492776 PMCID: PMC11007441 DOI: 10.1016/j.jbc.2024.107171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/28/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
Gemcitabine-based chemotherapy is a cornerstone of standard care for gallbladder cancer (GBC) treatment. Still, drug resistance remains a significant challenge, influenced by factors such as tumor-associated microbiota impacting drug concentrations within tumors. Enterococcus faecium, a member of tumor-associated microbiota, was notably enriched in the GBC patient cluster. In this study, we investigated the biochemical characteristics, catalytic activity, and kinetics of the cytidine deaminase of E. faecium (EfCDA). EfCDA showed the ability to convert gemcitabine to its metabolite 2',2'-difluorodeoxyuridine. Both EfCDA and E. faecium can induce gemcitabine resistance in GBC cells. Moreover, we determined the crystal structure of EfCDA, in its apo form and in complex with 2', 2'-difluorodeoxyuridine at high resolution. Mutation of key residues abolished the catalytic activity of EfCDA and reduced the gemcitabine resistance in GBC cells. Our findings provide structural insights into the molecular basis for recognizing gemcitabine metabolite by a bacteria CDA protein and may provide potential strategies to combat cancer drug resistance and improve the efficacy of gemcitabine-based chemotherapy in GBC treatment.
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Affiliation(s)
- Lin Jiang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China; Department of General Surgery, Shanghai Research Center of Biliary Tract Disease, Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lingxiao Zhang
- Department of General Surgery, Shanghai Research Center of Biliary Tract Disease, Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yijun Shu
- Department of General Surgery, Shanghai Research Center of Biliary Tract Disease, Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhan Zhang
- Department of General Surgery, Shanghai Research Center of Biliary Tract Disease, Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lili Gao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Shimei Qiu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Wenhua Zhang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Wenting Dai
- Department of General Surgery, Shanghai Research Center of Biliary Tract Disease, Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shili Chen
- Department of General Surgery, Shanghai Research Center of Biliary Tract Disease, Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Ying Huang
- Department of General Surgery, Shanghai Research Center of Biliary Tract Disease, Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yingbin Liu
- Department of Biliary-Pancreatic Surgery, Shanghai Key Laboratory for Cancer Systems Regulation and Clinical Translation, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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15
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Witzenberger M, Schwartz S. Directing RNA-modifying machineries towards endogenous RNAs: opportunities and challenges. Trends Genet 2024; 40:313-325. [PMID: 38350740 DOI: 10.1016/j.tig.2024.01.001] [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: 11/16/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 02/15/2024]
Abstract
Over 170 chemical modifications can be naturally installed on RNA, all of which are catalyzed by dedicated machineries. These modifications can alter RNA sequence structure, stability, and translation as well as serving as quality control marks that record aspects of RNA processing. The diverse roles played by RNAs within cells has motivated endeavors to exogenously introduce RNA modifications at target sites for diverse purposes ranging from recording RNA:protein interactions to therapeutic applications. Here, we discuss these applications and the approaches that have been employed to engineer RNA-modifying machineries, and highlight persisting challenges and perspectives.
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Affiliation(s)
- Monika Witzenberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel.
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel.
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16
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Lauring MC, Basu U. Somatic hypermutation mechanisms during lymphomagenesis and transformation. Curr Opin Genet Dev 2024; 85:102165. [PMID: 38428317 DOI: 10.1016/j.gde.2024.102165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 03/03/2024]
Abstract
B cells undergoing physiologically programmed or aberrant genomic alterations provide an opportune system to study the causes and consequences of genome mutagenesis. Activated B cells in germinal centers express activation-induced cytidine deaminase (AID) to accomplish physiological somatic hypermutation (SHM) of their antibody-encoding genes. In attempting to diversify their immunoglobulin (Ig) heavy- and light-chain genes, several B-cell clones successfully optimize their antigen-binding affinities. However, SHM can sometimes occur at non-Ig loci, causing genetic alternations that lay the foundation for lymphomagenesis, particularly diffuse large B-cell lymphoma. Thus, SHM acts as a double-edged sword, bestowing superb humoral immunity at the potential risk of initiating disease. We refer to off-target, non-Ig AID mutations - that are often but not always associated with disease - as aberrant SHM (aSHM). A key challenge in understanding SHM and aSHM is determining how AID targets and mutates specific DNA sequences in the Ig loci to generate antibody diversity and non-Ig genes to initiate lymphomagenesis. Herein, we discuss some current advances regarding the regulation of AID's DNA mutagenesis activity in B cells.
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Affiliation(s)
- Max C Lauring
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York 10032, USA.
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York 10032, USA.
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17
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Teng M, Xia ZJ, Lo N, Daud K, He HH. Assembling the RNA therapeutics toolbox. MEDICAL REVIEW (2021) 2024; 4:110-128. [PMID: 38680684 PMCID: PMC11046573 DOI: 10.1515/mr-2023-0062] [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] [Received: 12/01/2023] [Accepted: 02/29/2024] [Indexed: 05/01/2024]
Abstract
From the approval of COVID-19 mRNA vaccines to the 2023 Nobel Prize awarded for nucleoside base modifications, RNA therapeutics have entered the spotlight and are transforming drug development. While the term "RNA therapeutics" has been used in various contexts, this review focuses on treatments that utilize RNA as a component or target RNA for therapeutic effects. We summarize the latest advances in RNA-targeting tools and RNA-based technologies, including but not limited to mRNA, antisense oligos, siRNAs, small molecules and RNA editors. We focus on the mechanisms of current FDA-approved therapeutics but also provide a discussion on the upcoming workforces. The clinical utility of RNA-based therapeutics is enabled not only by the advances in RNA technologies but in conjunction with the significant improvements in chemical modifications and delivery platforms, which are also briefly discussed in the review. We summarize the latest RNA therapeutics based on their mechanisms and therapeutic effects, which include expressing proteins for vaccination and protein replacement therapies, degrading deleterious RNA, modulating transcription and translation efficiency, targeting noncoding RNAs, binding and modulating protein activity and editing RNA sequences and modifications. This review emphasizes the concept of an RNA therapeutic toolbox, pinpointing the readers to all the tools available for their desired research and clinical goals. As the field advances, the catalog of RNA therapeutic tools continues to grow, further allowing researchers to combine appropriate RNA technologies with suitable chemical modifications and delivery platforms to develop therapeutics tailored to their specific clinical challenges.
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Affiliation(s)
- Mona Teng
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ziting Judy Xia
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Nicholas Lo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Kashif Daud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Housheng Hansen He
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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18
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Kabir F, Plaisance E, Portman A, Marfo A, Cirrincione K, Silva D, Amadi V, Stringer J, Short L. Mpox Viral Lineage Analysis and Technique Development Using Next-generation Sequencing Approach. J Infect Dis 2024; 229:S163-S171. [PMID: 37968965 DOI: 10.1093/infdis/jiad504] [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: 08/16/2023] [Revised: 11/07/2023] [Accepted: 11/11/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND In response to Mpox endemic and public health emergency, DCHHS aimed to develop NGS based techniques to streamline Mpox viral clade and lineage analysis. METHODS The Mpox sequencing workflow started with DNA extraction and adapted Illumina's COVIDSeq assay using hMpox primer pools from Yale School of Public Health. Sequencing steps included cDNA amplification, tagmentation, PCR indexing, pooling libraries, sequencing on MiSeq, data analysis, and report generation. The bioinformatic analysis comprised read assembly and consensus sequence mapping to reference genomes and variant identification, and utilized pipelines including Illumina BaseSpace, NextClade, CLC Workbench, Terra.bio for data quality control (QC) and validation. RESULTS In total, 171 mpox samples were sequenced using modified COVIDSeq workflow and QC metrics were assessed for read quality, depth, and coverage. Multiple analysis pipelines identified the West African clade IIb as the only clade during peak Mpox infection from July through October 2022. Analyses also indicated lineage B.1.2 as the dominant variant comprising the majority of Mpox viral genomes (77.7%), implying its geographical distribution in the United States. Viral sequences were uploaded to GISAID EpiPox. CONCLUSIONS We developed NGS workflows to precisely detect and analyze mpox viral clade and lineages aiding in public health genomic surveillance.
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Affiliation(s)
- Farruk Kabir
- Dallas County Health and Human Services, Dallas, Texas, USA
| | - Erin Plaisance
- Dallas County Health and Human Services, Dallas, Texas, USA
| | | | - Agnes Marfo
- Dallas County Health and Human Services, Dallas, Texas, USA
| | | | - David Silva
- Dallas County Health and Human Services, Dallas, Texas, USA
| | - Victor Amadi
- Dallas County Health and Human Services, Dallas, Texas, USA
| | - Joey Stringer
- Dallas County Health and Human Services, Dallas, Texas, USA
| | - Luke Short
- Dallas County Health and Human Services, Dallas, Texas, USA
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19
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Rogozin IB, Saura A, Poliakov E, Bykova A, Roche-Lima A, Pavlov YI, Yurchenko V. Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2. Int J Mol Sci 2024; 25:3696. [PMID: 38612505 PMCID: PMC11011937 DOI: 10.3390/ijms25073696] [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: 02/25/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
SARS-CoV-2 has accumulated many mutations since its emergence in late 2019. Nucleotide substitutions leading to amino acid replacements constitute the primary material for natural selection. Insertions, deletions, and substitutions appear to be critical for coronavirus's macro- and microevolution. Understanding the molecular mechanisms of mutations in the mutational hotspots (positions, loci with recurrent mutations, and nucleotide context) is important for disentangling roles of mutagenesis and selection. In the SARS-CoV-2 genome, deletions and insertions are frequently associated with repetitive sequences, whereas C>U substitutions are often surrounded by nucleotides resembling the APOBEC mutable motifs. We describe various approaches to mutation spectra analyses, including the context features of RNAs that are likely to be involved in the generation of recurrent mutations. We also discuss the interplay between mutations and natural selection as a complex evolutionary trend. The substantial variability and complexity of pipelines for the reconstruction of mutations and the huge number of genomic sequences are major problems for the analyses of mutations in the SARS-CoV-2 genome. As a solution, we advocate for the development of a centralized database of predicted mutations, which needs to be updated on a regular basis.
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Affiliation(s)
- Igor B. Rogozin
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Eugenia Poliakov
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities—RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan 00936, Puerto Rico
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
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20
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Alhammadi MA, Bajbouj K, Talaat IM, Hamoudi R. The role of RNA-modifying proteins in renal cell carcinoma. Cell Death Dis 2024; 15:227. [PMID: 38503745 PMCID: PMC10951318 DOI: 10.1038/s41419-024-06479-y] [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: 07/06/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 03/21/2024]
Abstract
Gene expression is one of the most critical cellular processes. It is controlled by complex mechanisms at the genomic, epigenomic, transcriptomic, and proteomic levels. Any aberration in these mechanisms can lead to dysregulated gene expression. One recently discovered process that controls gene expression includes chemical modifications of RNA molecules by RNA-modifying proteins, a field known as epitranscriptomics. Epitranscriptomics can regulate mRNA splicing, nuclear export, stabilization, translation, or induce degradation of target RNA molecules. Dysregulation in RNA-modifying proteins has been found to contribute to many pathological conditions, such as cancer, diabetes, obesity, cardiovascular diseases, and neurological diseases, among others. This article reviews the role of epitranscriptomics in the pathogenesis and progression of renal cell carcinoma. It summarizes the molecular function of RNA-modifying proteins in the pathogenesis of renal cell carcinoma.
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Affiliation(s)
- Muna A Alhammadi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
| | - Khuloud Bajbouj
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Basic Sciences, College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States of America.
| | - Iman M Talaat
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Pathology Department, Faculty of Medicine, Alexandria University, 21131, Alexandria, Egypt.
| | - Rifat Hamoudi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Division of Surgery and Interventional Science, University College London, London, NW3 2PS, United Kingdom.
- ASPIRE Precision Medicine Research Institute Abu Dhabi, University of Sharjah, Sharjah, United Arab Emirates.
- BIMAI-Lab, Biomedically Informed Artificial Intelligence Laboratory, University of Sharjah, Sharjah, United Arab Emirates.
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21
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Ding JH, Li G, Xiong J, Liu FL, Xie NB, Ji TT, Wang M, Guo X, Feng YQ, Ci W, Yuan BF. Whole-Genome Mapping of Epigenetic Modification of 5-Formylcytosine at Single-Base Resolution by Chemical Labeling Enrichment and Deamination Sequencing. Anal Chem 2024; 96:4726-4735. [PMID: 38450632 DOI: 10.1021/acs.analchem.4c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
DNA cytosine methylation (5-methylcytosine, 5mC) is a predominant epigenetic modification that plays a critical role in a variety of biological and pathological processes in mammals. In active DNA demethylation, the 10-11 translocation (TET) dioxygenases can sequentially oxidize 5mC to generate three modified forms of cytosine, 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Beyond being a demethylation intermediate, recent studies have shown that 5fC has regulatory functions in gene expression and chromatin organization. While some methods have been developed to detect 5fC, genome-wide mapping of 5fC at base resolution is still highly desirable. Herein, we propose a chemical labeling enrichment and deamination sequencing (CLED-seq) method for detecting 5fC in genomic DNA at single-base resolution. The CLED-seq method utilizes selective labeling and enrichment of 5fC-containing DNA fragments, followed by deamination mediated by apolipoprotein B mRNA-editing catalytic polypeptide-like 3A (APOBEC3A or A3A) and sequencing. In the CLED-seq process, while all C, 5mC, and 5hmC are interpreted as T during sequencing, 5fC is still read as C, enabling the precise detection of 5fC in DNA. Using the proposed CLED-seq method, we accomplished genome-wide mapping of 5fC in mouse embryonic stem cells. The mapping study revealed that promoter regions enriched with 5fC overlapped with H3K4me1, H3K4me3, and H3K27ac marks. These findings suggest a correlation between 5fC marks and active gene expression in mESCs. In conclusion, CLED-seq is a straightforward, bisulfite-free method that offers a valuable tool for detecting 5fC in genomes at a single-base resolution.
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Affiliation(s)
- Jiang-Hui Ding
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Gaojie Li
- Key Laboratory of Genomics and Precision Medicine, and China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Xiong
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Fei-Long Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Neng-Bin Xie
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Tong-Tong Ji
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Min Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xia Guo
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yu-Qi Feng
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Weimin Ci
- Key Laboratory of Genomics and Precision Medicine, and China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bi-Feng Yuan
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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22
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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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23
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Zhang D, Zhu L, Gao Y, Wang Y, Li P. RNA editing enzymes: structure, biological functions and applications. Cell Biosci 2024; 14:34. [PMID: 38493171 PMCID: PMC10944622 DOI: 10.1186/s13578-024-01216-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
With the advancement of sequencing technologies and bioinformatics, over than 170 different RNA modifications have been identified. However, only a few of these modifications can lead to base pair changes, which are called RNA editing. RNA editing is a ubiquitous modification in mammalian transcriptomes and is an important co/posttranscriptional modification that plays a crucial role in various cellular processes. There are two main types of RNA editing events: adenosine to inosine (A-to-I) editing, catalyzed by ADARs on double-stranded RNA or ADATs on tRNA, and cytosine to uridine (C-to-U) editing catalyzed by APOBECs. This article provides an overview of the structure, function, and applications of RNA editing enzymes. We discuss the structural characteristics of three RNA editing enzyme families and their catalytic mechanisms in RNA editing. We also explain the biological role of RNA editing, particularly in innate immunity, cancer biogenesis, and antiviral activity. Additionally, this article describes RNA editing tools for manipulating RNA to correct disease-causing mutations, as well as the potential applications of RNA editing enzymes in the field of biotechnology and therapy.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
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24
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Yang H, Pacheco J, Kim K, Ebrahimi D, Ito F, Chen XS. Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584510. [PMID: 38559028 PMCID: PMC10980023 DOI: 10.1101/2024.03.11.584510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
APOBEC3G (A3G) belongs to the AID/APOBEC cytidine deaminase family and is essential for antiviral immunity. It contains two zinc-coordinated cytidine-deaminase (CD) domains. The N-terminal CD1 domain is non-catalytic but has a strong affinity for nucleic acids, whereas the C-terminal CD2 domain catalyzes C-to-U editing in single-stranded DNA. The interplay between the two domains in DNA binding and editing is not fully understood. Here, our studies on rhesus macaque A3G (rA3G) show that the DNA editing function in linear and hairpin loop DNA is greatly enhanced by AA or GA dinucleotide motifs present downstream (in the 3'-direction) but not upstream (in the 5'-direction) of the target-C editing sites. The effective distance between AA/GA and the target-C sites depends on the local DNA secondary structure. We present two co-crystal structures of rA3G bound to ssDNA containing AA and GA, revealing the contribution of the non-catalytic CD1 domain in capturing AA/GA DNA and explaining our biochemical observations. Our structural and biochemical findings elucidate the molecular mechanism underlying the cooperative function between the non-catalytic and the catalytic domains of A3G, which is critical for its antiviral role and its contribution to genome mutations in cancer.
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Affiliation(s)
- Hanjing Yang
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Josue Pacheco
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Kyumin Kim
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Diako Ebrahimi
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Fumiaki Ito
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA90095, USA
| | - Xiaojiang S. Chen
- Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
- Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089, USA
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25
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Ngo MH, AbuEed L, Kawasaki J, Oishi N, Pramono D, Kimura T, Sakurai M, Watanabe K, Mizukami Y, Ochi H, Anai Y, Odahara Y, Umehara D, Kawamura M, Watanabe S, Miyake A, Nishigaki K. Multiple recombination events between endogenous retroviral elements and feline leukemia virus. J Virol 2024; 98:e0140023. [PMID: 38240589 PMCID: PMC10878261 DOI: 10.1128/jvi.01400-23] [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: 09/11/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024] Open
Abstract
Feline leukemia virus (FeLV) is an exogenous retrovirus that causes malignant hematopoietic disorders in domestic cats, and its virulence may be closely associated with viral sequences. FeLV is classified into several subgroups, including A, B, C, D, E, and T, based on viral receptor interference properties or receptor usage. However, the transmission manner and disease specificity of the recombinant viruses FeLV-D and FeLV-B remain unclear. The aim of this study was to understand recombination events between exogenous and endogenous retroviruses within a host and elucidate the emergence and transmission of recombinant viruses. We observed multiple recombination events involving endogenous retroviruses (ERVs) in FeLV from a family of domestic cats kept in one house; two of these cats (ON-T and ON-C) presented with lymphoma and leukemia, respectively. Clonal integration of FeLV-D was observed in the ON-T case, suggesting an association with FeLV-D pathogenesis. Notably, the receptor usage of FeLV-B observed in ON-T was mediated by feline Pit1 and feline Pit2, whereas only feline Pit1 was used in ON-C. Furthermore, XR-FeLV, a recombinant FeLV containing an unrelated sequence referred to the X-region, which is homologous to a portion of the 5'-leader sequence of Felis catus endogenous gammaretrovirus 4 (FcERV-gamma4), was isolated. Genetic analysis suggested that most recombinant viruses occurred de novo; however, the possibility of FeLV-B transmission was also recognized in the family. This study demonstrated the occurrence of multiple recombination events between exogenous and endogenous retroviruses in domestic cats, highlighting the contribution of ERVs to pathogenic recombinant viruses.IMPORTANCEFeline leukemia virus subgroup A (FeLV-A) is primarily transmitted among cats. During viral transmission, genetic changes in the viral genome lead to the emergence of novel FeLV subgroups or variants with altered virulence. We isolated three FeLV subgroups (A, B, and D) and XR-FeLV from two cats and identified multiple recombination events in feline endogenous retroviruses (ERVs), such as enFeLV, ERV-DC, and FcERV-gamma4, which are present in the cat genome. This study highlights the pathogenic contribution of ERVs in the emergence of FeLV-B, FeLV-D, and XR-FeLV in a feline population.
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Affiliation(s)
- Minh Ha Ngo
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Loai AbuEed
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Junna Kawasaki
- Faculty of Science and Engineering, Waseda University, Okubo, Shinjuku-ku, Tokyo, Japan
| | | | - Didik Pramono
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Tohru Kimura
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Masashi Sakurai
- Laboratory of Veterinary Pathology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Kenji Watanabe
- Institute of Gene Research, Science Research Center, Yamaguchi University, Minami-kogushi, Ube, Japan
| | - Yoichi Mizukami
- Institute of Gene Research, Science Research Center, Yamaguchi University, Minami-kogushi, Ube, Japan
| | - Haruyo Ochi
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Yukari Anai
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Yuka Odahara
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Daigo Umehara
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Maki Kawamura
- Life Science Division, Advanced Technology Institute, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Shinya Watanabe
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Ariko Miyake
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Kazuo Nishigaki
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yoshida, Yamaguchi, Japan
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26
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Fukushima R, Suzuki T, Kobayakawa A, Kamiya H. Action-at-a-distance mutations induced by 8-oxo-7,8-dihydroguanine are dependent on APOBEC3. Mutagenesis 2024; 39:24-31. [PMID: 37471265 DOI: 10.1093/mutage/gead023] [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: 04/04/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023] Open
Abstract
DNA oxidation is a serious threat to genome integrity and is involved in mutations and cancer initiation. The G base is most frequently damaged, and 8-oxo-7,8-dihydroguanine (GO, 8-hydroxyguanine) is one of the predominant damaged bases. In human cells, GO causes a G:C→T:A transversion mutation at the modified site, and also induces untargeted substitution mutations at the G bases of 5'-GpA-3' dinucleotides (action-at-a-distance mutations). The 5'-GpA-3' sequences are complementary to the 5'-TpC-3' sequences, the preferred substrates for apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3 (APOBEC3) cytosine deaminases, and thus their contribution to mutagenesis has been considered. In this study, APOBEC3B, the most abundant APOBEC3 protein in human U2OS cells, was knocked down in human U2OS cells, and a GO-shuttle plasmid was then transfected into the cells. The action-at-a-distance mutations were reduced to ~25% by the knockdown, indicating that GO-induced action-at-a-distance mutations are highly dependent on APOBEC3B in this cell line.
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Affiliation(s)
- Ruriko Fukushima
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Tetsuya Suzuki
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Akari Kobayakawa
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Hiroyuki Kamiya
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
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Colson P, Delerce J, Pontarotti P, Devaux C, La Scola B, Fantini J, Raoult D. Resistance-associated mutations to the anti-SARS-CoV-2 agent nirmatrelvir: Selection not induction. J Med Virol 2024; 96:e29462. [PMID: 38363015 DOI: 10.1002/jmv.29462] [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: 11/20/2023] [Revised: 01/21/2024] [Accepted: 01/27/2024] [Indexed: 02/17/2024]
Abstract
Mutations associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resistance to antiprotease nirmatrelvir were reported. We aimed to detect them in SARS-CoV-2 genomes and quasispecies retrieved in our institute before drug availability in January 2022 and to analyze the impact of mutations on protease (3CLpro) structure. We sought for 38 3CLpro nirmatrelvir resistance mutations in a set of 62 673 SARS-CoV-2 genomes obtained in our institute from respiratory samples collected between 2020 and 2023 and for these mutations in SARS-CoV-2 quasispecies for 90 samples collected in 2020, using Python. SARS-CoV-2 protease with major mutation E166V was generated with Swiss Pdb Viewer and Molegro Molecular Viewer. We detected 22 (58%) of the resistance-associated mutations in 417 (0.67%) of the genomes analyzed; 325 (78%) of these genomes had been obtained from samples collected in 2020-2021. APOBEC signatures were found for 12/22 mutations. We also detected among viral quasispecies from 90 samples some minority reads harboring any of 15 nirmatrelvir resistance mutations, including E166V. Also, we predicted that E166V has a very limited effect on 3CLpro structure but may prevent drug attachment. Thus, we evidenced that mutations associated with nirmatrelvir resistance pre-existed in SARS-CoV-2 before drug availability. These findings further warrant SARS-CoV-2 genomic surveillance and SARS-CoV-2 quasispecies characterization.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Jérémy Delerce
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | | | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, Marseille, France
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Timmerman AL, Schönert ALM, van der Hoek L. Anelloviruses versus human immunity: how do we control these viruses? FEMS Microbiol Rev 2024; 48:fuae005. [PMID: 38337179 PMCID: PMC10883694 DOI: 10.1093/femsre/fuae005] [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: 11/09/2023] [Revised: 12/22/2023] [Accepted: 02/08/2024] [Indexed: 02/12/2024] Open
Abstract
One continuous companion and one of the major players in the human blood virome are members of the Anelloviridae family. Anelloviruses are probably found in all humans, infection occurs early in life and the composition (anellome) is thought to remain stable and personal during adulthood. The stable anellome implies a great balance between the host immune system and the virus. However, the lack of a robust culturing system hampers direct investigation of interactions between virus and host cells. Other techniques, however, including next generation sequencing, AnelloScan-antibody tests, evolution selection pressure analysis, and virus protein structures, do provide new insights into the interactions between anelloviruses and the host immune system. This review aims at providing an overview of the current knowledge on the immune mechanisms acting on anelloviruses and the countering viral mechanisms allowing immune evasion.
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Affiliation(s)
- Anne L Timmerman
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
| | - Antonia L M Schönert
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
| | - Lia van der Hoek
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
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Azad MTA, Sugi T, Qulsum U, Kato K. Detection of Developmental Asexual Stage-Specific RNA Editing Events in Plasmodium falciparum 3D7 Malaria Parasite. Microorganisms 2024; 12:137. [PMID: 38257964 PMCID: PMC10819399 DOI: 10.3390/microorganisms12010137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/24/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Transcriptional variation has been studied but post-transcriptional modification due to RNA editing has not been investigated in Plasmodium. We investigated developmental stage-specific RNA editing in selected genes in Plasmodium falciparum 3D7. We detected extensive amination- and deamination-type RNA editing at 8, 16, 24, 32, 40, and 46 h in tightly synchronized Plasmodium. Most of the editing events were observed in 8 and 16 h ring-stage parasites. Extensive A-to-G deamination-type editing was detected more during the 16 h ring stage (25%) than the 8 h ring stage (20%). Extensive U-to-C amination-type editing was detected more during the 16 h ring stage (31%) than the 8 h ring stage (22%). In 28S, rRNA editing converted the loop structure to the stem structure. The hemoglobin binding activity of PF3D7_0216900 was also altered due to RNA editing. Among the expressed 28S rRNA genes, PF3D7_0532000 and PF3D7_0726000 expression was higher. Increased amounts of the transcripts of these two genes were found, particularly PF3D7_0726000 in the ring stage and PF3D7_0532000 in the trophozoite and schizont stages. Adenosine deaminase (ADA) expression did not correlate with the editing level. This first experimental report of RNA editing will help to identify the editing machinery that might be useful for antimalarial drug discovery and malaria control.
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Affiliation(s)
- Md Thoufic Anam Azad
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Tatsuki Sugi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Nishi10-Kita 20, Sapporo 001-0020, Japan
| | - Umme Qulsum
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Kentaro Kato
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
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Devaux CA, Pontarotti P, Levasseur A, Colson P, Raoult D. Is it time to switch to a formulation other than the live attenuated poliovirus vaccine to prevent poliomyelitis? Front Public Health 2024; 11:1284337. [PMID: 38259741 PMCID: PMC10801389 DOI: 10.3389/fpubh.2023.1284337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
The polioviruses (PVs) are mainly transmitted by direct contact with an infected person through the fecal-oral route and respiratory secretions (or more rarely via contaminated water or food) and have a primary tropism for the gut. After their replication in the gut, in rare cases (far less than 1% of the infected individuals), PVs can spread to the central nervous system leading to flaccid paralysis, which can result in respiratory paralysis and death. By the middle of the 20th century, every year the wild polioviruses (WPVs) are supposed to have killed or paralyzed over half a million people. The introduction of the oral poliovirus vaccines (OPVs) through mass vaccination campaigns (combined with better application of hygiene measures), was a success story which enabled the World Health Organization (WHO) to set the global eradication of poliomyelitis as an objective. However this strategy of viral eradication has its limits as the majority of poliomyelitis cases today arise in individuals infected with circulating vaccine-derived polioviruses (cVDPVs) which regain pathogenicity following reversion or recombination. In recent years (between January 2018 and May 2023), the WHO recorded 8.8 times more cases of polio which were linked to the attenuated OPV vaccines (3,442 polio cases after reversion or recombination events) than cases linked to a WPV (390 cases). Recent knowledge of the evolution of RNA viruses and the exchange of genetic material among biological entities of the intestinal microbiota, call for a reassessment of the polio eradication vaccine strategies.
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Affiliation(s)
- Christian Albert Devaux
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), Marseille, France
| | - Pierre Pontarotti
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), Marseille, France
| | - Anthony Levasseur
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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31
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Wei L, Wu X, Wang L, Chen L, Wu X, Song T, Wang Y, Chang W, Guo A, Niu Y, Huang H. Expression and prognostic value of APOBEC2 in gastric adenocarcinoma and its association with tumor-infiltrating immune cells. BMC Cancer 2024; 24:15. [PMID: 38166744 PMCID: PMC10763203 DOI: 10.1186/s12885-023-11769-3] [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: 07/16/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 2 (APOBEC2) is associated with nucleotide alterations in the transcripts of tumor-related genes which are contributed to carcinogenesis. Expression and prognosis value of APOBEC2 in stomach adenocarcinoma (STAD) remains unclear. METHODS The APOBEC2 gene alteration frequency of STAD and APOBEC2 gene expression in STAD and normal tissues were investigated in cBioportal and GEPIA, respectively. We detected expression of APOBEC2, infiltration of CD66b+ tumor-associated neutrophils and CD163+ tumor-associated macrophages in tissue microarrays by immunohistochemistry. APOBEC2 gene expression was explored by western blot and qRT-PCR. Relationships between APOBEC2 and CD66b, CD163, and other clinicopathological characteristics were investigated. Associations among APOBEC2 expression status and patient survival outcome were further analyzed. RESULTS APOBEC2 gene alteration frequency was 5%, and APOBEC2 gene was downexpressed in STAD compared to normal tissues (P < 0.05). APOBEC2 expression status were associated with the infiltration of CD66b+ TANs, differentiation grade, TNM stage, histological type and gender (all P < 0.05) in STAD. Little or no APOBEC2 expression was detected in STAD and adjacent normal tissues by western blot. We failed to show that APOBEC2 was an independent risk factor for OS (Hazard Ratio 0.816, 95%CI 0.574-1.161, P = 0.259) or DFS (Hazard Ratio 0.821, 95%CI 0.578-1.166, P = 0.270) in STAD by multivariate Cox regression analysis, but APOBEC2 negative subgroup has a worse OS and DFS among patients with adjuvant chemotherapy. CONCLUSIONS APOBEC2 correlates with CD66b, differentiation grade, TNM stages, histological classification, and gender in STAD. APOBEC2 is not an independent prognostic factor for STAD, our results suggest that patients with positive APOBEC2 can benefit from postoperative chemotherapy, and combination of APOBEC2 and CD66b is helpful to further stratify patients into different groups with distinct prognoses.
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Affiliation(s)
- Lipan Wei
- Department of Pathology, Second affiliated Hospital of Medical College of Shantou University, Shantou, China
| | - Xiuqian Wu
- Department of Interventional Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Lan Wang
- Department of Pathology, Second affiliated Hospital of Medical College of Shantou University, Shantou, China
| | - Ling Chen
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Xuejun Wu
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Tiantian Song
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Yuanyuan Wang
- Department of Pathology, Shantou Central Hospital, Shantou, China
| | - Wenjun Chang
- Department of Environmental Hygiene, Second Military Medical University, Shanghai, China
| | - Aizhen Guo
- Department of General Practice, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Yongdong Niu
- Department of Pharmacology, Shantou University Medical College, Shantou, China.
| | - Haihua Huang
- Department of Pathology, Second affiliated Hospital of Medical College of Shantou University, Shantou, China.
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Fonzino A, Manzari C, Spadavecchia P, Munagala U, Torrini S, Conticello S, Pesole G, Picardi E. Unraveling C-to-U RNA editing events from direct RNA sequencing. RNA Biol 2024; 21:1-14. [PMID: 38090878 PMCID: PMC10732634 DOI: 10.1080/15476286.2023.2290843] [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] [Accepted: 10/29/2023] [Indexed: 12/18/2023] Open
Abstract
In mammals, RNA editing events involve the conversion of adenosine (A) in inosine (I) by ADAR enzymes or the hydrolytic deamination of cytosine (C) in uracil (U) by the APOBEC family of enzymes, mostly APOBEC1. RNA editing has a plethora of biological functions, and its deregulation has been associated with various human disorders. While the large-scale detection of A-to-I is quite straightforward using the Illumina RNAseq technology, the identification of C-to-U events is a non-trivial task. This difficulty arises from the rarity of such events in eukaryotic genomes and the challenge of distinguishing them from background noise. Direct RNA sequencing by Oxford Nanopore Technology (ONT) permits the direct detection of Us on sequenced RNA reads. Surprisingly, using ONT reads from wild-type (WT) and APOBEC1-knock-out (KO) murine cell lines as well as in vitro synthesized RNA without any modification, we identified a systematic error affecting the accuracy of the Cs call, thereby leading to incorrect identifications of C-to-U events. To overcome this issue in direct RNA reads, here we introduce a novel machine learning strategy based on the isolation Forest (iForest) algorithm in which C-to-U editing events are considered as sequencing anomalies. Using in vitro synthesized and human ONT reads, our model optimizes the signal-to-noise ratio improving the detection of C-to-U editing sites with high accuracy, over 90% in all samples tested. Our results suggest that iForest, known for its rapid implementation and minimal memory requirements, is a promising tool to denoise ONT reads and reliably identify RNA modifications.
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Affiliation(s)
- Adriano Fonzino
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
| | - Caterina Manzari
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
| | - Paola Spadavecchia
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
| | | | | | - Silvestro Conticello
- Core Research Laboratory, ISPRO, Florence, Italy
- National Research Council, Institute of Clinical Physiology, Pisa, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
- National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
- Consorzio Interuniversitario Biotecnologie, Trieste, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
- National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
- National Institute of Biostructures and Biosystems (INBB), Roma, Italy
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Xiang J, Xu W, Wu J, Luo Y, Yang B, Chen J. Nucleoside deaminases: the key players in base editing toolkit. BIOPHYSICS REPORTS 2023; 9:325-337. [PMID: 38524700 PMCID: PMC10960570 DOI: 10.52601/bpr.2023.230029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/28/2023] [Indexed: 03/26/2024] Open
Abstract
The development of nucleoside deaminase-containing base editors realized targeted single base change with high efficiency and precision. Such nucleoside deaminases include adenosine and cytidine deaminases, which can catalyze adenosine-to-inosine (A-to-I) and cytidine-to-uridine (C-to-U) conversion respectively. These nucleoside deaminases are under the spotlight because of their vast application potential in gene editing. Recent advances in the engineering of current nucleoside deaminases and the discovery of new nucleoside deaminases greatly broaden the application scope and improve the editing specificity of base editors. In this review, we cover current knowledge about the deaminases used in base editors, including their key structural features, working mechanisms, optimization, and evolution.
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Affiliation(s)
- Jiangchao Xiang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenchao Xu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jing Wu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yaxin Luo
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Bei Yang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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34
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Deneuve S, Fervers B, Senkin S, Bouaoun L, Pérol O, Chavanel B, Lu L, Coste I, Renno T, Zavadil J, Virard F. Molecular landscapes of oral cancers of unknown etiology. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.15.23299866. [PMID: 38168303 PMCID: PMC10760302 DOI: 10.1101/2023.12.15.23299866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The incidence of the mobile tongue cancer in young patients has been rising. This oral cancer (OC) type has no identified risk factors (NIRF), no established molecular markers and is not yet recognized as a distinct clinical entity. To understand this emerging malignancy, we innovatively analyzed the public head and neck cancer multi-omics data. We identified mutational signatures that successfully stratified 307 OC and 109 laryngeal cancer cases according to their clinico-pathological characteristics. The NIRF OCs exhibited significantly increased activities of endogenous clock-like and APOBEC-associated mutagenesis, alongside specific cancer driver gene mutations, distinct methylome patterns and prominent antimicrobial transcriptomic responses. Furthermore, we show that mutational signature SBS16 in OCs reflects the combined effects of alcohol drinking and tobacco smoking. Our study characterizes the unique disease histories and molecular programs of the NIRF OCs revealing that this emerging cancer subtype is likely driven by increased endogenous mutagenesis correlated with responses to microbial insults.
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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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Fan J, Li S, Zhang Y, Zheng J, Wang D, Liao Y, Cui Z, Zhao D, Barouch DH, Yu J. Early Emerging SARS-CoV-2 Spike Mutants Are Diversified in Virologic Properties but Elicit Compromised Antibody Responses. Viruses 2023; 15:2401. [PMID: 38140642 PMCID: PMC10747620 DOI: 10.3390/v15122401] [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: 11/21/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Despite the effective antivirals and vaccines, COVID-19 remains a public health concern. The mutations that occurred during the early stage of the pandemic can be valuable in assessing the viral fitness and evolutionary trajectory. In this study, we analyzed a panel of 2969 spike sequences deposited in GISAID before April 2020 and characterized nine representative spike single-point mutants in detail. Compared with the WA01/2020, most (8 out of 9) mutants demonstrated an equivalent or diminished protein expression or processing, pseudovirus infectivity, and cell-cell fusion. Interestingly, most of the mutants in native form elicited minimum antibody responses in mice despite unaltered CD4+ and CD8+ T cell responses. The mutants remained sensitive to the antisera and the type I interferon. Taken together, these data suggest that the early emerging mutants are virologically divergent, and some of which showed transmission fitness. Our findings have important implications for the retrospective tracing of the early SARS-CoV-2 transmission and future pandemic preparedness.
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Affiliation(s)
- Junhao Fan
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China;
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
| | - Shixiong Li
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yao Zhang
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jihao Zheng
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
| | - Dongfang Wang
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
| | - Yunxi Liao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; (Y.L.); (D.Z.)
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Zhibo Cui
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Dongyu Zhao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; (Y.L.); (D.Z.)
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jingyou Yu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China;
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
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37
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Baudat F, de Massy B. Mutation hotspots during meiosis. Science 2023; 382:997-998. [PMID: 38033058 DOI: 10.1126/science.adl2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Multiple pathways generate mutations at sites of meiotic recombination in humans.
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Affiliation(s)
- Frédéric Baudat
- Institut de Génétique Humaine, Université de Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
| | - Bernard de Massy
- Institut de Génétique Humaine, Université de Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
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Alonso de la Vega A, Temiz NA, Tasakis R, Somogyi K, Salgueiro L, Zimmer E, Ramos M, Diaz-Jimenez A, Chocarro S, Fernández-Vaquero M, Stefanovska B, Reuveni E, Ben-David U, Stenzinger A, Poth T, Heikenwälder M, Papavasiliou N, Harris RS, Sotillo R. Acute expression of human APOBEC3B in mice results in RNA editing and lethality. Genome Biol 2023; 24:267. [PMID: 38001542 PMCID: PMC10668425 DOI: 10.1186/s13059-023-03115-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND RNA editing has been described as promoting genetic heterogeneity, leading to the development of multiple disorders, including cancer. The cytosine deaminase APOBEC3B is implicated in tumor evolution through DNA mutation, but whether it also functions as an RNA editing enzyme has not been studied. RESULTS Here, we engineer a novel doxycycline-inducible mouse model of human APOBEC3B-overexpression to understand the impact of this enzyme in tissue homeostasis and address a potential role in C-to-U RNA editing. Elevated and sustained levels of APOBEC3B lead to rapid alteration of cellular fitness, major organ dysfunction, and ultimately lethality in mice. Importantly, RNA-sequencing of mouse tissues expressing high levels of APOBEC3B identifies frequent UCC-to-UUC RNA editing events that are not evident in the corresponding genomic DNA. CONCLUSIONS This work identifies, for the first time, a new deaminase-dependent function for APOBEC3B in RNA editing and presents a preclinical tool to help understand the emerging role of APOBEC3B as a driver of carcinogenesis.
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Affiliation(s)
- Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Nuri Alpay Temiz
- Health Informatics Institute, University of Minnesota, Minneapolis, 55455, USA
| | - Rafail Tasakis
- Division of Immune Diversity, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Kalman Somogyi
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Lorena Salgueiro
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Eleni Zimmer
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Maria Ramos
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Alberto Diaz-Jimenez
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Sara Chocarro
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Mirian Fernández-Vaquero
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bojana Stefanovska
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Eli Reuveni
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Uri Ben-David
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Tanja Poth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), Heidelberg, Germany.
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Desingu PA, Rubeni TP, Nagarajan K, Sundaresan NR. Sign of APOBEC editing, purifying selection, frameshift, and in-frame nonsense mutations in the microevolution of lumpy skin disease virus. Front Microbiol 2023; 14:1214414. [PMID: 38033577 PMCID: PMC10682384 DOI: 10.3389/fmicb.2023.1214414] [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: 04/29/2023] [Accepted: 10/25/2023] [Indexed: 12/02/2023] Open
Abstract
The lumpy skin disease virus (LSDV), which mostly affects ruminants and causes huge-economic loss, was endemic in Africa, caused outbreaks in the Middle East, and was recently detected in Russia, Serbia, Greece, Bulgaria, Kazakhstan, China, Taiwan, Vietnam, Thailand, and India. However, the role of evolutionary drivers such as codon selection, negative/purifying selection, APOBEC editing, and genetic variations such as frameshift and in-frame nonsense mutations in the LSDVs, which cause outbreaks in cattle in various countries, are still largely unknown. In the present study, a frameshift mutation in LSDV035, LSDV019, LSDV134, and LSDV144 genes and in-frame non-sense mutations in LSDV026, LSDV086, LSDV087, LSDV114, LSDV130, LSDV131, LSDV145, LSDV154, LSDV155, LSDV057, and LSDV081 genes were revealed among different clusters. Based on the available complete genome sequences, the prototype wild-type cluster-1.2.1 virus has been found in other than Africa only in India, the wild-type cluster-1.2.2 virus found in Africa were spread outside Africa, and the recombinant viruses spreading only in Asia and Russia. Although LSD viruses circulating in different countries form a specific cluster, the viruses detected in each specific country are distinguished by frameshift and in-frame nonsense mutations. Furthermore, the present study has brought to light that the selection pressure for codons usage bias is mostly exerted by purifying selection, and this process is possibly caused by APOBEC editing. Overall, the present study sheds light on microevolutions in LSDV, expected to help in future studies towards disturbed ORFs, epidemiological diagnostics, attenuation/vaccine reverts, and predicting the evolutionary direction of LSDVs.
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Affiliation(s)
| | - T. P. Rubeni
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - K. Nagarajan
- Department of Veterinary Pathology, Madras Veterinary College, Chennai, India
- Veterinary and Animal Sciences University (TANUVAS), Chennai, India
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40
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Pfeiffer LS, Stafforst T. Precision RNA base editing with engineered and endogenous effectors. Nat Biotechnol 2023; 41:1526-1542. [PMID: 37735261 DOI: 10.1038/s41587-023-01927-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/26/2023] [Indexed: 09/23/2023]
Abstract
RNA base editing refers to the rewriting of genetic information within an intact RNA molecule and serves various functions, such as evasion of the endogenous immune system and regulation of protein function. To achieve this, certain enzymes have been discovered in human cells that catalyze the conversion of one nucleobase into another. This natural process could be exploited to manipulate and recode any base in a target transcript. In contrast to DNA base editing, analogous changes introduced in RNA are not permanent or inheritable but rather allow reversible and doseable effects that appeal to various therapeutic applications. The current practice of RNA base editing involves the deamination of adenosines and cytidines, which are converted to inosines and uridines, respectively. In this Review, we summarize current site-directed RNA base-editing strategies and highlight recent achievements to improve editing efficiency, precision, codon-targeting scope and in vivo delivery into disease-relevant tissues. Besides engineered editing effectors, we focus on strategies to harness endogenous adenosine deaminases acting on RNA (ADAR) enzymes and discuss limitations and future perspectives to apply the tools in basic research and as a therapeutic modality. We expect the field to realize the first RNA base-editing drug soon, likely on a well-defined genetic disease. However, the long-term challenge will be to carve out the sweet spot of the technology where its unique ability is exploited to modulate signaling cues, metabolism or other clinically relevant processes in a safe and doseable manner.
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Affiliation(s)
- Laura S Pfeiffer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
- Gene and RNA Therapy Center, Faculty of Medicine, University of Tübingen, Tübingen, Germany.
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Colson P, Bader W, Fantini J, Dudouet P, Levasseur A, Pontarotti P, Devaux C, Raoult D. From viral democratic genomes to viral wild bunch of quasispecies. J Med Virol 2023; 95:e29209. [PMID: 37937701 DOI: 10.1002/jmv.29209] [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: 08/07/2023] [Revised: 10/05/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
The tremendous majority of RNA genomes from pathogenic viruses analyzed and deposited in databases are consensus or "democratic" genomes. They represent the genomes most frequently found in the clinical samples of patients but do not account for the huge genetic diversity of coexisting genomes, which is better described as quasispecies. A viral quasispecies is defined as the dynamic distribution of nonidentical but closely related mutants, variants, recombinant, or reassortant viral genomes. Viral quasispecies have collective behavior and dynamics and are the subject of internal interactions that comprise interference, complementation, or cooperation. In the setting of SARS-CoV-2 infection, intrahost SARS-CoV-2 genetic diversity was recently notably reported for immunocompromised, chronically infected patients, for patients treated with monoclonal antibodies targeting the viral spike protein, and for different body compartments of a single patient. A question that deserves attention is whether such diversity is generated postinfection from a clonal genome in response to selection pressure or is already present at the time of infection as a quasispecies. In the present review, we summarize the data supporting that hosts are infected by a "wild bunch" of viruses rather than by multiple virions sharing the same genome. Each virion in the "wild bunch" may have different virulence and tissue tropisms. As the number of viruses replicated during host infections is huge, a viral quasispecies at any time of infection is wide and is also influenced by host-specific selection pressure after infection, which accounts for the difficulty in deciphering and predicting the appearance of more fit variants and the evolution of epidemics of novel RNA viruses.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Wahiba Bader
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Pierre Dudouet
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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42
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Shen S, Zhang LS. The regulation of antiviral innate immunity through non-m 6A RNA modifications. Front Immunol 2023; 14:1286820. [PMID: 37915585 PMCID: PMC10616867 DOI: 10.3389/fimmu.2023.1286820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
The post-transcriptional RNA modifications impact the dynamic regulation of gene expression in diverse biological and physiological processes. Host RNA modifications play an indispensable role in regulating innate immune responses against virus infection in mammals. Meanwhile, the viral RNAs can be deposited with RNA modifications to interfere with the host immune responses. The N6-methyladenosine (m6A) has boosted the recent emergence of RNA epigenetics, due to its high abundance and a transcriptome-wide widespread distribution in mammalian cells, proven to impact antiviral innate immunity. However, the other types of RNA modifications are also involved in regulating antiviral responses, and the functional roles of these non-m6A RNA modifications have not been comprehensively summarized. In this Review, we conclude the regulatory roles of 2'-O-methylation (Nm), 5-methylcytidine (m5C), adenosine-inosine editing (A-to-I editing), pseudouridine (Ψ), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N6,2'-O-dimethyladenosine (m6Am), and N4-acetylcytidine (ac4C) in antiviral innate immunity. We provide a systematic introduction to the biogenesis and functions of these non-m6A RNA modifications in viral RNA, host RNA, and during virus-host interactions, emphasizing the biological functions of RNA modification regulators in antiviral responses. Furthermore, we discussed the recent research progress in the development of antiviral drugs through non-m6A RNA modifications. Collectively, this Review conveys knowledge and inspiration to researchers in multiple disciplines, highlighting the challenges and future directions in RNA epitranscriptome, immunology, and virology.
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Affiliation(s)
- Shenghai Shen
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
| | - Li-Sheng Zhang
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
- Department of Chemistry, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
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43
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Durfee C, Temiz NA, Levin-Klein R, Argyris PP, Alsøe L, Carracedo S, Alonso de la Vega A, Proehl J, Holzhauer AM, Seeman ZJ, Liu X, Lin YHT, Vogel RI, Sotillo R, Nilsen H, Harris RS. Human APOBEC3B promotes tumor development in vivo including signature mutations and metastases. Cell Rep Med 2023; 4:101211. [PMID: 37797615 PMCID: PMC10591044 DOI: 10.1016/j.xcrm.2023.101211] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/14/2023] [Accepted: 09/06/2023] [Indexed: 10/07/2023]
Abstract
The antiviral DNA cytosine deaminase APOBEC3B has been implicated as a source of mutation in many cancers. However, despite years of work, a causal relationship has yet to be established in vivo. Here, we report a murine model that expresses tumor-like levels of human APOBEC3B. Animals expressing full-body APOBEC3B appear to develop normally. However, adult males manifest infertility, and older animals of both sexes show accelerated rates of carcinogenesis, visual and molecular tumor heterogeneity, and metastasis. Both primary and metastatic tumors exhibit increased frequencies of C-to-T mutations in TC dinucleotide motifs consistent with the established biochemical activity of APOBEC3B. Enrichment for APOBEC3B-attributable single base substitution mutations also associates with elevated levels of insertion-deletion mutations and structural variations. APOBEC3B catalytic activity is required for all of these phenotypes. Together, these studies provide a cause-and-effect demonstration that human APOBEC3B is capable of driving both tumor initiation and evolution in vivo.
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Affiliation(s)
- Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rena Levin-Klein
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Prokopios P Argyris
- Division of Oral and Maxillofacial Pathology, College of Dentistry, Ohio State University, Columbus, OH 43210, USA
| | - Lene Alsøe
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Sergio Carracedo
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
| | - Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Joshua Proehl
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Anna M Holzhauer
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zachary J Seeman
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xingyu Liu
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Yu-Hsiu T Lin
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Hilde Nilsen
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
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44
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Li F, Zafar A, Luo L, Denning AM, Gu J, Bennett A, Yuan F, Zhang Y. R-Loops in Genome Instability and Cancer. Cancers (Basel) 2023; 15:4986. [PMID: 37894353 PMCID: PMC10605827 DOI: 10.3390/cancers15204986] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
R-loops are unique, three-stranded nucleic acid structures that primarily form when an RNA molecule displaces one DNA strand and anneals to the complementary DNA strand in a double-stranded DNA molecule. R-loop formation can occur during natural processes, such as transcription, in which the nascent RNA molecule remains hybridized with the template DNA strand, while the non-template DNA strand is displaced. However, R-loops can also arise due to many non-natural processes, including DNA damage, dysregulation of RNA degradation pathways, and defects in RNA processing. Despite their prevalence throughout the whole genome, R-loops are predominantly found in actively transcribed gene regions, enabling R-loops to serve seemingly controversial roles. On one hand, the pathological accumulation of R-loops contributes to genome instability, a hallmark of cancer development that plays a role in tumorigenesis, cancer progression, and therapeutic resistance. On the other hand, R-loops play critical roles in regulating essential processes, such as gene expression, chromatin organization, class-switch recombination, mitochondrial DNA replication, and DNA repair. In this review, we summarize discoveries related to the formation, suppression, and removal of R-loops and their influence on genome instability, DNA repair, and oncogenic events. We have also discussed therapeutical opportunities by targeting pathological R-loops.
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Affiliation(s)
- Fang Li
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Alyan Zafar
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Liang Luo
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ariana Maria Denning
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jun Gu
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ansley Bennett
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Fenghua Yuan
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Yanbin Zhang
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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Zhang D, Jin H, Sun Y, Yang Y, Li R, Li W, Zhang X, Li S, Chen Y, Wang Q, Pan Y. Genetic Features of 84 Genomes of Monkeypox Virus in Recent Circulation - Beijing Municipality, China, 2023. China CDC Wkly 2023; 5:918-921. [PMID: 37970070 PMCID: PMC10630903 DOI: 10.46234/ccdcw2023.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/07/2023] [Indexed: 11/17/2023] Open
Abstract
The first indigenous incidence of Mpox (previously known as monkeypox) within Chinese mainland was documented in May 2023, with subsequent local and imported cases identified. A comprehensive understanding of the Mpox virus's (MPXV) characteristics within Beijing remains incomplete. In this study, 84 MPXV genomes from 82 local incidents and two imported instances, detected between May and July 2023, were analyzed. All MPXV strains fell within lineage C.1 of the West African clade, displaying limited genetic heterogeneity, encompassing 76-87 nucleotide substitutions and holding nucleotide identities between 99.996% and 100%. Phylogenetic exploration indicated that all genomes exhibited high homology to those presently prevalent in neighboring East Asian and Southeast Asian regions. Forty-six distinct haplotypes were identified among the strains, with 36.90% of genomes corresponding to four common haplotypes, suggesting repeated cross-regional introductions and restrained distribution via recurrent local transmission. These findings elucidate the genetic diversity and phylogenesis of MPXVs during their nascent transmission within Beijing and provide vital information to enhance future Mpox containment strategies.
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Affiliation(s)
- Daitao Zhang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Haoyuan Jin
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yulan Sun
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yang Yang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Renqing Li
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Weihong Li
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Xin Zhang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Shuang Li
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yanwei Chen
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Quanyi Wang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yang Pan
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
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Devaux CA, Fantini J. Possible contribution of rare alleles of human ACE2 in the emergence of SARS-CoV-2 variants escaping the immune response. Front Immunol 2023; 14:1252367. [PMID: 37885880 PMCID: PMC10598458 DOI: 10.3389/fimmu.2023.1252367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Since the start of the SARS-CoV-2 pandemic, the rapid replacement of one lineage by another has been observed. Indeed, SARS-CoV-2 is evolving through a quasispecies mechanism leading to post-infection mutation selection under positive evolutionary pressure (host-driven viral evolution). These mutations may reduce the effectiveness of the specific neutralizing immune response against the virus. We provide here evidence that apart from the selection of SARS-CoV-2 variants by the immune system, selection by the cellular receptor can just as well select variants which escape neutralization.
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Affiliation(s)
- Christian A. Devaux
- Institut National des Sciences Biologiques (INSB), Centre National de la Recherche Scientifique (CNRS), Marseille, France
- Microbes, Evolution, Phylogénie et Infections, Faculté de Pharmacie, Aix Marseille Université, Marseille, France
| | - Jacques Fantini
- Institut National de la Santé et de la Recherche Médicale (INSERM) U_1072, Faculté des Sciences, Aix-Marseille Université, Marseille, France
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47
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Xin G, Kuang Q, Le S, Wu W, Gao Q, Gao H, Xu Z, Zheng Z, Lu G, Gong L, Wang H, Zhang G, Shi M, Sun Y. Origin, genomic diversity and evolution of African swine fever virus in East Asia. Virus Evol 2023; 9:vead060. [PMID: 37868933 PMCID: PMC10590196 DOI: 10.1093/ve/vead060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/29/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023] Open
Abstract
Since 2018, the outbreaks of genotype II African swine fever virus (ASFV) in China and several eastern Asian countries have caused a huge impact on the local swine industry, resulting in huge economic losses. However, little is known about the origin, genomic diversity, evolutionary features, and epidemiological history of the genotype II ASFV. Here, 14 high-quality complete genomes of ASFVs were generated via sequencing of samples collected from China over the course of 3 years, followed by phylogenetic and phylodynamic analyses. The strains identified were relatively homogeneous, with a total of 52 SNPs and 11 indels compared with the prototype strain HLJ/2018, among which there were four exceptionally large deletions (620-18,023 nt). Evolutionary analyses revealed that ASFV strains distributed in eastern Asia formed a monophyly and a 'star-like' structure centered around the prototype strain, suggesting a single origin. Additionally, phylogenetic network analysis and ancestral reconstruction of geographic state indicated that genotype II ASFV strains in eastern Asia likely originated from Western Europe. Overall, these results contribute to the understanding of the history and current status of genotype II ASFV strains in eastern Asian, which could be of considerable importance in disease control and prevention.
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Affiliation(s)
- Genyang Xin
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Qiyuan Kuang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Shijia Le
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Weichen Wu
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Qi Gao
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Han Gao
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Zhiying Xu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Zezhong Zheng
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Gang Lu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Lang Gong
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Heng Wang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Guihong Zhang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Yankuo Sun
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
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48
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Wang W, Zhang X, Garcia S, Leitch AR, Kovařík A. Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between? Heredity (Edinb) 2023; 131:179-188. [PMID: 37402824 PMCID: PMC10462631 DOI: 10.1038/s41437-023-00634-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.
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Affiliation(s)
- Wencai Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Xianzhi Zhang
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Sònia Garcia
- Institut Botànic de Barcelona, IBB (CSIC - Ajuntament de Barcelona), Barcelona, Spain
| | - Andrew R Leitch
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61200, Czech Republic.
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49
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Kim K, Shi AB, Kelley K, Chen XS. Unraveling the Enzyme-Substrate Properties for APOBEC3A-Mediated RNA Editing. J Mol Biol 2023; 435:168198. [PMID: 37442413 PMCID: PMC10528890 DOI: 10.1016/j.jmb.2023.168198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
The APOBEC3 family of human cytidine deaminases is involved in various cellular processes, including the innate and acquired immune system, mostly through inducing C-to-U in single-stranded DNA and/or RNA mutations. Although recent studies have examined RNA editing by APOBEC3A (A3A), its intracellular target specificity are not fully characterized. To address this gap, we performed in-depth analysis of cellular RNA editing using our recently developed sensitive cell-based fluorescence assay. Our findings demonstrate that A3A and an A3A-loop1-containing APOBEC3B (A3B) chimera are capable of RNA editing. We observed that A3A prefers to edit specific RNA substrates which are not efficiently deaminated by other APOBEC members. The editing efficiency of A3A is influenced by the RNA sequence contexts and distinct stem-loop secondary structures. Based on the identified RNA specificity features, we predicted potential A3A-editing targets in the encoding region of cellular mRNAs and discovered novel RNA transcripts that are extensively edited by A3A. Furthermore, we found a trend of increased synonymous mutations at the sites for more efficient A3A-editing, indicating evolutionary adaptation to the higher editing rate by A3A. Our results shed light on the intracellular RNA editing properties of A3A and provide insights into new RNA targets and potential impact of A3A-mediated RNA editing.
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Affiliation(s)
- Kyumin Kim
- Molecular and Computational Biology Program, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA. https://twitter.com/KYUMINK1324
| | - Alan B Shi
- Molecular and Computational Biology Program, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Kori Kelley
- Molecular and Computational Biology Program, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology Program, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA; Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA.
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50
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Xi B, Zeng X, Chen Z, Zeng J, Huang L, Du H. SARS-CoV-2 within-host diversity of human hosts and its implications for viral immune evasion. mBio 2023; 14:e0067923. [PMID: 37273216 PMCID: PMC10470530 DOI: 10.1128/mbio.00679-23] [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: 03/25/2023] [Accepted: 04/17/2023] [Indexed: 06/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously evolving, bringing great challenges to the control of the virus. In the present study, we investigated the characteristics of SARS-CoV-2 within-host diversity of human hosts and its implications for immune evasion using about 2,00,000 high-depth next-generation genome sequencing data of SARS-CoV-2. A total of 44% of the samples showed within-host variations (iSNVs), and the average number of iSNVs in the samples with iSNV was 1.90. C-to-U is the dominant substitution pattern for iSNVs. C-to-U/G-to-A and A-to-G/U-to-C preferentially occur in 5'-CG-3' and 5'-AU-3' motifs, respectively. In addition, we found that SARS-CoV-2 within-host variations are under negative selection. About 15.6% iSNVs had an impact on the content of the CpG dinucleotide (CpG) in SARS-CoV-2 genomes. We detected signatures of faster loss of CpG-gaining iSNVs, possibly resulting from zinc-finger antiviral protein-mediated antiviral activities targeting CpG, which could be the major reason for CpG depletion in SARS-CoV-2 consensus genomes. The non-synonymous iSNVs in the S gene can largely alter the S protein's antigenic features, and many of these iSNVs are distributed in the amino-terminal domain (NTD) and receptor-binding domain (RBD). These results suggest that SARS-CoV-2 interacts actively with human hosts and attempts to take different evolutionary strategies to escape human innate and adaptive immunity. These new findings further deepen and widen our understanding of the within-host evolutionary features of SARS-CoV-2. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pathogen of the coronavirus disease 2019, has evolved rapidly since it was discovered. Recent studies have pointed out that some mutations in the SARS-CoV-2 S protein could confer SARS-CoV-2 the ability to evade the human adaptive immune system. In addition, it is observed that the content of the CpG dinucleotide in SARS-CoV-2 genome sequences has decreased over time, reflecting the adaptation to the human host. The significance of our research is revealing the characteristics of SARS-CoV-2 within-host diversity of human hosts, identifying the causes of CpG depletion in SARS-CoV-2 consensus genomes, and exploring the potential impacts of non-synonymous within-host variations in the S gene on immune escape, which could further deepen and widen our understanding of the evolutionary features of SARS-CoV-2.
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Affiliation(s)
- Binbin Xi
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xi Zeng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zixi Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jiong Zeng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Lizhen Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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