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Jacob Bunu S, Cai H, Wu L, Zhang H, Zhou Z, Xu Z, Shi J, Zhu W. TRIP13 - a potential drug target in cancer pharmacotherapy. Bioorg Chem 2024; 151:107650. [PMID: 39042962 DOI: 10.1016/j.bioorg.2024.107650] [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: 03/25/2024] [Revised: 07/12/2024] [Accepted: 07/14/2024] [Indexed: 07/25/2024]
Abstract
ATPases Associated with Diverse Cellular Activity (AAA+ATPases) are important enzymatic functional proteins in human cells. Thyroid Hormone Receptor Interacting Protein-13 (TRIP13) is a member of this protein superfamily, that partly regulates DNA repair pathways and spindle assembly checkpoints during mitosis. TRIP13 is reported as an oncogene involving multiple pathways in many human malignancies, including multiple myeloma, brain tumors, etc. The structure of TRIP13 reveals the mechanisms for ATP binding and how TRIP13 recognizes the Mitotic Arrest Deficiency-2 (MAD2) protein, with p31comet acting as an adapter protein. DCZ0415, TI17, DCZ5417, and DCZ5418 are the reported small-molecule inhibitors of TRIP13, which have been demonstrated to inhibit TRIP13's biological functions significantly and effective in suppressing various types of malignant cells, indicating that TRIP13 is a significant anticancer drug target. Currently, no systematic reviews are cutting across the functions, structure, and novel inhibitors of TRIP13. This review provides a comprehensive overview of TRIP13's biological functions, its roles in eighteen different cancers, four small molecule inhibitors, different underlying molecular mechanisms, and its functionality as a potential anticancer drug target.
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Affiliation(s)
- Samuel Jacob Bunu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Haiyan Cai
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Leyun Wu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Hui Zhang
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Zhaoyin Zhou
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhijian Xu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Jumei Shi
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.
| | - Weiliang Zhu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.
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2
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Kusch S, Frantzeskakis L, Lassen BD, Kümmel F, Pesch L, Barsoum M, Walden KD, Panstruga R. A fungal plant pathogen overcomes mlo-mediated broad-spectrum disease resistance by rapid gene loss. THE NEW PHYTOLOGIST 2024. [PMID: 39155769 DOI: 10.1111/nph.20063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 08/03/2024] [Indexed: 08/20/2024]
Abstract
Hosts and pathogens typically engage in a coevolutionary arms race. This also applies to phytopathogenic powdery mildew fungi, which can rapidly overcome plant resistance and perform host jumps. Using experimental evolution, we show that the powdery mildew pathogen Blumeria hordei is capable of breaking the agriculturally important broad-spectrum resistance conditioned by barley loss-of-function mlo mutants. Partial mlo virulence of evolved B. hordei isolates is correlated with a distinctive pattern of adaptive mutations, including small-sized (c. 8-40 kb) deletions, of which one is linked to the de novo insertion of a transposable element. Occurrence of the mutations is associated with a transcriptional induction of effector protein-encoding genes that is absent in mlo-avirulent isolates on mlo mutant plants. The detected mutational spectrum comprises the same loci in at least two independently isolated mlo-virulent isolates, indicating convergent multigenic evolution. The mutational events emerged in part early (within the first five asexual generations) during experimental evolution, likely generating a founder population in which incipient mlo virulence was later stabilized by additional events. This work highlights the rapid dynamic genome evolution of an obligate biotrophic plant pathogen with a transposon-enriched genome.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Lamprinos Frantzeskakis
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Birthe D Lassen
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Florian Kümmel
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Lina Pesch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Mirna Barsoum
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Kim D Walden
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
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3
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Jiao L, Zhao J, Wang C, Liu X, Liu F, Li L, Shang R, Li Y, Ma W, Yang S. Nature-Inspired Intelligent Computing: A Comprehensive Survey. RESEARCH (WASHINGTON, D.C.) 2024; 7:0442. [PMID: 39156658 PMCID: PMC11327401 DOI: 10.34133/research.0442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/14/2024] [Indexed: 08/20/2024]
Abstract
Nature, with its numerous surprising rules, serves as a rich source of creativity for the development of artificial intelligence, inspiring researchers to create several nature-inspired intelligent computing paradigms based on natural mechanisms. Over the past decades, these paradigms have revealed effective and flexible solutions to practical and complex problems. This paper summarizes the natural mechanisms of diverse advanced nature-inspired intelligent computing paradigms, which provide valuable lessons for building general-purpose machines capable of adapting to the environment autonomously. According to the natural mechanisms, we classify nature-inspired intelligent computing paradigms into 4 types: evolutionary-based, biological-based, social-cultural-based, and science-based. Moreover, this paper also illustrates the interrelationship between these paradigms and natural mechanisms, as well as their real-world applications, offering a comprehensive algorithmic foundation for mitigating unreasonable metaphors. Finally, based on the detailed analysis of natural mechanisms, the challenges of current nature-inspired paradigms and promising future research directions are presented.
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Affiliation(s)
- Licheng Jiao
- School of Artificial Intelligence, Xidian University, Xi’an, China
| | - Jiaxuan Zhao
- School of Artificial Intelligence, Xidian University, Xi’an, China
| | - Chao Wang
- School of Artificial Intelligence, Xidian University, Xi’an, China
| | - Xu Liu
- School of Artificial Intelligence, Xidian University, Xi’an, China
| | - Fang Liu
- School of Artificial Intelligence, Xidian University, Xi’an, China
| | - Lingling Li
- School of Artificial Intelligence, Xidian University, Xi’an, China
| | - Ronghua Shang
- School of Artificial Intelligence, Xidian University, Xi’an, China
| | - Yangyang Li
- School of Artificial Intelligence, Xidian University, Xi’an, China
| | - Wenping Ma
- School of Artificial Intelligence, Xidian University, Xi’an, China
| | - Shuyuan Yang
- School of Artificial Intelligence, Xidian University, Xi’an, China
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Martinez S, Sentis S, Poulard C, Trédan O, Le Romancer M. Role of PRMT1 and PRMT5 in Breast Cancer. Int J Mol Sci 2024; 25:8854. [PMID: 39201539 PMCID: PMC11354362 DOI: 10.3390/ijms25168854] [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: 07/10/2024] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
Breast cancer is the most common cancer diagnosed in women worldwide. Early-stage breast cancer is curable in ~70-80% of patients, while advanced metastatic breast cancer is considered incurable with current therapies. Breast cancer is a highly heterogeneous disease categorized into three main subtypes based on key markers orientating specific treatment strategies for each subtype. The complexity of breast carcinogenesis is often associated with epigenetic modification regulating different signaling pathways, involved in breast tumor initiation and progression, particularly by the methylation of arginine residues. Protein arginine methyltransferases (PRMT1-9) have emerged, through their ability to methylate histones and non-histone substrates, as essential regulators of cancers. Here, we present an updated overview of the mechanisms by which PRMT1 and PRMT5, two major members of the PRMT family, control important signaling pathways impacting breast tumorigenesis, highlighting them as putative therapeutic targets.
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Affiliation(s)
- Sébastien Martinez
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
| | - Stéphanie Sentis
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
| | - Coralie Poulard
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
| | - Olivier Trédan
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
- Oncology Department, Centre Leon Bérard, F-69008 Lyon, France
| | - Muriel Le Romancer
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
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5
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Li S, Tang M, Xiong Y, Feng X, Wang C, Nie L, Huang M, Zhang H, Yin L, Zhu D, Yang C, Ma T, Chen J. Systematic investigation of BRCA1-A, -B, and -C complexes and their functions in DNA damage response and DNA repair. Oncogene 2024; 43:2621-2634. [PMID: 39068216 DOI: 10.1038/s41388-024-03108-y] [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: 04/17/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
BRCA1, a breast cancer susceptibility gene, has emerged as a central mediator that brings together multiple signaling complexes in response to DNA damage. The A, B, and C complexes of BRCA1, which are formed based on their phosphorylation-dependent interactions with the BRCA1-C-terminal domains, contribute to the roles of BRCA1 in DNA repair and cell cycle checkpoint control. However, their functions in DNA damage response remain to be fully appreciated. Specifically, there has been no systematic investigation of the roles of BRCA1-A, -B, and -C complexes in the regulation of BRCA1 localization and functions, in part because of cellular lethality associated with loss of CtIP protein, which is an essential component in BRCA1-C complex. To systematically investigate the functions of these complexes in DNA damage response, we depleted a key component in each of these complexes. We used the degradation tag system to inducibly deplete endogenous CtIP and obtained a series of RAP80/FANCJ/CtIP single-, double-, and triple-knockout cells. We showed that loss of BRCA1-B/FANCJ and BRCA1-C/CtIP, but not BRCA1-A/RAP80, resulted in reduced cell proliferation and increased sensitivity to DNA damage. BRCA1-C/CtIP and BRCA1-A/RAP80 were involved in BRCA1 recruitment to sites of DNA damage. However, BRCA1-A/RAP80 was not essential for damage-induced BRCA1 localization. Instead, RAP80/H2AX and CtIP have redundant roles in BRCA1 recruitment. Altogether, our systematic analysis uncovers functional differences between BRCA1-A, -B, and -C complexes and provides new insights into the roles of these BRCA1-associated protein complexes in DNA damage response and DNA repair.
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Affiliation(s)
- Siting Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yun Xiong
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Litong Nie
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Min Huang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ling Yin
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dandan Zhu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chang Yang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tiantian Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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6
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Xiao Y, Ni M, Zheng Z, Liu Y, Yin M, Mao S, Zhao Y, Tian B, Wang L, Xu H, Hua Y. POLM variant G312R promotes ovarian tumorigenesis through genomic instability and COL11A1-NF-κB axis. Am J Physiol Cell Physiol 2024; 327:C168-C183. [PMID: 38826139 DOI: 10.1152/ajpcell.00025.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024]
Abstract
In ovarian cancer (OC), identifying key molecular players in disease escalation and chemoresistance remains critical. Our investigation elucidates the role of the DNA polymerase mu (POLM), especially G312R mutation, in propelling oncogenesis through dual pathways. POLMG312R markedly augments the ribonucleotide insertion capability of POLM, precipitating genomic instability. In addition, our research reveals that POLMG312R perturbs collagen alpha-1 (XI) chain (COL11A1) expression-a gene that plays a key role in oncogenesis-and modulates the NF-κB signaling pathway, alters the secretion of downstream inflammatory cytokines, and promotes tumor-macrophage interactions. We illustrate a bidirectional regulatory interaction between POLM, particularly its G312R variant, and COL11A1. This interaction regulates NF-κB signaling, culminating in heightened malignancy and resistance to chemotherapy in OC cells. These insights position the POLM as a potential molecular target for OC therapy, shedding light on the intricate pathways underpinning POLM variant disease progression.NEW & NOTEWORTHY Our research reveals that POLM plays an important role in ovarian cancer development, especially the mutation G312R. We uncover the POLMG312R mutation as a driver of genomic instability in ovarian cancer via aberrant ribonucleotide incorporation. We reveal that POLMG312R upregulates COL11A1 and activates NF-κB signaling, contributing to tumor progression and chemoresistance. This study identifies the POLM-COL11A1-NF-κB axis as a novel oncogenic pathway.
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Affiliation(s)
- Yue Xiao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
| | - Maowei Ni
- Zhejiang Cancer Hospital, Hangzhou, People's Republic of China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, People's Republic of China
| | - Zhiguo Zheng
- Zhejiang Cancer Hospital, Hangzhou, People's Republic of China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, People's Republic of China
| | - Yufeng Liu
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
| | - Mingyu Yin
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
| | - Shuyu Mao
- Zhejiang Cancer Hospital, Hangzhou, People's Republic of China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, People's Republic of China
| | - Ye Zhao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
- Cancer Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Bing Tian
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
- Cancer Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Liangyan Wang
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
- Cancer Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Hong Xu
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
- Cancer Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Yuejin Hua
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
- Cancer Center, Zhejiang University, Hangzhou, People's Republic of China
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7
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Yilmaz I, Ozbek T. Genome editing in Acinetobacter baumannii through enhanced natural transformation. J Basic Microbiol 2024; 64:e2300644. [PMID: 38412427 DOI: 10.1002/jobm.202300644] [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: 10/28/2023] [Revised: 01/29/2024] [Accepted: 02/03/2024] [Indexed: 02/29/2024]
Abstract
Acinetobacter baumannii, a multidrug-resistant bacterium has become a significant cause of life-threatening infections acquired in hospitals worldwide. The existing drugs used to treat A. baumannii infections are rapidly losing efficacy, and the increasing antimicrobial resistance, which is expected to turn into a global health crisis, underscores the urgency to develop novel prevention and treatment strategies. We reasoned that the discovery of novel virulence targets for vaccine and therapy interventions requires a more enhanced method for the introduction of multiple elements of foreign DNA for genome editing than the current methods of natural transformation techniques. Herein, we employed a novel and a much-improved enhanced technique for the natural transformation of elements of the genome editing system CRISPR-Cas9 to suppress specific genomic regions linked to selectively suppress bacterial virulence. We modified the genome of the laboratory-adapted strain of A. baumannii BAA-747 by targeting the AmpC, as a marker gene, for disruption by three different genomic manipulation strategies, and created mutant strains of A. baumannii that are, at least, fourfold susceptible to ampicillin. This work has established an optimized enhanced natural transformation system that enables efficient genome editing of pathogenic bacteria in a laboratory setting, providing a valuable future tool for exploring the function of unidentified virulence genes in bacterial genomes.
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Affiliation(s)
- Ilknur Yilmaz
- Department of Molecular Biology and Genetics, Graduate School of Science & Engineering, Yildiz Technical University, Istanbul, Turkey
| | - Tulin Ozbek
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey
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8
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Clark-Hachtel CM, Hibshman JD, De Buysscher T, Stair ER, Hicks LM, Goldstein B. The tardigrade Hypsibius exemplaris dramatically upregulates DNA repair pathway genes in response to ionizing radiation. Curr Biol 2024; 34:1819-1830.e6. [PMID: 38614079 PMCID: PMC11078613 DOI: 10.1016/j.cub.2024.03.019] [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: 09/29/2023] [Revised: 01/19/2024] [Accepted: 03/13/2024] [Indexed: 04/15/2024]
Abstract
Tardigrades can survive remarkable doses of ionizing radiation, up to about 1,000 times the lethal dose for humans. How they do so is incompletely understood. We found that the tardigrade Hypsibius exemplaris suffers DNA damage upon gamma irradiation, but the damage is repaired. We show that this species has a specific and robust response to ionizing radiation: irradiation induces a rapid upregulation of many DNA repair genes. This upregulation is unexpectedly extreme-making some DNA repair transcripts among the most abundant transcripts in the animal. By expressing tardigrade genes in bacteria, we validate that increased expression of some repair genes can suffice to increase radiation tolerance. We show that at least one such gene is important in vivo for tardigrade radiation tolerance. We hypothesize that the tardigrades' ability to sense ionizing radiation and massively upregulate specific DNA repair pathway genes may represent an evolved solution for maintaining DNA integrity.
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Affiliation(s)
- Courtney M Clark-Hachtel
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Biology Department, The University of North Carolina at Asheville, Asheville, NC 28804, USA.
| | - Jonathan D Hibshman
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tristan De Buysscher
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Bioinformatics & Analytics Research Collaborative, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Evan R Stair
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Leslie M Hicks
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bob Goldstein
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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9
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Piñón Hofbauer J, Guttmann-Gruber C, Wally V, Sharma A, Gratz IK, Koller U. Challenges and progress related to gene editing in rare skin diseases. Adv Drug Deliv Rev 2024; 208:115294. [PMID: 38527624 DOI: 10.1016/j.addr.2024.115294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/01/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024]
Abstract
Genodermatoses represent a large group of inherited skin disorders encompassing clinically-heterogeneous conditions that manifest in the skin and other organs. Depending on disease variant, associated clinical manifestations and secondary complications can severely impact patients' quality of life and currently available treatments are transient and not curative. Multiple emerging approaches using CRISPR-based technologies offer promising prospects for therapy. Here, we explore current advances and challenges related to gene editing in rare skin diseases, including different strategies tailored to mutation type and structural organization of the affected gene, considerations for in vivo and ex vivo applications, the critical issue of delivery into the skin, and immune aspects of therapy. Against the backdrop of a landmark FDA approval for the first re-dosable gene replacement therapy for a rare genetic skin disorder, gene editing approaches are inching closer to the clinics and the possibility of a local permanent cure for patients affected by these disorders.
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Affiliation(s)
- Josefina Piñón Hofbauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Christina Guttmann-Gruber
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Verena Wally
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Anshu Sharma
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Iris K Gratz
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; Center for Tumor Biology and Immunology, University of Salzburg, 5020 Salzburg, Austria
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria.
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10
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Kitagawa Y, Kobayashi A, Cahill DP, Wakimoto H, Tanaka S. Molecular biology and novel therapeutics for IDH mutant gliomas: The new era of IDH inhibitors. Biochim Biophys Acta Rev Cancer 2024; 1879:189102. [PMID: 38653436 DOI: 10.1016/j.bbcan.2024.189102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/25/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Gliomas with Isocitrate dehydrogenase (IDH) mutation represent a discrete category of primary brain tumors with distinct and unique characteristics, behaviors, and clinical disease outcomes. IDH mutations lead to aberrant high-level production of the oncometabolite D-2-hydroxyglutarate (D-2HG), which act as a competitive inhibitor of enzymes regulating epigenetics, signaling pathways, metabolism, and various other processes. This review summarizes the significance of IDH mutations, resulting upregulation of D-2HG and the associated molecular pathways in gliomagenesis. With the recent finding of clinically effective IDH inhibitors in these gliomas, this article offers a comprehensive overview of the new era of innovative therapeutic approaches based on mechanistic rationales, encompassing both completed and ongoing clinical trials targeting gliomas with IDH mutations.
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Affiliation(s)
- Yosuke Kitagawa
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, 02114 Boston, MA, USA; Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, 02114 Boston, MA, USA; Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, 1138655 Bunkyo-ku, Tokyo, Japan
| | - Ami Kobayashi
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, 02115 Boston, MA, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, 02114 Boston, MA, USA; Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, 02114 Boston, MA, USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, 02114 Boston, MA, USA; Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, 02114 Boston, MA, USA.
| | - Shota Tanaka
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 7008558, Okayama, Japan
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11
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Selmoni O, Bay LK, Exposito-Alonso M, Cleves PA. Finding genes and pathways that underlie coral adaptation. Trends Genet 2024; 40:213-227. [PMID: 38320882 DOI: 10.1016/j.tig.2024.01.003] [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: 10/09/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
Mass coral bleaching is one of the clearest threats of climate change to the persistence of marine biodiversity. Despite the negative impacts of bleaching on coral health and survival, some corals may be able to rapidly adapt to warming ocean temperatures. Thus, a significant focus in coral research is identifying the genes and pathways underlying coral heat adaptation. Here, we review state-of-the-art methods that may enable the discovery of heat-adaptive loci in corals and identify four main knowledge gaps. To fill these gaps, we describe an experimental approach combining seascape genomics with CRISPR/Cas9 gene editing to discover and validate heat-adaptive loci. Finally, we discuss how information on adaptive genotypes could be used in coral reef conservation and management strategies.
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Affiliation(s)
- Oliver Selmoni
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA; Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
| | - Line K Bay
- Reef Recovery, Adaptation, and Restoration, Australian Institute of Marine Science; Townsville, QLD 4810, Australia
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Global Ecology, Carnegie Institution for Science, Stanford, CA 94305, USA.
| | - Phillip A Cleves
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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12
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Bischof J, Hierl M, Koller U. Emerging Gene Therapeutics for Epidermolysis Bullosa under Development. Int J Mol Sci 2024; 25:2243. [PMID: 38396920 PMCID: PMC10889532 DOI: 10.3390/ijms25042243] [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: 12/21/2023] [Revised: 02/01/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
The monogenetic disease epidermolysis bullosa (EB) is characterised by the formation of extended blisters and lesions on the patient's skin upon minimal mechanical stress. Causal for this severe condition are genetic mutations in genes, leading to the functional impairment, reduction, or absence of the encoded protein within the skin's basement membrane zone connecting the epidermis to the underlying dermis. The major burden of affected families justifies the development of long-lasting and curative therapies operating at the genomic level. The landscape of causal therapies for EB is steadily expanding due to recent breakthroughs in the gene therapy field, providing promising outcomes for patients suffering from this severe disease. Currently, two gene therapeutic approaches show promise for EB. The clinically more advanced gene replacement strategy was successfully applied in severe EB forms, leading to a ground-breaking in vivo gene therapy product named beremagene geperpavec (B-VEC) recently approved from the US Food and Drug Administration (FDA). In addition, the continuous innovations in both designer nucleases and gene editing technologies enable the efficient and potentially safe repair of mutations in EB in a potentially permanent manner, inspiring researchers in the field to define and reach new milestones in the therapy of EB.
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Affiliation(s)
- Johannes Bischof
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; (J.B.); (M.H.)
| | - Markus Hierl
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; (J.B.); (M.H.)
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; (J.B.); (M.H.)
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13
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Macarrón Palacios A, Korus P, Wilkens BGC, Heshmatpour N, Patnaik SR. Revolutionizing in vivo therapy with CRISPR/Cas genome editing: breakthroughs, opportunities and challenges. Front Genome Ed 2024; 6:1342193. [PMID: 38362491 PMCID: PMC10867117 DOI: 10.3389/fgeed.2024.1342193] [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: 11/21/2023] [Accepted: 01/11/2024] [Indexed: 02/17/2024] Open
Abstract
Genome editing using the CRISPR/Cas system has revolutionized the field of genetic engineering, offering unprecedented opportunities for therapeutic applications in vivo. Despite the numerous ongoing clinical trials focusing on ex vivo genome editing, recent studies emphasize the therapeutic promise of in vivo gene editing using CRISPR/Cas technology. However, it is worth noting that the complete attainment of the inherent capabilities of in vivo therapy in humans is yet to be accomplished. Before the full realization of in vivo therapeutic potential, it is crucial to achieve enhanced specificity in selectively targeting defective cells while minimizing harm to healthy cells. This review examines emerging studies, focusing on CRISPR/Cas-based pre-clinical and clinical trials for innovative therapeutic approaches for a wide range of diseases. Furthermore, we emphasize targeting cancer-specific sequences target in genes associated with tumors, shedding light on the diverse strategies employed in cancer treatment. We highlight the various challenges associated with in vivo CRISPR/Cas-based cancer therapy and explore their prospective clinical translatability and the strategies employed to overcome these obstacles.
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14
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Bao H, Chen Z, Wen Q, Wu Y, Fu Q. Effects of oxytetracycline on variation in intracellular and extracellular antibiotic resistance genes during swine manure composting. BIORESOURCE TECHNOLOGY 2024; 393:130127. [PMID: 38036151 DOI: 10.1016/j.biortech.2023.130127] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023]
Abstract
This research aimed to investigate the alterations in extracellular (eARGs) and intracellular (iARGs) antibiotic resistance genes in response to oxytetracycline (OTC), and unravel the dissemination mechanism of ARGs during composting. The findings revealed both low (L-OTC) and high contents (H-OTC) of OTC significantly enhanced absolute abundance (AA) of iARGs (p < 0.05), compared to CK (no OTC). Composting proved to be a proficient strategy for removing eARGs, while AA of eARGs was significantly enhanced in H-OTC (p < 0.05). OTC resulted in an increase in AA of mobile genetic elements (MGEs), ATP levels, antioxidant and DNA repair enzymes in bacteria in compost product. Structural equation model further demonstrated that OTC promoted bacterial DNA repair and antioxidant enzyme activities, altered bacterial community and enhanced MGEs abundance, thereby facilitating iARGs dissemination. This study highlights OTC can increase eARGs and iARGs abundance, underscoring the need for appropriate countermeasures to mitigate potential hazards.
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Affiliation(s)
- Huanyu Bao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Zhiqiang Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Qinxue Wen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China.
| | - Yiqi Wu
- Research Institute of Standards and Norms, Ministry of Housing and Urban-Rural Development, Beijing 100835, PR China
| | - Qiqi Fu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
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15
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Xu S, Neupane S, Wang H, Pham TP, Snyman M, Huynh TV, Wang L. Efficient CRISPR genome editing and integrative genomic analyses reveal the mosaicism of Cas-induced mutations and pleiotropic effects of scarlet gene in an emerging model system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577787. [PMID: 38352317 PMCID: PMC10862705 DOI: 10.1101/2024.01.29.577787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Despite the revolutionary impacts of CRISPR-Cas gene editing systems, the effective and widespread use of CRISPR technologies in emerging model organisms still faces significant challenges. These include the inefficiency in generating heritable mutations at the organismal level, limited knowledge about the genomic consequences of gene editing, and an inadequate understanding of the inheritance patterns of CRISPR-Cas-induced mutations. This study addresses these issues by 1) developing an efficient microinjection delivery method for CRISPR editing in the microcrustacean Daphnia pulex; 2) assessing the editing efficiency of Cas9 and Cas12a nucleases, examining mutation inheritance patterns, and analyzing the local and global mutation spectrum in the scarlet mutants; and 3) investigating the transcriptomes of scarlet mutants to understand the pleiotropic effects of scarlet underlying their swimming behavior changes. Our reengineered CRISPR microinjection method results in efficient biallelic editing with both nucleases. While indels are dominant in Cas-induced mutations, a few on-site large deletions (>1kb) are observed, most likely caused by microhomology-mediated end joining repair. Knock-in of a stop codon cassette to the scarlet locus was successful, despite complex induced mutations surrounding the target site. Moreover, extensive germline mosaicism exists in some mutants, which unexpectedly produce different phenotypes/genotypes in their asexual progenies. Lastly, our transcriptomic analyses unveil significant gene expression changes associated with scarlet knock-out and altered swimming behavior in mutants, including several genes (e.g., NMDA1, ABAT, CNTNAP2) involved in human neurodegenerative diseases. This study expands our understanding of the dynamics of gene editing in the tractable model organism Daphnia and highlights its promising potential as a neurological disease model.
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Affiliation(s)
- Sen Xu
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Swatantra Neupane
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Hongjun Wang
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Thinh Phu Pham
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Marelize Snyman
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Trung V. Huynh
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Li Wang
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
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16
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Wen X, Li J, Yang F, Zhang X, Li Y. Exploring the Effect of High-Energy Heavy Ion Beam on Rice Genome: Transposon Activation. Genes (Basel) 2023; 14:2178. [PMID: 38137000 PMCID: PMC10742395 DOI: 10.3390/genes14122178] [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: 10/30/2023] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
High-energy heavy ion beams are a new type of physical mutagen that can produce a wide range of phenotypic variations. In order to understand the mechanism of high-energy heavy ion beams, we resequenced the whole genome of individual plants with obvious phenotypic variations in rice. The sequence alignment results revealed a large number of SNPs and InDels, as well as genetic variations related to grain type and heading date. The distribution of SNP and InDel on chromosomes is random, but they often occur in the up/downstream regions and the intergenic region. Mutagenesis can cause changes in transposons such as Dasheng, mPing, Osr13 and RIRE2, affecting the stability of the genome. This study obtained the major gene mutation types, discovered differentially active transposons, screened out gene variants related to phenotype, and explored the mechanism of high-energy heavy ion beam radiation on rice genes.
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Affiliation(s)
- Xiaoting Wen
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.W.); (F.Y.); (X.Z.); (Y.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingpeng Li
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.W.); (F.Y.); (X.Z.); (Y.L.)
- Jilin Provincial Laboratory of Crop Germplasm Resources, Changchun 130299, China
| | - Fu Yang
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.W.); (F.Y.); (X.Z.); (Y.L.)
| | - Xin Zhang
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.W.); (F.Y.); (X.Z.); (Y.L.)
| | - Yiwei Li
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.W.); (F.Y.); (X.Z.); (Y.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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17
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O'Grady SM, Kita H. ATP functions as a primary alarmin in allergen-induced type 2 immunity. Am J Physiol Cell Physiol 2023; 325:C1369-C1386. [PMID: 37842751 PMCID: PMC10861152 DOI: 10.1152/ajpcell.00370.2023] [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: 08/07/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
Environmental allergens that interact with the airway epithelium can activate cellular stress pathways that lead to the release of danger signals known as alarmins. The mechanisms of alarmin release are distinct from damage-associated molecular patterns (DAMPs), which typically escape from cells after loss of plasma membrane integrity. Oxidative stress represents a form of allergen-induced cellular stress that stimulates oxidant-sensing mechanisms coupled to pathways, which facilitate alarmin mobilization and efflux across the plasma membrane. In this review, we highlight examples of alarmin release and discuss their roles in the initiation of type 2 immunity and allergic airway inflammation. In addition, we discuss the concept of alarmin amplification, where "primary" alarmins, which are directly released in response to a specific cellular stress, stimulate additional signaling pathways that lead to secretion of "secondary" alarmins that include proinflammatory cytokines, such as IL-33, as well as genomic and mitochondrial DNA that coordinate or amplify type 2 immunity. Accordingly, allergen-evoked cellular stress can elicit a hierarchy of alarmin signaling responses from the airway epithelium that trigger local innate immune reactions, impact adaptive immunity, and exacerbate diseases including asthma and other chronic inflammatory conditions that affect airway function.
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Affiliation(s)
- Scott M O'Grady
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, United States
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota, United States
| | - Hirohito Kita
- Division of Allergy, Asthma and Immunology, Mayo Clinic, Scottsdale, Arizona, United States
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18
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Lavi ES, Lin ZP, Ratner ES. Gene expression of non-homologous end-joining pathways in the prognosis of ovarian cancer. iScience 2023; 26:107934. [PMID: 37810216 PMCID: PMC10558711 DOI: 10.1016/j.isci.2023.107934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/04/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Ovarian cancer is the deadliest gynecologic malignancy in women, with a 46% five-year overall survival rate. The objective of the study was to investigate the effects of non-homologous end-joining (NHEJ) genes on clinical outcomes of ovarian cancer patients. To determine if these genes act as prognostic biomarkers of mortality and disease progression, the expression profiles of 48 NHEJ-associated genes were analyzed using an array of statistical and machine learning techniques: logistic regression models, decision trees, naive-Bayes, two sample t-tests, support vector machines, hierarchical clustering, principal component analysis, and neural networks. In this process, the correlation of genes with patient survival and disease progression and recurrence was noted. Also, multiple features from the gene set were found to have significant predictive capabilities. APTX, BRCA1, PAXX, LIG1, and TP53 were identified as most important out of all the candidate genes for predicting clinical outcomes of ovarian cancer patients.
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Affiliation(s)
- Ethan S. Lavi
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Z. Ping Lin
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Elena S. Ratner
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
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19
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Andrés CMC, de la Lastra JMP, Juan CA, Plou FJ, Pérez-Lebeña E. Chemical Insights into Oxidative and Nitrative Modifications of DNA. Int J Mol Sci 2023; 24:15240. [PMID: 37894920 PMCID: PMC10607741 DOI: 10.3390/ijms242015240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
This review focuses on DNA damage caused by a variety of oxidizing, alkylating, and nitrating species, and it may play an important role in the pathophysiology of inflammation, cancer, and degenerative diseases. Infection and chronic inflammation have been recognized as important factors in carcinogenesis. Under inflammatory conditions, reactive oxygen species (ROS) and reactive nitrogen species (RNS) are generated from inflammatory and epithelial cells, and result in the formation of oxidative and nitrative DNA lesions, such as 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8-nitroguanine. Cellular DNA is continuously exposed to a very high level of genotoxic stress caused by physical, chemical, and biological agents, with an estimated 10,000 modifications occurring every hour in the genetic material of each of our cells. This review highlights recent developments in the chemical biology and toxicology of 2'-deoxyribose oxidation products in DNA.
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Affiliation(s)
| | - José Manuel Pérez de la Lastra
- Institute of Natural Products and Agrobiology, CSIC-Spanish Research Council, Avda. AstrofísicoFco. Sánchez, 3, 38206 La Laguna, Spain
| | - Celia Andrés Juan
- Cinquima Institute and Department of Organic Chemistry, Faculty of Sciences, Valladolid University, Paseo de Belén, 7, 47011 Valladolid, Spain;
| | - Francisco J. Plou
- Institute of Catalysis and Petrochemistry, CSIC-Spanish Research Council, 28049 Madrid, Spain;
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20
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Soultanas P, Janniere L. The metabolic control of DNA replication: mechanism and function. Open Biol 2023; 13:230220. [PMID: 37582405 PMCID: PMC10427196 DOI: 10.1098/rsob.230220] [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: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023] Open
Abstract
Metabolism and DNA replication are the two most fundamental biological functions in life. The catabolic branch of metabolism breaks down nutrients to produce energy and precursors used by the anabolic branch of metabolism to synthesize macromolecules. DNA replication consumes energy and precursors for faithfully copying genomes, propagating the genetic material from generation to generation. We have exquisite understanding of the mechanisms that underpin and regulate these two biological functions. However, the molecular mechanism coordinating replication to metabolism and its biological function remains mostly unknown. Understanding how and why living organisms respond to fluctuating nutritional stimuli through cell-cycle dynamic changes and reproducibly and distinctly temporalize DNA synthesis in a wide-range of growth conditions is important, with wider implications across all domains of life. After summarizing the seminal studies that founded the concept of the metabolic control of replication, we review data linking metabolism to replication from bacteria to humans. Molecular insights underpinning these links are then presented to propose that the metabolic control of replication uses signalling systems gearing metabolome homeostasis to orchestrate replication temporalization. The remarkable replication phenotypes found in mutants of this control highlight its importance in replication regulation and potentially genetic stability and tumorigenesis.
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Affiliation(s)
- Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Laurent Janniere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
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21
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Stepchenkova EI, Zadorsky SP, Shumega AR, Aksenova AY. Practical Approaches for the Yeast Saccharomyces cerevisiae Genome Modification. Int J Mol Sci 2023; 24:11960. [PMID: 37569333 PMCID: PMC10419131 DOI: 10.3390/ijms241511960] [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: 06/29/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023] Open
Abstract
The yeast S. cerevisiae is a unique genetic object for which a wide range of relatively simple, inexpensive, and non-time-consuming methods have been developed that allow the performing of a wide variety of genome modifications. Among the latter, one can mention point mutations, disruptions and deletions of particular genes and regions of chromosomes, insertion of cassettes for the expression of heterologous genes, targeted chromosomal rearrangements such as translocations and inversions, directed changes in the karyotype (loss or duplication of particular chromosomes, changes in the level of ploidy), mating-type changes, etc. Classical yeast genome manipulations have been advanced with CRISPR/Cas9 technology in recent years that allow for the generation of multiple simultaneous changes in the yeast genome. In this review we discuss practical applications of both the classical yeast genome modification methods as well as CRISPR/Cas9 technology. In addition, we review methods for ploidy changes, including aneuploid generation, methods for mating type switching and directed DSB. Combined with a description of useful selective markers and transformation techniques, this work represents a nearly complete guide to yeast genome modification.
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Affiliation(s)
- Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.I.S.); (S.P.Z.); (A.R.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Sergey P. Zadorsky
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.I.S.); (S.P.Z.); (A.R.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Andrey R. Shumega
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.I.S.); (S.P.Z.); (A.R.S.)
| | - Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
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22
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Satoh K, Hoshino W, Hase Y, Kitamura S, Hayashi H, Furuta M, Oono Y. Lethal and mutagenic effects of different LET radiations on Bacillus subtilis spores. Mutat Res 2023; 827:111835. [PMID: 37562181 DOI: 10.1016/j.mrfmmm.2023.111835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/23/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023]
Abstract
New, useful microorganism resources have been generated by ionizing radiation breeding technology. However, the mutagenic effects of ionizing radiation on microorganisms have not been systematically clarified. For a deeper understanding and characterization of ionizing radiation-induced mutations in microorganisms, we investigated the lethal effects of seven different linear energy transfer (LET) radiations based on the survival fraction (SF) and whole-genome sequencing analysis of the mutagenic effects of a dose resulting in an SF of around 1% in Bacillus subtilis spores. Consequently, the lower LET radiations (gamma [surface LET: 0.2 keV/µm] and 4He2+ [24 keV/µm]) showed low lethality and high mutation frequency (MF), resulting in the major induction of single-base substitutions. Whereas higher LET radiations (12C5+ [156 keV/µm] and 12C6+ [179 keV/µm]) showed high lethality and low MF, resulting in the preferential induction of deletion mutations. In addition, 12C6+ (111) ion beams likely possess characteristics of both low- and high-LET radiations simultaneously. A decrease in the relative biological effectiveness and an evaluation of the inactivation cross section indicated that 20Ne8+ (468 keV/µm) and 40Ar13+ (2214 keV/µm) ion beams had overkill effects. In conclusion, in the mutation breeding of microorganisms, it should be possible to regulate the proportions, types, and frequencies of induced mutations by selecting an ionizing radiation of an appropriate LET in accordance with the intended purpose.
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Affiliation(s)
- Katsuya Satoh
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan.
| | - Wataru Hoshino
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan; Faculty of Engineering, Maebashi Institute of Technology, 460-1 Kamisadori, Maebashi, Gunma 371-0816, Japan
| | - Yoshihiro Hase
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
| | - Satoshi Kitamura
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
| | - Hidenori Hayashi
- Faculty of Engineering, Maebashi Institute of Technology, 460-1 Kamisadori, Maebashi, Gunma 371-0816, Japan
| | - Masakazu Furuta
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531, Japan
| | - Yutaka Oono
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
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Komic L, Kumric M, Urlic H, Rizikalo A, Grahovac M, Kelam J, Tomicic M, Rusic D, Ticinovic Kurir T, Bozic J. Obesity and Clonal Hematopoiesis of Indeterminate Potential: Allies in Cardiovascular Diseases and Malignancies. Life (Basel) 2023; 13:1365. [PMID: 37374147 PMCID: PMC10304718 DOI: 10.3390/life13061365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/04/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The clonal hematopoiesis of indeterminate potential (CHIP) is a term used to describe individuals who have detectable somatic mutations in genes commonly found in individuals with hematologic cancers but without any apparent evidence of such conditions. The mortality rate in individuals with CHIP is remarkably higher than the influence ascribed to hematologic malignancies, and it is plausible that cardiovascular diseases (CVD) could elucidate the apparent disparity. Studies have shown that the most frequently altered genes in CHIP are associated with the increased incidence of CVDs, type 2 diabetes mellitus (T2DM) and myeloid malignancies, as well as obesity. Additionally, multiple research studies have confirmed that obesity is also independently associated with these conditions, particularly the development and progression of atherosclerotic CVD. Considering the shared pathogenetic mechanisms of obesity and CHIP, our objective in this review was to investigate both preclinical and clinical evidence regarding the correlation between obesity and CHIP and the resulting implications of this interaction on the pathophysiology of CVDs and malignancies. The pro-inflammatory condition induced by obesity and CHIP enhances the probability of developing both diseases and increases the likelihood of developing CVDs, T2DM and malignancies, suggesting that a dangerous vicious loop may exist. However, it is vital to conduct additional research that will suggest targeted treatment options for obese individuals with CHIP in order to reduce harmful effects connected to these conditions.
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Affiliation(s)
- Luka Komic
- Department of Family Medicine, Split-Dalmatia County Health Center, 21000 Split, Croatia; (L.K.); (J.K.); (M.T.)
| | - Marko Kumric
- Department of Pathophysiology, University of Split School of Medicine, 21000 Split, Croatia; (M.K.); (H.U.); (T.T.K.)
- Laboratory for Cardiometabolic Research, University of Split School of Medicine, 21000 Split, Croatia
| | - Hrvoje Urlic
- Department of Pathophysiology, University of Split School of Medicine, 21000 Split, Croatia; (M.K.); (H.U.); (T.T.K.)
| | - Azer Rizikalo
- Department of Anatomy, School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina;
| | - Marko Grahovac
- Department of Pharmacology, University of Split School of Medicine, 21000 Split, Croatia;
| | - Jelena Kelam
- Department of Family Medicine, Split-Dalmatia County Health Center, 21000 Split, Croatia; (L.K.); (J.K.); (M.T.)
| | - Marion Tomicic
- Department of Family Medicine, Split-Dalmatia County Health Center, 21000 Split, Croatia; (L.K.); (J.K.); (M.T.)
- Department of Family Medicine, University of Split School of Medicine, 21000 Split, Croatia
| | - Doris Rusic
- Department of Pharmacy, University of Split School of Medicine, 21000 Split, Croatia;
| | - Tina Ticinovic Kurir
- Department of Pathophysiology, University of Split School of Medicine, 21000 Split, Croatia; (M.K.); (H.U.); (T.T.K.)
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Hospital of Split, 21000 Split, Croatia
| | - Josko Bozic
- Department of Pathophysiology, University of Split School of Medicine, 21000 Split, Croatia; (M.K.); (H.U.); (T.T.K.)
- Laboratory for Cardiometabolic Research, University of Split School of Medicine, 21000 Split, Croatia
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24
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Rădoi VE, Țurcan M, Maioru OV, Dan A, Bohîlțea LC, Dumitrescu EA, Gheorghe AS, Stănculeanu DL, Thodi G, Loukas YL, Săbău ID. Homologous Recombination Deficiency Score Determined by Genomic Instability in a Romanian Cohort. Diagnostics (Basel) 2023; 13:1896. [PMID: 37296748 PMCID: PMC10252278 DOI: 10.3390/diagnostics13111896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/02/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The Homologous Recombination Deficiency (HRD) Score, determined by evaluating genomic instability through the assessment of loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale state transitions (LST), serves as a crucial biomarker for identifying patients who might benefit from targeted therapies, such as PARP inhibitors (PARPi). This study aimed to investigate the efficacy of HRD testing in high-grade serous ovarian carcinoma, tubal, and peritoneal cancer patients who are negative for somatic BRCA1 and BRCA2 mutations and to evaluate the impact of HRD status on Bevacizumab and PARPi therapy response. A cohort of 100 Romanian female patients, aged 42-77, was initially selected. Among them, 30 patients had unsuitable samples for HRD testing due to insufficient tumor content or DNA integrity. Using the OncoScan C.N.V. platform, HRD testing was successfully performed on the remaining 70 patients, with 20 testing negative and 50 testing positive for HRD. Among the HRD-positive patients, 35 were eligible for and benefited from PARPi maintenance therapy, resulting in a median progression-free survival (PFS) increase from 4 months to 8.2 months. Our findings support the importance of HRD testing in ovarian cancer patients, demonstrating the potential therapeutic advantage of PARPi therapy in HRD-positive patients without somatic BRCA1/2 mutations.
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Affiliation(s)
- Viorica-Elena Rădoi
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-E.R.); (O.V.M.); (A.D.); (L.C.B.); (I.-D.S.)
- “Alessandrescu-Rusescu” National Institute for Maternal and Child Health, 20382 Bucharest, Romania
- Independent Researcher, 010987 Bucharest, Romania
- Sanador, 011026 Bucharest, Romania
| | - Mihaela Țurcan
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-E.R.); (O.V.M.); (A.D.); (L.C.B.); (I.-D.S.)
- Independent Researcher, 010987 Bucharest, Romania
| | - Ovidiu Virgil Maioru
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-E.R.); (O.V.M.); (A.D.); (L.C.B.); (I.-D.S.)
| | - Andra Dan
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-E.R.); (O.V.M.); (A.D.); (L.C.B.); (I.-D.S.)
| | - Laurentiu Camil Bohîlțea
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-E.R.); (O.V.M.); (A.D.); (L.C.B.); (I.-D.S.)
- “Alessandrescu-Rusescu” National Institute for Maternal and Child Health, 20382 Bucharest, Romania
| | - Elena Adriana Dumitrescu
- Department of Oncology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.A.D.); (D.L.S.)
| | - Adelina Silvana Gheorghe
- Department of Oncology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.A.D.); (D.L.S.)
- Department of Medical Oncology I, Institute of Oncology “Prof. Dr. Al. Trestioreanu” Bucharest, 022328 Bucharest, Romania
| | - Dana Lucia Stănculeanu
- Department of Oncology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.A.D.); (D.L.S.)
- Department of Medical Oncology I, Institute of Oncology “Prof. Dr. Al. Trestioreanu” Bucharest, 022328 Bucharest, Romania
| | - Georgia Thodi
- Neoscreen Diagnostic Laboratory, Voreiou Ipeirou, 15235 Athens, Greece;
| | - Yannis L. Loukas
- School of Pharmacy, University of Athens, Panepistimiolopis, 15771 Zografou, Greece;
| | - Ileana-Delia Săbău
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-E.R.); (O.V.M.); (A.D.); (L.C.B.); (I.-D.S.)
- Independent Researcher, 010987 Bucharest, Romania
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25
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Feng Z, Du Y, Chen J, Chen X, Ren W, Wang L, Zhou L. Comparison and Characterization of Phenotypic and Genomic Mutations Induced by a Carbon-Ion Beam and Gamma-ray Irradiation in Soybean ( Glycine max (L.) Merr.). Int J Mol Sci 2023; 24:ijms24108825. [PMID: 37240171 DOI: 10.3390/ijms24108825] [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: 04/26/2023] [Revised: 05/07/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Soybean (Glycine max (L.) Merr.) is a nutritious crop that can provide both oil and protein. A variety of mutagenesis methods have been proposed to obtain better soybean germplasm resources. Among the different types of physical mutagens, carbon-ion beams are considered to be highly efficient with high linear energy transfer (LET), and gamma rays have also been widely used for mutation breeding. However, systematic knowledge of the mutagenic effects of these two mutagens during development and on phenotypic and genomic mutations has not yet been elucidated in soybean. To this end, dry seeds of Williams 82 soybean were irradiated with a carbon-ion beam and gamma rays. The biological effects of the M1 generation included changes in survival rate, yield and fertility. Compared with gamma rays, the relative biological effectiveness (RBE) of the carbon-ion beams was between 2.5 and 3.0. Furthermore, the optimal dose for soybean was determined to be 101 Gy to 115 Gy when using the carbon-ion beam, and it was 263 Gy to 343 Gy when using gamma rays. A total of 325 screened mutant families were detected from out of 2000 M2 families using the carbon-ion beam, and 336 screened mutant families were found using gamma rays. Regarding the screened phenotypic M2 mutations, the proportion of low-frequency phenotypic mutations was 23.4% when using a carbon ion beam, and the proportion was 9.8% when using gamma rays. Low-frequency phenotypic mutations were easily obtained with the carbon-ion beam. After screening the mutations from the M2 generation, their stability was verified, and the genome mutation spectrum of M3 was systemically profiled. A variety of mutations, including single-base substitutions (SBSs), insertion-deletion mutations (INDELs), multinucleotide variants (MNVs) and structural variants (SVs) were detected with both carbon-ion beam irradiation and gamma-ray irradiation. Overall, 1988 homozygous mutations and 9695 homozygous + heterozygous genotype mutations were detected when using the carbon-ion beam. Additionally, 5279 homozygous mutations and 14,243 homozygous + heterozygous genotype mutations were detected when using gamma rays. The carbon-ion beam, which resulted in low levels of background mutations, has the potential to alleviate the problems caused by linkage drag in soybean mutation breeding. Regarding the genomic mutations, when using the carbon-ion beam, the proportion of homozygous-genotype SVs was 0.45%, and that of homozygous + heterozygous-genotype SVs was 6.27%; meanwhile, the proportions were 0.04% and 4.04% when using gamma rays. A higher proportion of SVs were detected when using the carbon ion beam. The gene effects of missense mutations were greater under carbon-ion beam irradiation, and the gene effects of nonsense mutations were greater under gamma-ray irradiation, which meant that the changes in the amino acid sequences were different between the carbon-ion beam and gamma rays. Taken together, our results demonstrate that both carbon-ion beam and gamma rays are effective techniques for rapid mutation breeding in soybean. If one would like to obtain mutations with a low-frequency phenotype, low levels of background genomic mutations and mutations with a higher proportion of SVs, carbon-ion beams are the best choice.
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Affiliation(s)
- Zhuo Feng
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Du
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingmin Chen
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xia Chen
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weibin Ren
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lulu Wang
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Libin Zhou
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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26
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Vijg J, Schumacher B, Abakir A, Antonov M, Bradley C, Cagan A, Church G, Gladyshev VN, Gorbunova V, Maslov AY, Reik W, Sharifi S, Suh Y, Walsh K. Mitigating age-related somatic mutation burden. Trends Mol Med 2023:S1471-4914(23)00072-2. [PMID: 37121869 DOI: 10.1016/j.molmed.2023.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 05/02/2023]
Abstract
Genomes are inherently unstable and require constant DNA repair to maintain their genetic information. However, selective pressure has optimized repair mechanisms in somatic cells only to allow transmitting genetic information to the next generation, not to maximize sequence integrity long beyond the reproductive age. Recent studies have confirmed that somatic mutations, due to errors during genome repair and replication, accumulate in tissues and organs of humans and model organisms. Here, we describe recent advances in the quantitative analysis of somatic mutations in vivo. We also review evidence for or against a possible causal role of somatic mutations in aging. Finally, we discuss options to prevent, delay or eliminate de novo, random somatic mutations as a cause of aging.
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Affiliation(s)
- Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Center for Single-Cell Omics, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, University and University Hospital of Cologne, Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - Abdulkadir Abakir
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK
| | | | | | - Alex Cagan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wolf Reik
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK; Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK; Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | | | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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27
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Develtere W, Waegneer E, Debray K, De Saeger J, Van Glabeke S, Maere S, Ruttink T, Jacobs TB. SMAP design: a multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation. Nucleic Acids Res 2023; 51:e37. [PMID: 36718951 PMCID: PMC10123101 DOI: 10.1093/nar/gkad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 12/14/2022] [Accepted: 01/12/2023] [Indexed: 02/01/2023] Open
Abstract
Multiplex amplicon sequencing is a versatile method to identify genetic variation in natural or mutagenized populations through eco-tilling or multiplex CRISPR screens. Such genotyping screens require reliable and specific primer designs, combined with simultaneous gRNA design for CRISPR screens. Unfortunately, current tools are unable to combine multiplex gRNA and primer design in a high-throughput and easy-to-use manner with high design flexibility. Here, we report the development of a bioinformatics tool called SMAP design to overcome these limitations. We tested SMAP design on several plant and non-plant genomes and obtained designs for more than 80-90% of the target genes, depending on the genome and gene family. We validated the designs with Illumina multiplex amplicon sequencing and Sanger sequencing in Arabidopsis, soybean, and maize. We also used SMAP design to perform eco-tilling by tilling PCR amplicons across nine candidate genes putatively associated with haploid induction in Cichorium intybus. We screened 60 accessions of chicory and witloof and identified thirteen knockout haplotypes and their carriers. SMAP design is an easy-to-use command-line tool that generates highly specific gRNA and/or primer designs for any number of loci for CRISPR or natural variation screens and is compatible with other SMAP modules for seamless downstream analysis.
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Affiliation(s)
- Ward Develtere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, (Technologiepark-Zwijnaarde 71) 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark-Zwijnaarde 71), 9052, Ghent, Belgium
| | - Evelien Waegneer
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, (Caritasstraat 39), 9090, Melle, Belgium
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Kevin Debray
- Department of Plant Biotechnology and Bioinformatics, Ghent University, (Technologiepark-Zwijnaarde 71) 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark-Zwijnaarde 71), 9052, Ghent, Belgium
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, (Caritasstraat 39), 9090, Melle, Belgium
| | - Jonas De Saeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, (Technologiepark-Zwijnaarde 71) 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark-Zwijnaarde 71), 9052, Ghent, Belgium
| | - Sabine Van Glabeke
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, (Caritasstraat 39), 9090, Melle, Belgium
| | - Steven Maere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, (Technologiepark-Zwijnaarde 71) 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark-Zwijnaarde 71), 9052, Ghent, Belgium
| | - Tom Ruttink
- Department of Plant Biotechnology and Bioinformatics, Ghent University, (Technologiepark-Zwijnaarde 71) 9052, Ghent, Belgium
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, (Caritasstraat 39), 9090, Melle, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, (Technologiepark-Zwijnaarde 71) 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark-Zwijnaarde 71), 9052, Ghent, Belgium
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28
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Shadfar S, Parakh S, Jamali MS, Atkin JD. Redox dysregulation as a driver for DNA damage and its relationship to neurodegenerative diseases. Transl Neurodegener 2023; 12:18. [PMID: 37055865 PMCID: PMC10103468 DOI: 10.1186/s40035-023-00350-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/16/2023] [Indexed: 04/15/2023] Open
Abstract
Redox homeostasis refers to the balance between the production of reactive oxygen species (ROS) as well as reactive nitrogen species (RNS), and their elimination by antioxidants. It is linked to all important cellular activities and oxidative stress is a result of imbalance between pro-oxidants and antioxidant species. Oxidative stress perturbs many cellular activities, including processes that maintain the integrity of DNA. Nucleic acids are highly reactive and therefore particularly susceptible to damage. The DNA damage response detects and repairs these DNA lesions. Efficient DNA repair processes are therefore essential for maintaining cellular viability, but they decline considerably during aging. DNA damage and deficiencies in DNA repair are increasingly described in age-related neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and Huntington's disease. Furthermore, oxidative stress has long been associated with these conditions. Moreover, both redox dysregulation and DNA damage increase significantly during aging, which is the biggest risk factor for neurodegenerative diseases. However, the links between redox dysfunction and DNA damage, and their joint contributions to pathophysiology in these conditions, are only just emerging. This review will discuss these associations and address the increasing evidence for redox dysregulation as an important and major source of DNA damage in neurodegenerative disorders. Understanding these connections may facilitate a better understanding of disease mechanisms, and ultimately lead to the design of better therapeutic strategies based on preventing both redox dysregulation and DNA damage.
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Affiliation(s)
- Sina Shadfar
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia.
| | - Sonam Parakh
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia
| | - Md Shafi Jamali
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia
| | - Julie D Atkin
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia.
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29
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Khatpe AS, Dirks R, Bhat-Nakshatri P, Mang H, Batic K, Swiezy S, Olson J, Rao X, Wang Y, Tanaka H, Liu S, Wan J, Chen D, Liu Y, Fang F, Althouse S, Hulsey E, Granatir MM, Addison R, Temm CJ, Sandusky G, Lee-Gosselin A, Nephew K, Miller KD, Nakshatri H. TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer. Cancer Res 2023; 83:1345-1360. [PMID: 37057595 PMCID: PMC10107402 DOI: 10.1158/0008-5472.can-22-3667] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/13/2023] [Accepted: 02/03/2023] [Indexed: 04/15/2023]
Abstract
Study of genomic aberrations leading to immortalization of epithelial cells has been technically challenging due to the lack of isogenic models. To address this, we used healthy primary breast luminal epithelial cells of different genetic ancestry and their hTERT-immortalized counterparts to identify transcriptomic changes associated with immortalization. Elevated expression of TONSL (Tonsoku-like, DNA repair protein) was identified as one of the earliest events during immortalization. TONSL, which is located on chromosome 8q24.3, was found to be amplified in approximately 20% of breast cancers. TONSL alone immortalized primary breast epithelial cells and increased telomerase activity, but overexpression was insufficient for neoplastic transformation. However, TONSL-immortalized primary cells overexpressing defined oncogenes generated estrogen receptor-positive adenocarcinomas in mice. Analysis of a breast tumor microarray with approximately 600 tumors revealed poor overall and progression-free survival of patients with TONSL-overexpressing tumors. TONSL increased chromatin accessibility to pro-oncogenic transcription factors, including NF-κB and limited access to the tumor-suppressor p53. TONSL overexpression resulted in significant changes in the expression of genes associated with DNA repair hubs, including upregulation of several genes in the homologous recombination (HR) and Fanconi anemia pathways. Consistent with these results, TONSL-overexpressing primary cells exhibited upregulated DNA repair via HR. Moreover, TONSL was essential for growth of TONSL-amplified breast cancer cell lines in vivo, and these cells were sensitive to TONSL-FACT complex inhibitor CBL0137. Together, these findings identify TONSL as a regulator of epithelial cell immortalization to facilitate cancer initiation and as a target for breast cancer therapy. SIGNIFICANCE The chr.8q24.3 amplicon-resident gene TONSL is upregulated during the initial steps of tumorigenesis to support neoplastic transformation by increasing DNA repair and represents a potential therapeutic target for treating breast cancer.
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Affiliation(s)
- Aditi S Khatpe
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rebecca Dirks
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Henry Mang
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Katie Batic
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sarah Swiezy
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jacob Olson
- Decatur Central High School, Indianapolis, IN 46221, USA
| | - Xi Rao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, IN 46202, USA
| | - Yue Wang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, IN 46202, USA
| | - Hiromi Tanaka
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, IN 46202, USA
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, IN 46202, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN 46202, USA
| | - Duojiao Chen
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN 46202, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN 46202, USA
| | - Fang Fang
- Medical Science Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Sandra Althouse
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, IN 46202, USA
| | - Emily Hulsey
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, IN 46202, USA
| | - Maggie M Granatir
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, IN 46202, USA
| | - Rebekah Addison
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, IN 46202, USA
| | - Constance J. Temm
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, IN 46202, USA
| | - George Sandusky
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, IN 46202, USA
| | - Audrey Lee-Gosselin
- Stark Neurosciences Research Institute, Indiana University School of Medicine, IN 46202, USA
| | - Kenneth Nephew
- Medical Science Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Kathy D. Miller
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN 46202, USA
- VA Roudebush Medical Center, Indianapolis, IN 46202, USA
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30
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Holland A, Pitoulias M, Soultanas P, Janniere L. The Replicative DnaE Polymerase of Bacillus subtilis Recruits the Glycolytic Pyruvate Kinase (PykA) When Bound to Primed DNA Templates. Life (Basel) 2023; 13:life13040965. [PMID: 37109494 PMCID: PMC10143966 DOI: 10.3390/life13040965] [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: 02/28/2023] [Revised: 03/21/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
The glycolytic enzyme PykA has been reported to drive the metabolic control of replication through a mechanism involving PykA moonlighting functions on the essential DnaE polymerase, the DnaC helicase and regulatory determinants of PykA catalytic activity in Bacillus subtilis. The mutants of this control suffer from critical replication and cell cycle defects, showing that the metabolic control of replication plays important functions in the overall rate of replication. Using biochemical approaches, we demonstrate here that PykA interacts with DnaE for modulating its activity when the replication enzyme is bound to a primed DNA template. This interaction is mediated by the CAT domain of PykA and possibly allosterically regulated by its PEPut domain, which also operates as a potent regulator of PykA catalytic activity. Furthermore, using fluorescence microscopy we show that the CAT and PEPut domains are important for the spatial localization of origins and replication forks, independently of their function in PykA catalytic activity. Collectively, our data suggest that the metabolic control of replication depends on the recruitment of PykA by DnaE at sites of DNA synthesis. This recruitment is likely highly dynamic, as DnaE is frequently recruited to and released from replication machineries to extend the several thousand RNA primers generated from replication initiation to termination. This implies that PykA and DnaE continuously associate and dissociate at replication machineries for ensuring a highly dynamic coordination of the replication rate with metabolism.
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Affiliation(s)
- Alexandria Holland
- Biodiscovery Institute, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Matthaios Pitoulias
- Biodiscovery Institute, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Laurent Janniere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, CEDEX, France
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31
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Bottillo I, Savino E, Majore S, Mulargia C, Valiante M, Ferraris A, Rossi V, Svegliati F, Ciccone MP, Brusco F, Grammatico B, Di Giacomo G, Bargiacchi S, D'Angelantonio D, Grammatico P. Two unrelated cases with biallelic CHEK2 variants:a novel condition with constitutional chromosomal instability? Eur J Hum Genet 2023; 31:474-478. [PMID: 36529819 PMCID: PMC10133322 DOI: 10.1038/s41431-022-01270-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 12/03/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Constitutional heterozygous mutations in CHEK2 gene have been associated with hereditary cancer risk. To date, only a few homozygous CHEK2 mutations have been reported in families with cancer susceptibility. Here, we report two unrelated individuals with a personal and familial cancer history in whom biallelic CHEK2 alterations were identified. The first case resulted homozygous for the CHEK2 c.793-1 G > A (p.Asp265Thrfs*10) variant, and the second one was found to be compound heterozygous for the c.1100delC (p.Thr367Metfs*15) and the c.1312 G > T (p.Asp438Tyr) variants. Multiple cytogenetic anomalies were demonstrated on peripheral lymphocytes of both patients. A literature revision showed that a single other CHEK2 homozygous variant was previously associated to a constitutional randomly occurring multi-translocation karyotype from peripheral blood in humans. We hypothesize that, at least some biallelic CHEK2 mutations might be associated with a novel disorder, further expanding the group of chromosome instability syndromes. Additional studies on larger cohorts are needed to confirm if chromosomal instability could represent a marker for CHEK2 constitutionally mutated recessive genotypes, and to investigate the cancer risk and the occurrence of other anomalies typically observed in chromosome instability syndromes.
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Affiliation(s)
- Irene Bottillo
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy.
| | - Emanuele Savino
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Silvia Majore
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Claudia Mulargia
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Michele Valiante
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Alessandro Ferraris
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Valentina Rossi
- Breast Oncology Unit, San Camillo-Forlanini Hospital, Rome, Italy
| | | | - Maria Pia Ciccone
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Francesca Brusco
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Barbara Grammatico
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Gianluca Di Giacomo
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Simone Bargiacchi
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Daniela D'Angelantonio
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Paola Grammatico
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
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32
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Du G, Yang R, Qiu J, Xia J. Multifaceted Influence of Histone Deacetylases on DNA Damage Repair: Implications for Hepatocellular Carcinoma. J Clin Transl Hepatol 2023; 11:231-243. [PMID: 36406320 PMCID: PMC9647118 DOI: 10.14218/jcth.2022.00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most commonly diagnosed cancers and a leading cause of cancer-related mortality worldwide, but its pathogenesis remains largely unknown. Nevertheless, genomic instability has been recognized as one of the facilitating characteristics of cancer hallmarks that expedites the acquisition of genetic diversity. Genomic instability is associated with a greater tendency to accumulate DNA damage and tumor-specific DNA repair defects, which gives rise to gene mutations and chromosomal damage and causes oncogenic transformation and tumor progression. Histone deacetylases (HDACs) have been shown to impair a variety of cellular processes of genome stability, including the regulation of DNA damage and repair, reactive oxygen species generation and elimination, and progression to mitosis. In this review, we provide an overview of the role of HDAC in the different aspects of DNA repair and genome instability in HCC as well as the current progress on the development of HDAC-specific inhibitors as new cancer therapies.
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Affiliation(s)
- Gan Du
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
- The First Clinical College, Chongqing Medical University, Chongqing, China
| | - Ruizhe Yang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
- The First Clinical College, Chongqing Medical University, Chongqing, China
| | - Jianguo Qiu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Correspondence to: Jie Xia, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, No. 1 Yi Xue Yuan Road, Yuzhong District, Chongqing 400016, China. ORCID: https://orcid.org/0000-0003-4574-9376. Tel/Fax: +86-23-68486780, E-mail: ; Jianguo Qiu, Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No.1 You Yi Road, Yuzhong District, Chongqing 400016, China. ORCID: https://orcid.org/0000-0003-4574-9376. Tel: +86-23-68486780, Fax: +86-23-89011016, E-mail:
| | - Jie Xia
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
- Correspondence to: Jie Xia, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, No. 1 Yi Xue Yuan Road, Yuzhong District, Chongqing 400016, China. ORCID: https://orcid.org/0000-0003-4574-9376. Tel/Fax: +86-23-68486780, E-mail: ; Jianguo Qiu, Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No.1 You Yi Road, Yuzhong District, Chongqing 400016, China. ORCID: https://orcid.org/0000-0003-4574-9376. Tel: +86-23-68486780, Fax: +86-23-89011016, E-mail:
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Molecular targets that sensitize cancer to radiation killing: From the bench to the bedside. Biomed Pharmacother 2023; 158:114126. [PMID: 36521246 DOI: 10.1016/j.biopha.2022.114126] [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: 10/19/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Radiotherapy is a standard cytotoxic therapy against solid cancers. It uses ionizing radiation to kill tumor cells through damage to DNA, either directly or indirectly. Radioresistance is often associated with dysregulated DNA damage repair processes. Most radiosensitizers enhance radiation-mediated DNA damage and reduce the rate of DNA repair ultimately leading to accumulation of DNA damages, cell-cycle arrest, and cell death. Recently, agents targeting key signals in DNA damage response such as DNA repair pathways and cell-cycle have been developed. This new class of molecularly targeted radiosensitizing agents is being evaluated in preclinical and clinical studies to monitor their activity in potentiating radiation cytotoxicity of tumors and reducing normal tissue toxicity. The molecular pathways of DNA damage response are reviewed with a focus on the repair mechanisms, therapeutic targets under current clinical evaluation including ATM, ATR, CDK1, CDK4/6, CHK1, DNA-PKcs, PARP-1, Wee1, & MPS1/TTK and potential new targets (BUB1, and DNA LIG4) for radiation sensitization.
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34
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Tang T, Chen Y, Du Y, Yao B, Liu M. Effects of functional modules and bacterial clusters response on transmission performance of antibiotic resistance genes under antibiotic stress during anaerobic digestion of livestock wastewater. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129870. [PMID: 36063716 DOI: 10.1016/j.jhazmat.2022.129870] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/06/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
The formation and transmission of antibiotic resistance genes (ARGs) have attracted increasing attention. It is unclear whether the internal mechanisms by which antibiotics affect horizontal gene transfer (HGT) of ARGs during anaerobic digestion (AD) were influenced by dose and type. We investigated the effects of two major antibiotics (oxytetracycline, OTC, and sulfamethoxazole, SMX) on ARGs during AD according to antibiotic concentration in livestock wastewater influent. The low-dose antibiotic (0.5 mg/L) increased ROS and SOS responses, promoting the formation of ARGs. Meanwhile, low-dose antibiotics could also promote the spread of ARGs by promoting pili, communication responses, and the type IV secretion system (T4SS). However, different types and doses of antibiotics would lead to changes in the above functional modules and then affect the enrichment of ARGs. With the increasing dose of SMX, the advantages of pili and communication responses would gradually change. In the OTC system, low-dose has the strongest promoting ability in both pili and communication responses. Similarly, an increase in the dose of SMX would change T4SS from facilitation to inhibition, while OTC completely inhibits T4SS. Microbial and network analysis also revealed that low-dose antibiotics were more favorable for the growth of host bacteria.
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Affiliation(s)
- Taotao Tang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Ying Chen
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Ye Du
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Bing Yao
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Min Liu
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China.
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35
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Schaeffer L, Lindner L, Pavlovic G, Hérault Y, Birling MC. CRISMERE Chromosome Engineering in Mouse and Rat. Methods Mol Biol 2023; 2631:277-297. [PMID: 36995673 DOI: 10.1007/978-1-0716-2990-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
CRISPR/Cas9 technology is a versatile tool for engineering biology that has dramatically transformed our ability to manipulate genomes. In this protocol, we use its capacity to generate two double-strand breaks simultaneously, at precise positions in the genome, to generate mouse or rat lines with deletion, inversion, and duplication of a specific genomic segment. The technic is called CRISMERE for CRISpr-MEdiated REarrangement. This protocol describes the different steps to generate and validate the different chromosomal rearrangements that can be obtained with the technology. These new genetic configurations can be useful to model rare diseases with copy number variation, understand the genomic organization, or provide genetic tools (like balancer chromosome) to keep lethal mutations.
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Affiliation(s)
- Laurence Schaeffer
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Loic Lindner
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Guillaume Pavlovic
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Yann Hérault
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Marie-Christine Birling
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France.
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36
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Novotny JP, Mariño-Enríquez A, Fletcher JA. Targeting DNA-PK. Cancer Treat Res 2023; 186:299-312. [PMID: 37978142 DOI: 10.1007/978-3-031-30065-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
This chapter explores the multifaceted roles of DNA-PK with particular focus on its functions in non-homologous end-joining (NHEJ) DNA repair. DNA-PK is the primary orchestrator of NHEJ but also regulates other biologic processes. The growing understanding of varied DNA-PK biologic roles highlights new avenues for cancer treatment. However, these multiple roles also imply challenges, particularly in combination therapies, with perhaps a higher risk of clinical toxicities than was previously envisioned. These considerations underscore the need for compelling and innovative strategies to accomplish effective clinical translation.
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37
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Geci R, Willis K, Burt A. Gene drive designs for efficient and localisable population suppression using Y-linked editors. PLoS Genet 2022; 18:e1010550. [PMID: 36574454 PMCID: PMC9829173 DOI: 10.1371/journal.pgen.1010550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 01/09/2023] [Accepted: 11/29/2022] [Indexed: 12/28/2022] Open
Abstract
The sterile insect technique (SIT) has been successful in controlling some pest species but is not practicable for many others due to the large number of individuals that need to be reared and released. Previous computer modelling has demonstrated that the release of males carrying a Y-linked editor that kills or sterilises female descendants could be orders of magnitude more efficient than SIT while still remaining spatially restricted, particularly if combined with an autosomal sex distorter. In principle, further gains in efficiency could be achieved by using a self-propagating double drive design, in which each of the two components (the Y-linked editor and the sex ratio distorter) boosted the transmission of the other. To better understand the expected dynamics and impact of releasing constructs of this new design we have analysed a deterministic population genetic and population dynamic model. Our modelling demonstrates that this design can suppress a population from very low release rates, with no invasion threshold. Importantly, the design can work even if homing rates are low and sex chromosomes are silenced at meiosis, potentially expanding the range of species amenable to such control. Moreover, the predicted dynamics and impacts can be exquisitely sensitive to relatively small (e.g., 25%) changes in allele frequencies in the target population, which could be exploited for sequence-based population targeting. Analysis of published Anopheles gambiae genome sequences indicates that even for weakly differentiated populations with an FST of 0.02 there may be thousands of suitably differentiated genomic sites that could be used to restrict the spread and impact of a release. Our proposed design, which extends an already promising development pathway based on Y-linked editors, is therefore a potentially useful addition to the menu of options for genetic biocontrol.
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Affiliation(s)
- René Geci
- Dept. of Life Sciences, Imperial College London, Silwood Park, United Kingdom
| | - Katie Willis
- Dept. of Life Sciences, Imperial College London, Silwood Park, United Kingdom
| | - Austin Burt
- Dept. of Life Sciences, Imperial College London, Silwood Park, United Kingdom
- * E-mail:
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38
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Lama J, Srivastav S, Tasnim S, Hubbard D, Hadjipanteli S, Smith BR, Macdonald SJ, Green L, Kelleher ES. Genetic variation in P-element dysgenic sterility is associated with double-strand break repair and alternative splicing of TE transcripts. PLoS Genet 2022; 18:e1010080. [PMID: 36477699 PMCID: PMC9762592 DOI: 10.1371/journal.pgen.1010080] [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: 02/07/2022] [Revised: 12/19/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022] Open
Abstract
The germline mobilization of transposable elements (TEs) by small RNA mediated silencing pathways is conserved across eukaryotes and critical for ensuring the integrity of gamete genomes. However, genomes are recurrently invaded by novel TEs through horizontal transfer. These invading TEs are not targeted by host small RNAs, and their unregulated activity can cause DNA damage in germline cells and ultimately lead to sterility. Here we use hybrid dysgenesis-a sterility syndrome of Drosophila caused by transposition of invading P-element DNA transposons-to uncover host genetic variants that modulate dysgenic sterility. Using a panel of highly recombinant inbred lines of Drosophila melanogaster, we identified two linked quantitative trait loci (QTL) that determine the severity of dysgenic sterility in young and old females, respectively. We show that ovaries of fertile genotypes exhibit increased expression of splicing factors that suppress the production of transposase encoding transcripts, which likely reduces the transposition rate and associated DNA damage. We also show that fertile alleles are associated with decreased sensitivity to double-stranded breaks and enhanced DNA repair, explaining their ability to withstand high germline transposition rates. Together, our work reveals a diversity of mechanisms whereby host genotype modulates the cost of an invading TE, and points to genetic variants that were likely beneficial during the P-element invasion.
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Affiliation(s)
- Jyoti Lama
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Satyam Srivastav
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Sadia Tasnim
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Donald Hubbard
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Savana Hadjipanteli
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Brittny R. Smith
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Stuart J. Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Llewellyn Green
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Erin S. Kelleher
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
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39
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Chen X, Niu X, Liu Y, Zheng R, Yang L, Lu J, Yin S, Wei Y, Pan J, Sayed A, Ma X, Liu M, Jing F, Liu M, Hu J, Wang L, Li D. Long-term correction of hemophilia B through CRISPR/Cas9 induced homology-independent targeted integration. J Genet Genomics 2022; 49:1114-1126. [PMID: 35691554 DOI: 10.1016/j.jgg.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 01/14/2023]
Abstract
CRISPR/Cas9-mediated site-specific insertion of exogenous genes holds potential for clinical applications. However, it is still infeasible because homologous recombination (HR) is inefficient, especially for non-dividing cells. To overcome the challenge, we report that a homology-independent targeted integration (HITI) strategy is used for permanent integration of high-specificity-activity Factor IX variant (F9 Padua, R338L) at the albumin (Alb) locus in a novel hemophilia B (HB) rat model. The knock-in efficiency reaches 3.66%, as determined by droplet digital PCR (ddPCR). The clotting time is reduced to a normal level four weeks after treatment, and the circulating factor IX (FIX) level is gradually increased up to 52% of the normal level over nine months even after partial hepatectomy, demonstrating the amelioration of hemophilia. Through primer-extension-mediated sequencing (PEM-seq), no significant off-target effect is detected. This study not only provides a novel model for HB but also identifies a promising therapeutic approach for rare inherited diseases.
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Affiliation(s)
- Xi Chen
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xuran Niu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yang Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Genome Editing Research Center, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Rui Zheng
- Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Lei Yang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jian Lu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Shuming Yin
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yu Wei
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiahao Pan
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Ahmed Sayed
- Biochemistry Laboratory, Chemistry Department, Faculty of Science, Assiut University, Assiut 71516, Egypt
| | - Xueyun Ma
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Meizhen Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | | | - Mingyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Genome Editing Research Center, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| | - Liren Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.
| | - Dali Li
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.
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40
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CRISPR-Cas12a induced DNA double-strand breaks are repaired by multiple pathways with different mutation profiles in Magnaporthe oryzae. Nat Commun 2022; 13:7168. [PMID: 36418866 PMCID: PMC9684475 DOI: 10.1038/s41467-022-34736-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/01/2022] [Indexed: 11/24/2022] Open
Abstract
CRISPR-Cas mediated genome engineering has revolutionized functional genomics. However, understanding of DNA repair following Cas-mediated DNA cleavage remains incomplete. Using Cas12a ribonucleoprotein genome editing in the fungal pathogen, Magnaporthe oryzae, we detail non-canonical DNA repair outcomes from hundreds of transformants. Sanger and nanopore sequencing analysis reveals significant variation in DNA repair profiles, ranging from small INDELs to kilobase size deletions and insertions. Furthermore, we find the frequency of DNA repair outcomes varies between loci. The results are not specific to the Cas-nuclease or selection procedure. Through Ku80 deletion analysis, a key protein required for canonical non-homologous end joining, we demonstrate activity of an alternative end joining mechanism that creates larger DNA deletions, and uses longer microhomology compared to C-NHEJ. Together, our results suggest preferential DNA repair pathway activity in the genome that can create different mutation profiles following repair, which could create biased genome variation and impact genome engineering and genome evolution.
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41
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Zattera ML, Bruschi DP. Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome. Cells 2022; 11:cells11213373. [PMID: 36359770 PMCID: PMC9659126 DOI: 10.3390/cells11213373] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 12/02/2022] Open
Abstract
The impact of transposable elements (TEs) on the evolution of the eukaryote genome has been observed in a number of biological processes, such as the recruitment of the host’s gene expression network or the rearrangement of genome structure. However, TEs may also provide a substrate for the emergence of novel repetitive elements, which contribute to the generation of new genomic components during the course of the evolutionary process. In this review, we examine published descriptions of TEs that give rise to tandem sequences in an attempt to comprehend the relationship between TEs and the emergence of de novo satellite DNA families in eukaryotic organisms. We evaluated the intragenomic behavior of the TEs, the role of their molecular structure, and the chromosomal distribution of the paralogous copies that generate arrays of repeats as a substrate for the emergence of new repetitive elements in the genome. We highlight the involvement and importance of TEs in the eukaryote genome and its remodeling processes.
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Affiliation(s)
- Michelle Louise Zattera
- Departamento de Genética, Programa de Pós-Graduação em Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba 81530-000, PR, Brazil
| | - Daniel Pacheco Bruschi
- Departamento de Genética, Laboratorio de Citogenética Evolutiva e Conservação Animal, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba 81530-000, PR, Brazil
- Correspondence:
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Chu YY, Yam C, Yamaguchi H, Hung MC. Biomarkers beyond BRCA: promising combinatorial treatment strategies in overcoming resistance to PARP inhibitors. J Biomed Sci 2022; 29:86. [PMID: 36284291 PMCID: PMC9594904 DOI: 10.1186/s12929-022-00870-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) exploit the concept of synthetic lethality and offer great promise in the treatment of tumors with deficiencies in homologous recombination (HR) repair. PARPi exert antitumor activity by blocking Poly(ADP-ribosyl)ation (PARylation) and trapping PARP1 on damaged DNA. To date, the U.S. Food and Drug Administration (FDA) has approved four PARPi for the treatment of several cancer types including ovarian, breast, pancreatic and prostate cancer. Although patients with HR-deficient tumors benefit from PARPi, majority of tumors ultimately develop acquired resistance to PARPi. Furthermore, even though BRCA1/2 mutations are commonly used as markers of PARPi sensitivity in current clinical practice, not all patients with BRCA1/2 mutations have PARPi-sensitive disease. Thus, there is an urgent need to elucidate the molecular mechanisms of PARPi resistance to support the development of rational effective treatment strategies aimed at overcoming resistance to PARPi, as well as reliable biomarkers to accurately identify patients who will most likely benefit from treatment with PARPi, either as monotherapy or in combination with other agents, so called marker-guided effective therapy (Mget). In this review, we summarize the molecular mechanisms driving the efficacy of and resistance to PARPi as well as emerging therapeutic strategies to overcome PARPi resistance. We also highlight the identification of potential markers to predict PARPi resistance and guide promising PARPi-based combination strategies.
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Affiliation(s)
- Yu-Yi Chu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Clinton Yam
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hirohito Yamaguchi
- Research Center for Cancer Biology, and Center for Molecular Medicine, Graduate Institute of Biomedical Sciences, China Medical University, 100, Sec 1, Jingmao Rd., Beitun, Taichung, 40402, Taiwan, ROC
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Research Center for Cancer Biology, and Center for Molecular Medicine, Graduate Institute of Biomedical Sciences, China Medical University, 100, Sec 1, Jingmao Rd., Beitun, Taichung, 40402, Taiwan, ROC. .,Department of Biotechnology, Asia University, Taichung, 413, Taiwan.
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Deshpande M, Paniza T, Jalloul N, Nanjangud G, Twarowski J, Koren A, Zaninovic N, Zhan Q, Chadalavada K, Malkova A, Khiabanian H, Madireddy A, Rosenwaks Z, Gerhardt J. Error-prone repair of stalled replication forks drives mutagenesis and loss of heterozygosity in haploinsufficient BRCA1 cells. Mol Cell 2022; 82:3781-3793.e7. [PMID: 36099913 DOI: 10.1016/j.molcel.2022.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/21/2022] [Accepted: 08/16/2022] [Indexed: 01/05/2023]
Abstract
Germline mutations in the BRCA genes are associated with a higher risk of carcinogenesis, which is linked to an increased mutation rate and loss of the second unaffected BRCA allele (loss of heterozygosity, LOH). However, the mechanisms triggering mutagenesis are not clearly understood. The BRCA genes contain high numbers of repetitive DNA sequences. We detected replication forks stalling, DNA breaks, and deletions at these sites in haploinsufficient BRCA cells, thus identifying the BRCA genes as fragile sites. Next, we found that stalled forks are repaired by error-prone pathways, such as microhomology-mediated break-induced replication (MMBIR) in haploinsufficient BRCA1 breast epithelial cells. We detected MMBIR mutations in BRCA1 tumor cells and noticed deletions-insertions (>50 bp) at the BRCA1 genes in BRCA1 patients. Altogether, these results suggest that under stress, error-prone repair of stalled forks is upregulated and induces mutations, including complex genomic rearrangements at the BRCA genes (LOH), in haploinsufficient BRCA1 cells.
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Affiliation(s)
- Madhura Deshpande
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Theodore Paniza
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Nahed Jalloul
- Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08903, USA
| | - Gouri Nanjangud
- Molecular Cytogenetics Core Facility, Sloan Kettering Institute, New York, NY 10065, USA
| | - Jerzy Twarowski
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Nikica Zaninovic
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Qiansheng Zhan
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Kalyani Chadalavada
- Molecular Cytogenetics Core Facility, Sloan Kettering Institute, New York, NY 10065, USA
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Hossein Khiabanian
- Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08903, USA
| | - Advaitha Madireddy
- Department of Pediatric Hematology/Oncology, Rutgers University, New Brunswick, NJ 08903, USA
| | - Zev Rosenwaks
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jeannine Gerhardt
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY 10021, USA.
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Ren P, Dong X, Vijg J. Age-related somatic mutation burden in human tissues. FRONTIERS IN AGING 2022; 3:1018119. [PMID: 36213345 PMCID: PMC9534562 DOI: 10.3389/fragi.2022.1018119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022]
Abstract
The genome of multicellular organisms carries the hereditary information necessary for the development of all organs and tissues and to maintain function in adulthood. To ensure the genetic stability of the species, genomes are protected against changes in sequence information. However, genomes are not static. De novo mutations in germline cells are passed on to offspring and generate the variation needed in evolution. Moreover, postzygotic mutations occur in all somatic cells during development and aging. These somatic mutations remain limited to the individual, generating tissues that are genome mosaics. Insight into such mutations and their consequences has been limited due to their extremely low abundance, with most mutations unique for each cell. Recent advances in sequencing, including whole genome sequencing at the single-cell level, have now led to the first insights into somatic mutation burdens in human tissues. Here, we will first briefly describe the latest methodology for somatic mutation analysis, then review our current knowledge of somatic mutation burden in human tissues and, finally, briefly discuss the possible functional impact of somatic mutations on the aging process and age-related diseases, including cancer and diseases other than cancer.
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Affiliation(s)
- Peijun Ren
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Peijun Ren, ; Xiao Dong, ; Jan Vijg, ,
| | - Xiao Dong
- Department of Genetics, Cell Biology and Development, Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, United States,*Correspondence: Peijun Ren, ; Xiao Dong, ; Jan Vijg, ,
| | - Jan Vijg
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Department of Genetics, Albert Einstein College of Medicine, New York City, NY, United States,*Correspondence: Peijun Ren, ; Xiao Dong, ; Jan Vijg, ,
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Mahmoud R, Dhakal S. Single-Molecule Analysis of DNA Branch Migration under Biomimetic Environments. J Phys Chem B 2022; 126:7252-7261. [DOI: 10.1021/acs.jpcb.2c03153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roaa Mahmoud
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
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A mechanistic mathematical model of initiation and malignant transformation in sporadic vestibular schwannoma. Br J Cancer 2022; 127:1843-1857. [PMID: 36097176 DOI: 10.1038/s41416-022-01955-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 07/13/2022] [Accepted: 08/08/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND A vestibular schwannoma (VS) is a relatively rare, benign tumour of the eighth cranial nerve, often involving alterations to the gene NF2. Previous mathematical models of schwannoma incidence have not attempted to account for alterations in specific genes, and could not distinguish between nonsense mutations and loss of heterozygosity (LOH). METHODS Here, we present a mechanistic approach to modelling initiation and malignant transformation in schwannoma. Each parameter is associated with a specific gene or mechanism operative in Schwann cells, and can be determined by combining incidence data with empirical frequencies of pathogenic variants and LOH. RESULTS This results in new estimates for the base-pair mutation rate u = 4.48 × 10-10 and the rate of LOH = 2.03 × 10-6/yr in Schwann cells. In addition to new parameter estimates, we extend the approach to estimate the risk of both spontaneous and radiation-induced malignant transformation. DISCUSSION We conclude that radiotherapy is likely to have a negligible excess risk of malignancy for sporadic VS, with a possible exception of rapidly growing tumours.
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Katerji M, Bertucci A, Filippov V, Vazquez M, Chen X, Duerksen-Hughes PJ. Proton-induced DNA damage promotes integration of foreign plasmid DNA into human genome. Front Oncol 2022; 12:928545. [PMID: 36119491 PMCID: PMC9478911 DOI: 10.3389/fonc.2022.928545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/16/2022] [Indexed: 11/20/2022] Open
Abstract
High-risk human papillomaviruses (HPVs) cause virtually all cervical cancer cases and are also associated with other types of anogenital and oropharyngeal cancers. Normally, HPV exists as a circular episomal DNA in the infected cell. However, in some instances, it integrates into the human genome in such a way as to enable increased expression of viral oncogenes, thereby leading to carcinogenesis. Since viral integration requires breaks in both viral and human genomes, DNA damage likely plays a key role in this critical process. One potentially significant source of DNA damage is exposure to elevated doses of ionizing radiation. Natural background radiation is ubiquitous; however, some populations, including radiological workers, radiotherapy patients, and astronauts, are exposed to significantly higher radiation doses, as well as to different types of radiation such as particle radiation. We hypothesize that ionizing radiation-induced DNA damage facilitates the integration of HPV into the human genome, increasing the risk of developing HPV-related cancers in the exposed population. To test this, we first determined the kinetics of DNA damage in keratinocytes exposed to ionizing radiation (protons) by assessing γ-H2AX foci formation using immunofluorescence (direct damage), and also measured ROS and 8-oxoG levels via DCFDA and Avidin-FITC (indirect damage).As anticipated, direct DNA damage was observed promptly, within 30 min, whereas indirect DNA damage was delayed due to the time required for ROS to accumulate and cause oxidative damage. Although radiation was lethal at high doses, we were able to establish an experimental system where radiation exposure (protons and X-rays) induced DNA damage dose-dependently without causing major cytotoxic effects as assessed by several cytotoxicity assays. Most importantly, we explored the impact of radiation exposure on integration frequency using a clonogenic assay and demonstrated that as predicted, proton-induced DNA damage promotes the integration of HPV-like foreign DNA in oral keratinocytes. Overall, the insights gained from this work enable us to better understand the contribution of radiation exposure and DNA damage to HPV-mediated carcinogenesis and direct us toward strategies aimed at preventing malignancies in HPV-infected individuals.
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Affiliation(s)
- Meghri Katerji
- Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, United States
| | - Antonella Bertucci
- Department of Radiation Medicine, Loma Linda University Medical Center, Loma Linda, CA, United States
| | - Valery Filippov
- Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, United States
| | - Marcelo Vazquez
- Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, United States
- Department of Radiation Medicine, Loma Linda University Medical Center, Loma Linda, CA, United States
| | - Xin Chen
- Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, United States
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, United States
| | - Penelope J. Duerksen-Hughes
- Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, United States
- *Correspondence: Penelope J. Duerksen-Hughes,
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Ji Y, Feng S, Wu L, Fang Q, Brüniche-Olsen A, DeWoody JA, Cheng Y, Zhang D, Hao Y, Song G, Qu Y, Suh A, Zhang G, Hackett SJ, Lei F. Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds. SCIENCE ADVANCES 2022; 8:eabo0099. [PMID: 36044583 PMCID: PMC9432842 DOI: 10.1126/sciadv.abo0099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
The rate of mutation accumulation in germline cells can be affected by cell replication and/or DNA damage, which are further related to life history traits such as generation time and body mass. Leveraging the existing datasets of 233 neoavian bird species, here, we investigated whether generation time and body mass contribute to the interspecific variation of orthologous microsatellite length, transposable element (TE) length, and deletion length and how these genomic attributes affect genome sizes. In nonpasserines, we found that generation time is correlated to both orthologous microsatellite length and TE length, and body mass is negatively correlated to DNA deletions. These patterns are less pronounced in passerines. In all species, we found that DNA deletions relate to genome size similarly as TE length, suggesting a role of body mass dynamics in genome evolution. Our results indicate that generation time and body mass shape the evolution of genomic attributes in neoavian birds.
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Affiliation(s)
- Yanzhu Ji
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
- Evolutionary and Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, China
| | - Lei Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Fang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Anna Brüniche-Olsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - J. Andrew DeWoody
- Departments of Forestry and Natural Resources and Biological Sciences, Purdue University, West Lafayette, IN 47906, USA
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Alexander Suh
- School of Biological Sciences, Organism and Environment, University of East Anglia, NR4 7TU, Norwich, UK
- Department of Organismal Biology, Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala SE-752 36, Sweden
| | - Guojie Zhang
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
- Evolutionary and Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Women’s Hospital, School of Medicine, Zhejiang University, Shangcheng District, Hangzhou, 310006, China
| | - Shannon J. Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
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49
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Holmes TH, Winn LM. DNA damage, DNA repair gene expression, and topoisomerase IIα activity in CD-1 mice following in utero benzene exposure. Toxicol Lett 2022; 368:47-55. [PMID: 35963423 DOI: 10.1016/j.toxlet.2022.08.002] [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: 03/24/2022] [Revised: 07/16/2022] [Accepted: 08/08/2022] [Indexed: 11/19/2022]
Abstract
Benzene is an environmental toxicant and known human carcinogen. Recent epidemiological studies show a relationship between exposure to benzene in pregnant women and increased incidence of childhood leukemias. Studies in murine models demonstrate a relationship between carcinogenicity and in utero benzene exposure which was sex dependent, thus the cellular mechanisms of benzene toxicity by sex require further studies. A hypothesized mechanism of benzene-induced in utero carcinogenicity is through increased DNA damage and reduced fetal DNA repair capacity. This includes the potential inhibition of topoisomerase IIα (topo IIα), in part, to generate double stranded DNA (dsDNA) breaks and induction of error-prone DNA repair. Using a mouse model of transplacental benzene carcinogenicity, gestational day (GD) 14 fetal livers were harvested 2, 6, and 24 h following maternal exposure to 200 mg/kg benzene and used to assess DNA damage, DNA repair gene expression and topo IIα activity. DNA damage, measured by levels of modified histone H2AX (γH2AX), is significantly increased in benzene exposed pups, with sex-dependent significance seen only in female pups. Comet assay results confirmed that benzene exposure in utero induces dsDNA damage in the GD14 fetal liver. Genes involved in DNA repair were assessed, and DNA repair gene expression changes were observed after 24 h in genes related to nucleotide excision repair, homologous recombination, and non-homologous end-joining. There were no significant differences in topo IIα activity in GD14 fetal livers at any timepoint, or between sexes. Overall, this study shows that 200 mg/kg benzene exposure induces dsDNA damage and alters fetal DNA repair gene expression in utero, without perturbing fetal topo IIα in CD-1 mice.
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Affiliation(s)
- Trent H Holmes
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Louise M Winn
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada; School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada.
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Valcz G, Újvári B, Buzás EI, Krenács T, Spisák S, Kittel Á, Tulassay Z, Igaz P, Takács I, Molnár B. Small extracellular vesicle DNA-mediated horizontal gene transfer as a driving force for tumor evolution: Facts and riddles. Front Oncol 2022; 12:945376. [PMID: 36003770 PMCID: PMC9393732 DOI: 10.3389/fonc.2022.945376] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
The basis of the conventional gene-centric view on tumor evolution is that vertically inherited mutations largely define the properties of tumor cells. In recent years, however, accumulating evidence shows that both the tumor cells and their microenvironment may acquire external, non-vertically inherited genetic properties via horizontal gene transfer (HGT), particularly through small extracellular vesicles (sEVs). Many phases of sEV-mediated HGT have been described, such as DNA packaging into small vesicles, their release, uptake by recipient cells, and incorporation of sEV-DNA into the recipient genome to modify the phenotype and properties of cells. Recent techniques in sEV separation, genome sequencing and editing, as well as the identification of new secretion mechanisms, shed light on a number of additional details of this phenomenon. Here, we discuss the key features of this form of gene transfer and make an attempt to draw relevant conclusions on the contribution of HGT to tumor evolution.
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Affiliation(s)
- Gábor Valcz
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, Budapest, Hungary
- *Correspondence: Gábor Valcz,
| | - Beáta Újvári
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Waurn Ponds, VIC, Australia
| | - Edit I. Buzás
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
- ELKH-SE Immune-Proteogenomics Extracellular Vesicle Research Group, Semmelweis University, Budapest, Hungary
- HCEMM-SU Extracellular Vesicle Research Group, Semmelweis University, Budapest, Hungary
| | - Tibor Krenács
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Sándor Spisák
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ágnes Kittel
- Institute of Experimental Medicine, Eötvös Loránd Research Network, Budapest, Hungary
| | - Zsolt Tulassay
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, Budapest, Hungary
| | - Péter Igaz
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
- Department of Endocrinology, Semmelweis University, Budapest, Hungary
| | - István Takács
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Béla Molnár
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
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