1
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Přibylová A, Fischer L. How to use CRISPR/Cas9 in plants - from target site selection to DNA repair. J Exp Bot 2024:erae147. [PMID: 38648173 DOI: 10.1093/jxb/erae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Indexed: 04/25/2024]
Abstract
A tool for precise, target-specific, efficient and affordable genome editing, it is a dream for many researchers, from those who do basic research to those who use it for applied research. Since 2012, we have the tool that almost fulfils such requirements; it is based on CRISPR/Cas systems. However, even CRISPR/Cas has limitations and obstacles that might surprise its users. In this review, we focus on the most frequently used variant, CRISPR/Cas9 from Streptococcus pyogenes, and highlight the key factors affecting its mutagenesis outcomes. Firstly, factors affecting the CRISPR/Cas9 activity, such as the effect of the target sequence, chromatin state or Cas9 variant, and how long it remains in place after cleavage. Secondly, factors affecting the follow-up DNA repair mechanisms include mostly the cell type and cell cycle phase, but also, for example, the type of DNA ends produced by Cas9 cleavage (blunt/staggered). Moreover, we note some differences between using CRISPR/Cas9 in plants, yeasts and animals, as knowledge from individual kingdoms is not fully transferable. Awareness of these factors can increase the likelihood of achieving the expected results of plant genome editing, for which we provide detailed guidelines.
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Affiliation(s)
- Adéla Přibylová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12800, Prague 2, Czech Republic
| | - Lukáš Fischer
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12800, Prague 2, Czech Republic
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2
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Hahn R, Avraham KB. Gene Therapy for Inherited Hearing Loss: Updates and Remaining Challenges. Audiol Res 2023; 13:952-966. [PMID: 38131808 PMCID: PMC10740825 DOI: 10.3390/audiolres13060083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/13/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
Hearing loss stands as the most prevalent sensory deficit among humans, posing a significant global health challenge. Projections indicate that by 2050, approximately 10% of the world's population will grapple with disabling hearing impairment. While approximately half of congenital hearing loss cases have a genetic etiology, traditional interventions such as hearing aids and cochlear implants do not completely restore normal hearing. The absence of biological treatment has prompted significant efforts in recent years, with a strong focus on gene therapy to address hereditary hearing loss. Although several studies have exhibited promising recovery from common forms of genetic deafness in mouse models, existing challenges must be overcome to make gene therapy applicable in the near future. Herein, we summarize the primary gene therapy strategies employed over past years, provide an overview of the recent achievements in preclinical studies for genetic hearing loss, and outline the current key obstacles to cochlear gene therapy.
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Affiliation(s)
| | - Karen B. Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel;
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3
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Dulic M, Krpan N, Gruic-Sovulj I. Gly56 in the synthetic site of isoleucyl-tRNA synthetase confers specificity and maintains communication with the editing site. FEBS Lett 2023; 597:3114-3124. [PMID: 38015921 DOI: 10.1002/1873-3468.14780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 11/30/2023]
Abstract
Isoleucyl-tRNA synthetase (IleRS) links isoleucine to cognate tRNA via the Ile-AMP intermediate. Non-cognate valine is often mistakenly recognized as the IleRS substrate; therefore, to maintain the accuracy of translation, IleRS hydrolyzes Val-AMP within the synthetic site (pre-transfer editing). As this activity is not efficient enough, Val-tRNAIle is formed and hydrolyzed in the distant post-transfer editing site. A strictly conserved synthetic site residue Gly56 was previously shown to safeguard Ile-to-Val discrimination during aminoacyl (aa)-AMP formation. Here, we show that the Gly56Ala variant lost its specificity in pre-transfer editing, confirming that this residue ensures the selectivity of all synthetic site reactions. Moreover, we found that the Gly56Ala mutation affects IleRS interaction with aa-tRNA likely by disturbing tRNA-dependent communication between the two active sites.
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Affiliation(s)
- Morana Dulic
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
| | - Nina Krpan
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
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4
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Zheng WQ, Zhang JH, Li ZH, Liu X, Zhang Y, Huang S, Li J, Zhou B, Eriani G, Wang ED, Zhou XL. Mammalian mitochondrial translation infidelity leads to oxidative stress-induced cell cycle arrest and cardiomyopathy. Proc Natl Acad Sci U S A 2023; 120:e2309714120. [PMID: 37669377 PMCID: PMC10500172 DOI: 10.1073/pnas.2309714120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/08/2023] [Indexed: 09/07/2023] Open
Abstract
Proofreading (editing) of mischarged tRNAs by cytoplasmic aminoacyl-tRNA synthetases (aaRSs), whose impairment causes neurodegeneration and cardiac diseases, is of high significance for protein homeostasis. However, whether mitochondrial translation needs fidelity and the significance of editing by mitochondrial aaRSs have been unclear. Here, we show that mammalian cells critically depended on the editing of mitochondrial threonyl-tRNA synthetase (mtThrRS, encoded by Tars2), disruption of which accumulated Ser-tRNAThr and generated a large abundance of Thr-to-Ser misincorporated peptides in vivo. Such infidelity impaired mitochondrial translation and oxidative phosphorylation, causing oxidative stress and cell cycle arrest in the G0/G1 phase. Notably, reactive oxygen species (ROS) scavenging by N-acetylcysteine attenuated this abnormal cell proliferation. A mouse model of heart-specific defective mtThrRS editing was established. Increased ROS levels, blocked cardiomyocyte proliferation, contractile dysfunction, dilated cardiomyopathy, and cardiac fibrosis were observed. Our results elucidate that mitochondria critically require a high level of translational accuracy at Thr codons and highlight the cellular dysfunctions and imbalance in tissue homeostasis caused by mitochondrial mistranslation.
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Affiliation(s)
- Wen-Qiang Zheng
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Jian-Hui Zhang
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
| | - Zi-Han Li
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Xiuxiu Liu
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Yong Zhang
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Shuo Huang
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Jinsong Li
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
| | - Bin Zhou
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
| | - Gilbert Eriani
- Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg67084, France
| | - En-Duo Wang
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Xiao-Long Zhou
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
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5
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Sanz-Aznar J, Bruni LE, Soto-Faraco S. Cinematographic continuity edits across shot scales and camera angles: an ERP analysis. Front Neurosci 2023; 17:1173704. [PMID: 37521689 PMCID: PMC10375706 DOI: 10.3389/fnins.2023.1173704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023] Open
Abstract
Film editing has attracted great theoretical and practical interest since the beginnings of cinematography. In recent times, the neural correlates of visual transitions at edit cuts have been at the focus of attention in neurocinematics. Many Event Related Potential (ERP) studies studies have reported the consequences of cuts involving narrative discontinuities, and violations of standard montage rules. However, less is known about edits that are meant to induce continuity. Here, we addressed the neural correlates of continuity editing involving scale, and angle variations across the cut within the same scene, two of the most popular devices used for continuity editing. We recorded the electroencephalographic signal obtained from 20 viewers as they watched four different cinematographic excerpts to extract ERPs at edit points. First, we were able to reproduce the general time and scalp distribution of the typical ERPs to filmic cuts in prior studies. Second, we found significant ERP modulations triggered by scale changes (scale out, scale in, or maintaining the same scale). Edits involving an increase in scale (scale out) led to amplification of the ERP deflection, and scale reduction (scale in) led to decreases, compared to edits that kept scale across the cut. These modulations coincide with the time window of the N300 and N400 components and, according to previous findings, their amplitude has been associated with the likelihood of consciously detecting the edit. Third, we did not detect similar modulations as a function of angle variations across the cut. Based on these findings, we suggest that cuts involving reduction of scale are more likely to go unnoticed, than ones that scale out. This relationship between scale in/out and visibility is documented in film edition manuals. Specifically, in order to achieve fluidity in a scene, the edition is designed from the most opened shots to the most closed ones.
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Affiliation(s)
- Javier Sanz-Aznar
- Section of Communication, Department of Hispanic Studies, Literary Theory and Communication, University of Barcelona, Barcelona, Spain
| | - Luis Emilio Bruni
- Augmented Cognition Lab, Section for Media Technology, Department of Architecture, Design and Media Technology, The Technical Faculty of IT and Design, Aalborg University, Copenhagen, Denmark
| | - Salvador Soto-Faraco
- Multisensory Research Group, The Center for Brain and Cognition, Pompeu Fabra University, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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6
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Wang HM, Qiao YY, Cai BY, Tan J, Na L, Wang Y, Lu H, Tang YD. Genome editing of pseudorabies virus in the CRISPR/Cas9 era: a mini-review. Front Vet Sci 2023; 10:1237186. [PMID: 37476821 PMCID: PMC10354360 DOI: 10.3389/fvets.2023.1237186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 06/22/2023] [Indexed: 07/22/2023] Open
Abstract
Pseudorabies virus (PRV) is an important swine virus that has a significant impact on the global swine industry. PRV is a member of the herpesvirus family, specifically the alphaherpesvirus subfamily, and has been extensively utilized as a prototype herpesvirus. Notably, recent studies have reported that PRV sporadically spills over into humans. The PRV genome is approximately 150 kb in size and is difficult to manipulate at the genomic level. The development of clustered regularly interspaced short palindromic repeat-associated protein (CRISPR/Cas9) technology has revolutionized PRV genome editing. CRISPR/Cas9 has been widely used in the construction of reporter viruses, knock-out/knock-in of genes of interest, single virus tracking and antiviral strategies. Most importantly, for vaccine development, virulence gene knockout PRV vaccine candidates can be obtained within 2 weeks using CRISPR/Cas9. In this mini-review, we provide a concise overview of the application of CRISPR/Cas9 in PRV research and mainly share our experience with methods for efficiently editing the PRV genome. Through this review, we hope to give researchers better insight into the genome editing of pseudorabies virus.
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Affiliation(s)
- Hai-Ming Wang
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Yang-Yang Qiao
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Bing-Yan Cai
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Ju Tan
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Lei Na
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Vocational College Agriculture and Forestry, Taizhou, Jiangsu, China
| | - Yu Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hui Lu
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Yan-Dong Tang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
- Heilongjiang Provincial Research Center for Veterinary Biomedicine, Harbin, China
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7
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Hoekstra M, Van Eck M, Van Berkel TJC. Perspective: Hepatocyte-Directed Base Editing as Novel Treatment for Human Dyslipidemia-Current Status and Remaining Challenges. Arterioscler Thromb Vasc Biol 2023; 43:832-835. [PMID: 37128922 DOI: 10.1161/atvbaha.122.318354] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Hyperlipidemia is a major risk factor for the development of atherosclerotic cardiovascular disease. Lipid-lowering drug therapies therefore still form the heart of the ongoing battle against the occurrence of cardiovascular events. However, in light of the important improvements in gene interference and editing that have been made during the last 2 decades, gene therapy-the genetic modification of cells to produce a permanent therapeutic effect-is currently employed to relief hypercholesterolemic subjects from their potential (chronic) cardiovascular disease burden. In this perspective, we review the current status regarding hepatocyte-directed base editing to treat human dyslipidemia and provide suggestions for further technological improvement.
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Affiliation(s)
- Menno Hoekstra
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands. (M.H., M.V.E., T.J.C.V.B.)
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands. (M.H., M.V.E.)
| | - Miranda Van Eck
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands. (M.H., M.V.E., T.J.C.V.B.)
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands. (M.H., M.V.E.)
- Pharmacy Leiden, The Netherlands (M.V.E.)
| | - Theo J C Van Berkel
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands. (M.H., M.V.E., T.J.C.V.B.)
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8
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Bose SK, Kennedy K, Peranteau WH. Foetal genome editing. Curr Opin Obstet Gynecol 2023; 35:134-139. [PMID: 36924409 PMCID: PMC10027366 DOI: 10.1097/gco.0000000000000854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
PURPOSE OF REVIEW The development of modern gene editing tools alongside promising innovations in gene sequencing and prenatal diagnostics as well as a shifting regulatory climate around targeted therapeutics offer an opportunity to address monogenic diseases prior to the onset of pathology. In this review, we seek to highlight recent progress in preclinical studies evaluating the potential in-utero gene editing as a treatment for monogenic diseases that cause morbidity or mortality before or shortly after birth. RECENT FINDINGS There has been significant recent progress in clinical trials for postnatal gene editing. Corresponding advances have been made with respect to in-utero cell and enzyme replacement therapies. These precedents establish the foundation for 'one-shot' treatments by way in-utero gene editing. Compelling preclinical data in liver, pulmonary and multisystemic diseases demonstrate the potential benefits of in-utero editing approaches. SUMMARY Recent proof-of-concept studies have demonstrated the safety and feasibility of in-utero gene editing across multiple organ systems and in numerous diseases. Clinical translation will require continued evolution of vectors and editing approaches to maximize efficiency and minimize unwanted treatment effects.
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Affiliation(s)
- Sourav K Bose
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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Yan S, Xu X, Qi F, Guo X, Luo J, Li Y. Editorial: Application of gene editing in pathology dissection of neurodegenerative diseases. Front Neurosci 2023; 16:1092176. [PMID: 36685233 PMCID: PMC9850221 DOI: 10.3389/fnins.2022.1092176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Affiliation(s)
- Sen Yan
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of Central Nervous System (CNS) Regeneration, Jinan University, Guangzhou, China,*Correspondence: Sen Yan ✉
| | - Xingshun Xu
- The Institute of Neuroscience, Soochow University, Suzhou, China,Xingshun Xu ✉
| | - Fangfang Qi
- Department of Anatomy and Neurobiology, Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China,Fangfang Qi ✉
| | - Xing Guo
- Department of Neurobiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu, China,Xing Guo ✉
| | - Junhong Luo
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China,Junhong Luo ✉
| | - Yujing Li
- Department of Human Genetics, Emory University, Atlanta, GA, United States,Yujing Li ✉
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Seidman CS. That's All She Wrote. J Appalach Health 2022; 4:5-8. [PMID: 35769507 PMCID: PMC9200455 DOI: 10.13023/jah.0401.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
With the publication of this issue, I am retiring and formally handing over the reins as managing editor of the Journal of Appalachian Health to Rachel Dixon. I have had a 50+ year career and have been blessed to have had the opportunity to meet and work with the best health professionals in preventive medicine and public health.
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11
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Khalfi P, Suspène R, Caval V, Thiers V, Beauclair G, Marchio A, Bekondi C, Amougou Atsama M, Camengo-Police SM, Noah Noah D, Njouom R, Blanc H, Vallet T, Vignuzzi M, Pineau P, Vartanian JP. APOBEC3C S188I polymorphism enhances context specific editing of Hepatitis B virus genome. J Infect Dis 2022; 226:891-895. [PMID: 35022749 DOI: 10.1093/infdis/jiac003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 01/10/2022] [Indexed: 11/12/2022] Open
Abstract
A single nucleotide polymorphism in APOBEC3C (serine to isoleucine in position 188) is present in ~10% of African populations and greatly enhances restriction against HIV-1 and SIV by improving dimerization and DNA processivity of the enzyme. In this study, we demonstrated in culture and in infected patients that HBV could be edited by APOBEC3CS188I. Using next generation sequencing, we demonstrated that APOBEC3CS188I led to an enhanced editing activity in a more specific 5'TpCpA->5'TpTpA context. This constitutes a new hallmark of this enzyme which could be used to determine its impact on HBV or nuclear DNA.
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Affiliation(s)
- Pierre Khalfi
- Department of Virology, Institut Pasteur, Université de Paris, Paris, France.,Complexité du Vivant, ED515, Sorbonne Université, Paris, France
| | - Rodolphe Suspène
- Department of Virology, Institut Pasteur, Université de Paris, Paris, France
| | - Vincent Caval
- Department of Virology, Institut Pasteur, Université de Paris, Paris, France
| | - Valérie Thiers
- Department of Virology, Institut Pasteur, Université de Paris, Paris, France
| | - Guillaume Beauclair
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Agnès Marchio
- Nuclear Organization and Oncogenesis unit, INSERM U993, Institut Pasteur, Université de Paris, Paris, France
| | - Claudine Bekondi
- Retrovirology and Oncogenic Viruses unit, Institut Pasteur de Bangui, Bangui, République Centrafricaine
| | | | | | - Dominique Noah Noah
- Gastroenterology Service, Hôpital de l'Amitié, Bangui, République Centrafricaine
| | - Richard Njouom
- Virology Service, Centre Pasteur du Cameroun, Yaoundé, Cameroun
| | - Hervé Blanc
- Viral Populations and Pathogenesis unit, Institut Pasteur, Université de Paris, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis unit, Institut Pasteur, Université de Paris, Paris, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis unit, Institut Pasteur, Université de Paris, Paris, France
| | - Pascal Pineau
- Nuclear Organization and Oncogenesis unit, INSERM U993, Institut Pasteur, Université de Paris, Paris, France
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12
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Gerber A, Le Gal F, Dziri S, Alloui C, Roulot D, Dény P, Sureau C, Brichler S, Gordien E. Comprehensive Analysis of Hepatitis Delta Virus Assembly Determinants According to Genotypes: Lessons From a Study of 526 Hepatitis Delta Virus Clinical Strains. Front Microbiol 2021; 12:751531. [PMID: 34867871 PMCID: PMC8636853 DOI: 10.3389/fmicb.2021.751531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/24/2021] [Indexed: 12/31/2022] Open
Abstract
Human hepatitis Delta virus (HDV) infection is associated to the most severe viral hepatic disease, including severe acute liver decompensation and progression to cirrhosis, and hepatocellular carcinoma. HDV is a satellite of hepatitis B virus (HBV) that requires the HBV envelope proteins for assembly of HDV virions. HDV and HBV exhibit a large genetic diversity that extends, respectively to eight (HDV-1 to -8) and to ten (HBV/A to/J) genotypes. Molecular determinants of HDV virion assembly consist of a C-terminal Proline-rich domain in the large Hepatitis Delta Antigen (HDAg) protein, also known as the Delta packaging domain (DPD) and of a Tryptophan-rich domain, the HDV matrix domain (HMD) in the C-terminal region of the HBV envelope proteins. In this study, we performed a systematic genotyping of HBV and HDV in a cohort 1,590 HDV-RNA-positive serum samples collected between 2001 to 2014, from patients originated from diverse parts of the world, thus reflecting a large genetic diversity. Among these samples, 526 HBV (HBV/A, B, C, D, E, and G) and HDV (HDV-1, 2, 3, and 5 to -8) genotype couples could be obtained. We provide results of a comprehensive analysis of the amino-acid sequence conservation within the HMD and structural and functional features of the DPD that may account for the yet optimal interactions between HDV and its helper HBV.
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Affiliation(s)
- Athenaïs Gerber
- Laboratoire de Microbiologie Clinique, Université Paris Nord, Sorbonne Paris Cité, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France.,Centre National de Référence des Hépatites B, C et Delta, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France
| | - Frédéric Le Gal
- Laboratoire de Microbiologie Clinique, Université Paris Nord, Sorbonne Paris Cité, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France.,Centre National de Référence des Hépatites B, C et Delta, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France.,INSERM U955, Équipe 18, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Samira Dziri
- Laboratoire de Microbiologie Clinique, Université Paris Nord, Sorbonne Paris Cité, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France.,Centre National de Référence des Hépatites B, C et Delta, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France
| | - Chakib Alloui
- Laboratoire de Microbiologie Clinique, Université Paris Nord, Sorbonne Paris Cité, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France.,Centre National de Référence des Hépatites B, C et Delta, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France.,INSERM U955, Équipe 18, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Dominique Roulot
- Centre National de Référence des Hépatites B, C et Delta, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France.,INSERM U955, Équipe 18, Institut Mondor de Recherche Biomédicale, Créteil, France.,Unité d'Hépatologie, Université Paris Nord, Sorbonne Paris Cité, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France
| | - Paul Dény
- Laboratoire de Microbiologie Clinique, Université Paris Nord, Sorbonne Paris Cité, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France.,Inserm, U1052 - UMR CNRS 5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Camille Sureau
- Laboratoire de Virologie Moléculaire, Institut National de la Transfusion Sanguine, Paris, France
| | - Ségolène Brichler
- Laboratoire de Microbiologie Clinique, Université Paris Nord, Sorbonne Paris Cité, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France.,Centre National de Référence des Hépatites B, C et Delta, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France.,INSERM U955, Équipe 18, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Emmanuel Gordien
- Laboratoire de Microbiologie Clinique, Université Paris Nord, Sorbonne Paris Cité, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France.,Centre National de Référence des Hépatites B, C et Delta, Hôpitaux Universitaires de Paris-Seine-Saint-Denis, Bobigny, France.,INSERM U955, Équipe 18, Institut Mondor de Recherche Biomédicale, Créteil, France
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13
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Gregori J, Cortese MF, Piñana M, Campos C, Garcia-Cehic D, Andrés C, Abril JF, Codina MG, Rando A, Esperalba J, Sulleiro E, Joseph J, Saubí N, Colomer-Castell S, Martin MC, Castillo C, Esteban JI, Pumarola T, Rodriguez-Frias F, Antón A, Quer J. Host-dependent editing of SARS-CoV-2 in COVID-19 patients. Emerg Microbes Infect 2021; 10:1777-1789. [PMID: 34402744 PMCID: PMC8425778 DOI: 10.1080/22221751.2021.1969868] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A common trait among RNA viruses is their high capability to acquire genetic variability due to viral and host mechanisms. Next-generation sequencing (NGS) analysis enables the deep study of the viral quasispecies in samples from infected individuals. In this study, the viral quasispecies complexity and single nucleotide polymorphisms of the SARS-CoV-2 spike gene of coronavirus disease 2019 (COVID-19) patients with mild or severe disease were investigated using next-generation sequencing (Illumina platform). SARS-CoV-2 spike variability was higher in patients with long-lasting infection. Most substitutions found were present at frequencies lower than 1%, and had an A → G or T → C pattern, consistent with variants caused by adenosine deaminase acting on RNA-1 (ADAR1). ADAR1 affected a small fraction of replicating genomes, but produced multiple, mainly non-synonymous mutations. ADAR1 editing during replication rather than the RNA-dependent RNA polymerase (nsp12) was the predominant mechanism generating SARS-CoV-2 genetic variability. However, the mutations produced are not fixed in the infected human population, suggesting that ADAR1 may have an antiviral role, whereas nsp12-induced mutations occurring in patients with high viremia and persistent infection are the main source of new SARS-CoV-2 variants.
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Affiliation(s)
- Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics SL, Barcelona, Spain
| | - Maria Francesca Cortese
- Biochemistry and Microbiology Departments, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Maria Piñana
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Andrés
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Josep Francesc Abril
- Computational Genomics Lab, Genetics, Microbiology and Statistics Department, Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Maria Gema Codina
- Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Ariadna Rando
- Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Juliana Esperalba
- Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Elena Sulleiro
- Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Joan Joseph
- Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Narcís Saubí
- Biochemistry and Microbiology Departments, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Mari Carmen Martin
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carla Castillo
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Tomas Pumarola
- Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Microbiology Departments, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Spain
- Andrés Antón Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Pg Vall d’Hebron 119-129, Barcelona08035, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Josep Quer , Virus Translational Research Unit, Liver Diseases, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, Barcelona08035, Spain
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14
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Bellido AM, Souza Canadá ED, Permingeat HR, Echenique V. Genetic Transformation of Apomictic Grasses: Progress and Constraints. Front Plant Sci 2021; 12:768393. [PMID: 34804102 PMCID: PMC8602796 DOI: 10.3389/fpls.2021.768393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/05/2021] [Indexed: 05/17/2023]
Abstract
The available methods for plant transformation and expansion beyond its limits remain especially critical for crop improvement. For grass species, this is even more critical, mainly due to drawbacks in in vitro regeneration. Despite the existence of many protocols in grasses to achieve genetic transformation through Agrobacterium or biolistic gene delivery, their efficiencies are genotype-dependent and still very low due to the recalcitrance of these species to in vitro regeneration. Many plant transformation facilities for cereals and other important crops may be found around the world in universities and enterprises, but this is not the case for apomictic species, many of which are C4 grasses. Moreover, apomixis (asexual reproduction by seeds) represents an additional constraint for breeding. However, the transformation of an apomictic clone is an attractive strategy, as the transgene is immediately fixed in a highly adapted genetic background, capable of large-scale clonal propagation. With the exception of some species like Brachiaria brizantha which is planted in approximately 100 M ha in Brazil, apomixis is almost non-present in economically important crops. However, as it is sometimes present in their wild relatives, the main goal is to transfer this trait to crops to fix heterosis. Until now this has been a difficult task, mainly because many aspects of apomixis are unknown. Over the last few years, many candidate genes have been identified and attempts have been made to characterize them functionally in Arabidopsis and rice. However, functional analysis in true apomictic species lags far behind, mainly due to the complexity of its genomes, of the trait itself, and the lack of efficient genetic transformation protocols. In this study, we review the current status of the in vitro culture and genetic transformation methods focusing on apomictic grasses, and the prospects for the application of new tools assayed in other related species, with two aims: to pave the way for discovering the molecular pathways involved in apomixis and to develop new capacities for breeding purposes because many of these grasses are important forage or biofuel resources.
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Affiliation(s)
- Andrés M. Bellido
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS – CCT – CONICET Bahía Blanca), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | | | | | - Viviana Echenique
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS – CCT – CONICET Bahía Blanca), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
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15
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Meneghini V, Peviani M, Luciani M, Zambonini G, Gritti A. Delivery Platforms for CRISPR/Cas9 Genome Editing of Glial Cells in the Central Nervous System. Front Genome Ed 2021; 3:644319. [PMID: 34713256 PMCID: PMC8525379 DOI: 10.3389/fgeed.2021.644319] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 01/21/2021] [Indexed: 12/14/2022] Open
Abstract
Glial cells (astrocytes, oligodendrocytes, and microglia) are emerging as key players in several physiological and pathological processes of the central nervous system (CNS). Astrocytes and oligodendrocytes are not only supportive cells that release trophic factors or regulate energy metabolism, but they also actively modulate critical neuronal processes and functions in the tripartite synapse. Microglia are defined as CNS-resident cells that provide immune surveillance; however, they also actively contribute to shaping the neuronal microenvironment by scavenging cell debris or regulating synaptogenesis and pruning. Given the many interconnected processes coordinated by glial cells, it is not surprising that both acute and chronic CNS insults not only cause neuronal damage but also trigger complex multifaceted responses, including neuroinflammation, which can critically contribute to the disease progression and worsening of symptoms in several neurodegenerative diseases. Overall, this makes glial cells excellent candidates for targeted therapies to treat CNS disorders. In recent years, the application of gene editing technologies has redefined therapeutic strategies to treat genetic and age-related neurological diseases. In this review, we discuss the advantages and limitations of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based gene editing in the treatment of neurodegenerative disorders, focusing on the development of viral- and nanoparticle-based delivery methods for in vivo glial cell targeting.
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Affiliation(s)
- Vasco Meneghini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco Peviani
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Marco Luciani
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giada Zambonini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angela Gritti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
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16
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Feng W, Cao Z, Lim PX, Zhao H, Luo H, Mao N, Lee YS, Rivera AA, Choi D, Wu C, Han T, Romero R, de Stanchina E, Carver BS, Wang Q, Jasin M, Sawyers CL. Rapid interrogation of cancer cell of origin through CRISPR editing. Proc Natl Acad Sci U S A 2021; 118:e2110344118. [PMID: 34353917 PMCID: PMC8364185 DOI: 10.1073/pnas.2110344118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The increasing complexity of different cell types revealed by single-cell analysis of tissues presents challenges in efficiently elucidating their functions. Here we show, using prostate as a model tissue, that primary organoids and freshly isolated epithelial cells can be CRISPR edited ex vivo using Cas9-sgRNA (guide RNA) ribotnucleoprotein complex technology, then orthotopically transferred in vivo into immunocompetent or immunodeficient mice to generate cancer models with phenotypes resembling those seen in traditional genetically engineered mouse models. Large intrachromosomal (∼2 Mb) or multigenic deletions can be engineered efficiently without the need for selection, including in isolated subpopulations to address cell-of-origin questions.
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Affiliation(s)
- Weiran Feng
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Zhen Cao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10021
| | - Pei Xin Lim
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Huiyong Zhao
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Hanzhi Luo
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Ninghui Mao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Young Sun Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Aura Agudelo Rivera
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Danielle Choi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Chao Wu
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Teng Han
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Rodrigo Romero
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Brett S Carver
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Division of Urology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology of Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
- HHMI, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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17
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Dziri S, Rodriguez C, Gerber A, Brichler S, Alloui C, Roulot D, Dény P, Pawlotsky JM, Gordien E, Le Gal F. Variable In Vivo Hepatitis D Virus (HDV) RNA Editing Rates According to the HDV Genotype. Viruses 2021; 13:v13081572. [PMID: 34452437 PMCID: PMC8402866 DOI: 10.3390/v13081572] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/26/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022] Open
Abstract
Human hepatitis delta virus (HDV) is a small defective RNA satellite virus that requires hepatitis B virus (HBV) envelope proteins to form its own virions. The HDV genome possesses a single coding open reading frame (ORF), located on a replicative intermediate, the antigenome, encoding the small (s) and the large (L) isoforms of the delta antigen (s-HDAg and L-HDAg). The latter is produced following an editing process, changing the amber/stop codon on the s-HDAg-ORF into a tryptophan codon, allowing L-HDAg synthesis by the addition of 19 (or 20) C-terminal amino acids. The two delta proteins play different roles in the viral cell cycle: s-HDAg activates genome replication, while L-HDAg blocks replication and favors virion morphogenesis and propagation. L-HDAg has also been involved in HDV pathogenicity. Understanding the kinetics of viral editing rates in vivo is key to unravel the biology of the virus and understand its spread and natural history. We developed and validated a new assay based on next-generation sequencing and aimed at quantifying HDV RNA editing in plasma. We analyzed plasma samples from 219 patients infected with different HDV genotypes and showed that HDV editing capacity strongly depends on the genotype of the strain.
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Affiliation(s)
- Samira Dziri
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
| | - Christophe Rodriguez
- Centre National de référence des Hépatites Virales B, C et Delta, Département de Virologie, Hôpital Henri Mondor, Assistance Publique-Hôpitaux de Paris, Université Paris-Est, 94000 Créteil, France; (C.R.); (J.M.P.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Athenaïs Gerber
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
| | - Ségolène Brichler
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Chakib Alloui
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Dominique Roulot
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
- Unité d’hépatologie, Hôpital Avicenne, Assistance Publique-Hôpitaux de Paris, Université Sorbonne-Paris-Cité, 93000 Bobigny, France
| | - Paul Dény
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052-UMR CNRS 5286, 69001 Lyon, France
| | - Jean Michel Pawlotsky
- Centre National de référence des Hépatites Virales B, C et Delta, Département de Virologie, Hôpital Henri Mondor, Assistance Publique-Hôpitaux de Paris, Université Paris-Est, 94000 Créteil, France; (C.R.); (J.M.P.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Emmanuel Gordien
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Frédéric Le Gal
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
- Correspondence:
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18
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Paris Z, Svobodová M, Kachale A, Horáková E, Nenarokova A, Lukeš J. A mitochondrial cytidine deaminase is responsible for C to U editing of tRNA Trp to decode the UGA codon in Trypanosoma brucei. RNA Biol 2021; 18:278-286. [PMID: 34224320 PMCID: PMC8677022 DOI: 10.1080/15476286.2021.1940445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In kinetoplastid protists, all mitochondrial tRNAs are encoded in the nucleus and imported from the cytoplasm to maintain organellar translation. This also applies to the tryptophanyl tRNA (tRNATrp) encoded by a single-copy nuclear gene, with a CCA anticodon to read UGG codon used in the cytosolic translation. Yet, in the mitochondrion it is unable to decode the UGA codon specifying tryptophan. Following mitochondrial import of tRNATrp, this problem is solved at the RNA level by a single C34 to U34 editing event that creates the UCA anticodon, recognizing UGA. To identify the enzyme responsible for this critical editing activity, we scrutinized the genome of Trypanosoma brucei for putative cytidine deaminases as the most likely candidates. Using RNAi silencing and poisoned primer extension, we have identified a novel deaminase enzyme, named here TbmCDAT for mitochondrial Cytidine Deaminase Acting on tRNA, which is responsible for this organelle-specific activity in T. brucei. The ablation of TbmCDAT led to the downregulation of mitochondrial protein synthesis, supporting its role in decoding the UGA tryptophan codon.
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Affiliation(s)
- Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Budweis, Czech Republic
| | - Michaela Svobodová
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic
| | - Ambar Kachale
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Budweis, Czech Republic
| | - Eva Horáková
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic
| | - Anna Nenarokova
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Budweis, Czech Republic
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19
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Deelchand DK, Marjańska M, Henry PG, Terpstra M. MEGA-PRESS of GABA+: Influences of acquisition parameters. NMR Biomed 2021; 34:e4199. [PMID: 31658398 PMCID: PMC7186154 DOI: 10.1002/nbm.4199] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/11/2019] [Accepted: 09/15/2019] [Indexed: 05/13/2023]
Abstract
γ-aminobutyric acid (GABA) was the first molecule that was edited with MEGA-PRESS. GABA edited spectroscopy is challenged by limited selectivity of editing pulses. Coediting of resonances from macromolecules (MM) is the greatest single limitation of GABA edited spectroscopy. In this contribution, relative signal contributions from GABA, MM and homocarnosine to the total MEGA-PRESS edited signal at ~3 ppm, i.e., GABA+, are simulated at 3 tesla using several acquisition schemes. The base scheme is modeled after those currently supplied by vendors: it uses typical pulse shapes and lengths, it minimizes the first echo time (TE), and the delay between the editing pulses is kept at TE/2. Edited spectra are simulated for imperfect acquisition parameters such as incorrect frequency, larger chemical shift displacement, incorrect transmit B1 -field calibration for localization and editing pulses, and longer TE. An alternative timing scheme and longer editing pulses are also considered. Additional simulations are performed for symmetric editing around the MM frequency to suppress the MM signal. The relative influences of these acquisition parameters on the constituents of GABA+ are examined from the perspective of modern experimental designs for investigating brain GABA concentration differences in healthy and diseased humans. Other factors that influence signal contributions, such as T1 and T2 relaxation times are also considered.
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Affiliation(s)
- Dinesh K Deelchand
- Center for Magnetic Resonance Research and Department of Radiology, University of, Minnesota, Minneapolis, MN, USA
| | - Małgorzata Marjańska
- Center for Magnetic Resonance Research and Department of Radiology, University of, Minnesota, Minneapolis, MN, USA
| | - Pierre-Gilles Henry
- Center for Magnetic Resonance Research and Department of Radiology, University of, Minnesota, Minneapolis, MN, USA
| | - Melissa Terpstra
- Center for Magnetic Resonance Research and Department of Radiology, University of, Minnesota, Minneapolis, MN, USA
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Breton C, Furmanak T, Avitto AN, Smith MK, Latshaw C, Yan H, Greig JA, Wilson JM. Increasing the Specificity of AAV-Based Gene Editing through Self-Targeting and Short-Promoter Strategies. Mol Ther 2021; 29:1047-1056. [PMID: 33359790 DOI: 10.1016/j.ymthe.2020.12.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 12/28/2022] Open
Abstract
Our group previously used adeno-associated viral vectors (AAVs) to express an engineered meganuclease specific for a sequence in the PCSK9 gene (M2PCSK9), a clinical target for treating coronary heart disease. Upon testing this nuclease in non-human primates, we observed specific editing characterized by several insertions and deletions (indels) in the target sequence as well as indels in similar genomic sequences. We hypothesized that high nuclease expression increases off-target editing. Here, we reduced nuclease expression using two strategies. The first was a self-targeting strategy that involved inserting the M2PCSK9 target sequence into the AAV genome that expresses the nuclease and/or fusing the nuclease to a specific peptide to promote its degradation. The second strategy used a shortened version of the parental promoter to reduce nuclease expression. Mice administered with these second-generation AAV vectors showed reduced PCSK9 expression due to the nuclease on-target activity and reduced off-target activity. All vectors induced a stable reduction of PCSK9 in primates treated with self-targeting and short-promoter AAVs. Compared to the meganuclease-expressing parental AAV vector, we observed a significant reduction in off-target activity. In conclusion, we increased the in vivo nuclease specificity using a clinically relevant strategy that can be applied to other genome-editing nucleases.
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Affiliation(s)
- Camilo Breton
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas Furmanak
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexa N Avitto
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melanie K Smith
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Caitlin Latshaw
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hanying Yan
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jenny A Greig
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James M Wilson
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Lange CA, Hammes SR. Publish or Perish: Five Steps to Navigating a Less Painful Peer Review. Endocrinology 2021; 162:6124510. [PMID: 33516156 DOI: 10.1210/endocr/bqaa225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Indexed: 11/19/2022]
Abstract
UNLABELLED This Perspective presents comments intended for junior researchers by Carol A. Lange, Editor-in-Chief, Endocrinology, and Stephen R. Hammes, former Editor-in-Chief, Molecular Endocrinology, and former co-Editor-in-Chief, Endocrinology. PRINCIPAL POINTS 1. Know when you are ready and identify your target audience.2. Select an appropriate journal.3. Craft your title and abstract to capture your key words and deliver your message.4. Tell a clear and impactful story.5. Review, polish, and perfect your manuscript.
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Affiliation(s)
- Carol A Lange
- Departments of Medicine and Pharmacology, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
| | - Stephen R Hammes
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
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Gutmann B, Millman M, Vincis Pereira Sanglard L, Small I, Colas des Francs-Small C. The Pentatricopeptide Repeat Protein MEF100 Is Required for the Editing of Four Mitochondrial Editing Sites in Arabidopsis. Cells 2021; 10:468. [PMID: 33671598 PMCID: PMC7926422 DOI: 10.3390/cells10020468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/30/2021] [Accepted: 02/17/2021] [Indexed: 11/20/2022] Open
Abstract
In Arabidopsis thaliana there are more than 600 C-to-U RNA editing events in the mitochondria and at least 44 in the chloroplasts. Pentatricopeptide repeat (PPR) proteins provide the specificity for these reactions. They recognize RNA sequences in a partially predictable fashion via key amino acids at the fifth and last position in each PPR motif that bind to individual ribonucleotides. A combined approach of RNA-Seq, mutant complementation, electrophoresis of mitochondrial protein complexes and Western blotting allowed us to show that MEF100, a PPR protein identified in a genetic screen for mutants resistant to an inhibitor of γ -glutamylcysteine synthetase, is required for the editing of nad1-493, nad4-403, nad7-698 and ccmFN2-356 sites in Arabidopsis mitochondria. The absence of editing in mef100 leads to a decrease in mitochondrial Complex I activity, which probably explains the physiological phenotype. Some plants have lost the requirement for MEF100 at one or more of these sites through mutations in the mitochondrial genome. We show that loss of the requirement for MEF100 editing leads to divergence in the MEF100 binding site.
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Affiliation(s)
| | | | | | | | - Catherine Colas des Francs-Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia; (B.G.); (M.M.); (L.V.P.S.); (I.S.)
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Lee MS, Hsieh KY, Kuo CI, Lee SH, Garde S, Reddy M, Chang CI. Structural Basis for the Peptidoglycan- Editing Activity of YfiH. mBio 2021; 13:e0364621. [PMID: 35164571 DOI: 10.1128/mbio.03646-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Bacterial cells are encased in peptidoglycan (PG), a polymer of disaccharide N-acetylglucosamine (GlcNAc) and N-acetyl-muramic acid (MurNAc) cross-linked by peptide stems. PG is synthesized in the cytoplasm as UDP-MurNAc-peptide precursors, of which the amino acid composition of the peptide is unique, with l-Ala added at the first position in most bacteria but with l-Ser or Gly in some bacteria. YfiH is a PG-editing factor whose absence causes misincorporation of l-Ser instead of l-Ala into peptide stems, but its mechanistic function is unknown. Here, we report the crystal structures of substrate-bound and product-bound YfiH, showing that YfiH is a cytoplasmic amidase that controls the incorporation of the correct amino acid to the nucleotide precursors by preferentially cleaving the nucleotide precursor by-product UDP-MurNAc-l-Ser. This work reveals an editing mechanism in the cytoplasmic steps of peptidoglycan biosynthesis. IMPORTANCE YfiH is a peptidoglycan (PG)-editing factor required for the maintenance of specific amino acid compositions of the stem peptides. However, the activity of YfiH has not been deciphered, and the editing mechanism involving YfiH has remained a mystery. Through X-ray crystallographic and biochemical analyses, we demonstrate that YfiH is a hydrolase with a previously unknown activity specific for the UDP-MurNAc-monopeptide, one of the nucleotide precursors from the cytoplasmic steps of the PG biosynthesis pathway. YfiH selectively hydrolyzes UDP-MurNAc-Ser, an incorrect by-product of the biosynthesis reaction, to ensure that only the correct PG precursor, UDP-MurNAc-Ala, is incorporated. Therefore, this work reveals coupled synthetic and editing reactions in the cytoplasmic steps of PG biosynthesis.
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Tusup M, Cheng PF, Picardi E, Raziunaite A, Dummer R, Levesque MP, French LE, Guenova E, Kundig TM, Pascolo S. Evaluation of the Interplay between the ADAR Editome and Immunotherapy in Melanoma. Noncoding RNA 2021; 7:ncrna7010005. [PMID: 33445472 PMCID: PMC7838980 DOI: 10.3390/ncrna7010005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 01/09/2023] Open
Abstract
Background: RNA editing is a highly conserved posttranscriptional mechanism that contributes to transcriptome diversity. In mammals, it includes nucleobase deaminations that convert cytidine (C) into uridine (U) and adenosine (A) into inosine (I). Evidence from cancer studies indicates that RNA-editing enzymes promote certain mechanisms of tumorigenesis. On the other hand, recoding editing in mRNA can generate mutations in proteins that can participate in the Major Histocompatibility Complex (MHC) ligandome and can therefore be recognized by the adaptive immune system. Anti-cancer treatment based on the administration of immune checkpoint inhibitors enhance these natural anti-cancer immune responses. Results: Based on RNA-Seq datasets, we evaluated the editome of melanoma cell lines generated from patients pre- and post-immunotherapy with immune checkpoint inhibitors. Our results reveal a differential editing in Arthrobacter luteus (Alu) sequences between samples pre-therapy and relapses during therapy with immune checkpoint inhibitors. Conclusion: These data pave the way towards the development of new diagnostics and therapies targeted to editing that could help in preventing relapses during immunotherapies.
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Affiliation(s)
- Marina Tusup
- Department of Dermatology, University Hospital of Zürich, Gloriastrasse 31, 8091 Zürich, Switzerland; (M.T.); (P.F.C.); (A.R.); (R.D.); (M.P.L.); (L.E.F.); (E.G.); (T.M.K.)
- Faculty of Medicine, University of Zürich, 8091 Zürich, Switzerland
| | - Phil F. Cheng
- Department of Dermatology, University Hospital of Zürich, Gloriastrasse 31, 8091 Zürich, Switzerland; (M.T.); (P.F.C.); (A.R.); (R.D.); (M.P.L.); (L.E.F.); (E.G.); (T.M.K.)
- Faculty of Medicine, University of Zürich, 8091 Zürich, Switzerland
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, 70121 Bari, Italy;
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, 70126 Bari, Italy
| | - Austeja Raziunaite
- Department of Dermatology, University Hospital of Zürich, Gloriastrasse 31, 8091 Zürich, Switzerland; (M.T.); (P.F.C.); (A.R.); (R.D.); (M.P.L.); (L.E.F.); (E.G.); (T.M.K.)
- Faculty of Medicine, University of Zürich, 8091 Zürich, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University Hospital of Zürich, Gloriastrasse 31, 8091 Zürich, Switzerland; (M.T.); (P.F.C.); (A.R.); (R.D.); (M.P.L.); (L.E.F.); (E.G.); (T.M.K.)
- Faculty of Medicine, University of Zürich, 8091 Zürich, Switzerland
| | - Mitchell P. Levesque
- Department of Dermatology, University Hospital of Zürich, Gloriastrasse 31, 8091 Zürich, Switzerland; (M.T.); (P.F.C.); (A.R.); (R.D.); (M.P.L.); (L.E.F.); (E.G.); (T.M.K.)
- Faculty of Medicine, University of Zürich, 8091 Zürich, Switzerland
| | - Lars E. French
- Department of Dermatology, University Hospital of Zürich, Gloriastrasse 31, 8091 Zürich, Switzerland; (M.T.); (P.F.C.); (A.R.); (R.D.); (M.P.L.); (L.E.F.); (E.G.); (T.M.K.)
- Faculty of Medicine, University of Zürich, 8091 Zürich, Switzerland
- Department of Dermatology and Allergy, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Emmanuella Guenova
- Department of Dermatology, University Hospital of Zürich, Gloriastrasse 31, 8091 Zürich, Switzerland; (M.T.); (P.F.C.); (A.R.); (R.D.); (M.P.L.); (L.E.F.); (E.G.); (T.M.K.)
- Faculty of Medicine, University of Zürich, 8091 Zürich, Switzerland
- Department of Dermatology, Lausanne University Hospital and Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Thomas M. Kundig
- Department of Dermatology, University Hospital of Zürich, Gloriastrasse 31, 8091 Zürich, Switzerland; (M.T.); (P.F.C.); (A.R.); (R.D.); (M.P.L.); (L.E.F.); (E.G.); (T.M.K.)
- Faculty of Medicine, University of Zürich, 8091 Zürich, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital of Zürich, Gloriastrasse 31, 8091 Zürich, Switzerland; (M.T.); (P.F.C.); (A.R.); (R.D.); (M.P.L.); (L.E.F.); (E.G.); (T.M.K.)
- Faculty of Medicine, University of Zürich, 8091 Zürich, Switzerland
- Correspondence:
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Johansson‐Malmeling C, Wengelin Å, Henriksson I. Aphasia and spelling to dictation: Analysis of spelling errors and editing. Int J Lang Commun Disord 2021; 56:145-160. [PMID: 33368870 PMCID: PMC7898650 DOI: 10.1111/1460-6984.12591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
INTRODUCTION Spelling difficulty is a common symptom of aphasia and can entail editing difficulties. Previous research has shown that extensive editing is related to a lower production rate in text writing for persons with aphasia, yet editing difficulty is not commonly examined. It is not known if editing difficulty is related to reading and writing skills or to aspects of the word. AIMS To analyse spelling and editing processes as well as errors in a dictation task performed by Swedish-speaking adults with post-stroke aphasia. Furthermore, the study aimed to identify any relationships between spelling and editing difficulties and characteristics of individual words. Finally, relationships between successful edits and reading and phonological ability were investigated and specific editing strategies or behaviours identified. Correlation analyses were performed between measures of spelling and editing and word frequency and length as well as participants' scores on tests of reading, phonological spelling and phonological decoding. METHODS & PROCEDURES A total of 16 Swedish speaking participants with post-stroke aphasia wrote a word-dictation task in a keystroke logging program and were tested for phonological spelling, phonological decoding and reading ability. Spelling errors were categorized and analysed. OUTCOMES & RESULTS The most common error type was omission of letter(s) and there was evidence of aphasia-specific writing errors. Both spelling and editing difficulty were related to word frequency and word length. Successful editing was related to participants' scores on the phonological spelling task, but not to phonological decoding or reading ability. Specific editing strategies could be identified, and some strategies were individual, while others were more commonly used. CONCLUSIONS & IMPLICATIONS Word length and word frequency should be taken into consideration in spelling tests for persons with aphasia, and the presence of editing difficulty should be taken into account when assessing spelling difficulties. Treatment for writing difficulties in aphasia should include training in successful editing strategies and individual fitting of digital writing aids. What this paper adds What is already known on the subject Post-stroke aphasia often causes writing and spelling difficulties. Spelling difficulties may entail editing difficulties, in turn causing extensive and/or unsuccessful editing. Extensive editing is known to impede productivity in text writing. Still, editing behaviour, abilities relating to editing or what features of a word that causes editing difficulty has not been investigated for persons with aphasia. What this paper adds to existing knowledge This study adds an in-depth analysis of spelling ability, spelling errors and editing behaviour for persons with aphasia, using keystroke logging and a single-word dictation task. Results showed that both features of the target word (frequency and word length) and the individual abilities of the person with aphasia (score on a phonological spelling task) related to spelling and editing difficulty, editing behaviour and successful editing. Specific editing strategies were analysed and described. What are the potential or actual clinical implications of this work? Word length and word frequency should be taken into consideration when testing single-word spelling for persons with aphasia. When assessing spelling difficulties, both correctness of spelling as well as the presence and nature of any editing difficulties should be taken into account and treatment for writing difficulties in should include training in successful editing strategies. The fitting of digital writing aids for persons with aphasia should be individual, since many of the editing strategies used were individual.
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Affiliation(s)
- Charlotte Johansson‐Malmeling
- Institute of Neuroscience and Physiology, Speech and Language Pathology Unit, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Åsa Wengelin
- Department of SwedishUniversity of GothenburgGothenburgSweden
| | - Ingrid Henriksson
- Institute of Neuroscience and Physiology, Speech and Language Pathology Unit, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
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Ma J, Li K, Gu S. Efficient Editing of Silver Nanoclusters by Changing Simply One Cytosine in a DNA Template. Chembiochem 2020; 22:1210-1214. [PMID: 33174392 DOI: 10.1002/cbic.202000640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/09/2020] [Indexed: 11/07/2022]
Abstract
DNA with genetic information was edited to regulate and repair the structure and function of a protein. In DNA nanotechnology, DNA with programmable information can be designed to edit the fluorescence intensity and emissive colors of DNA-stabilized silver nanoclusters (DNA/AgNCs). By introducing and moving one cytosine in the spacer of the emitter domain, we have built up a simple strategy to regulate the excitation and emission wavelengths of AgNCs. When replacing thymine in the spacer of the emitter with one cytosine, the expected excitation and emission change do not occur. However, after moving the introduced cytosine, DNA templates produce AgNCs with extremely different excitation and emission wavelengths from those of the initial template, leading to a template for near-infrared (NIR) emissive species with the highest fluorescence intensity. The formation of AgNCs induces the DNA template into condensed secondary structure based on an altered migration rate in PAGE. The simple strategy of moving one cytosine in a spacer in the emitter domain can enrich the library of templates for synthesizing diverse DNA/AgNCs and has great potential in bioimaging and probe design.
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Affiliation(s)
- Jinliang Ma
- College of Food and Bioengineering, Henan University of Science and Technology, 471023, Luoyang, Henan, P. R. China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, P. R. China
| | - Kexin Li
- College of Food and Bioengineering, Henan University of Science and Technology, 471023, Luoyang, Henan, P. R. China
| | - Shaobin Gu
- College of Food and Bioengineering, Henan University of Science and Technology, 471023, Luoyang, Henan, P. R. China
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Serra ME. Scientific paper management. How do articles get published in medical journals? ARCH ARGENT PEDIATR 2020; 118:433-437. [PMID: 33231053 DOI: 10.5546/aap.2020.eng.433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 11/12/2022]
Abstract
The life-cycle of a manuscript from writing to publication is not usually taught during health care professionals' training. This article reviews the process that goes from from the authors' decision to communicate to its eventual publication, detailing practical aspects to be considered in each step. The responsibilities of the different roles involved are specified: author, editor, and reviewer. International guidelines supporting the writing of medical-scientific papers are also described.
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Affiliation(s)
- María E Serra
- Archivos Argentinos de Pediatría.,Fundación para la Salud Materno Infantil (FUNDASAMIN), Ciudad Autónoma de Buenos Aires, Argentina.
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Vargas-Rodriguez O, Bakhtina M, McGowan D, Abid J, Goto Y, Suga H, Musier-Forsyth K. Human trans- editing enzyme displays tRNA acceptor-stem specificity and relaxed amino acid selectivity. J Biol Chem 2020; 295:16180-16190. [PMID: 33051185 PMCID: PMC7705315 DOI: 10.1074/jbc.ra120.015981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/06/2020] [Indexed: 01/20/2023] Open
Abstract
Accurate translation of genetic information into proteins is vital for cell sustainability. ProXp-ala prevents proteome-wide Pro-to-Ala mutations by hydrolyzing misacylated Ala-tRNAPro, which is synthesized by prolyl-tRNA synthetase. Bacterial ProXp-ala was previously shown to combine a size-based exclusion mechanism with conformational and chemical selection for the recognition of the alanyl moiety, whereas tRNAPro is selected via recognition of tRNA acceptor-stem elements G72 and A73. The identity of these critical bases changed during evolution with eukaryotic cytosolic tRNAPro possessing a cytosine at the corresponding positions. The mechanism by which eukaryotic ProXp-ala adapted to these changes remains unknown. In this work, recognition of the aminoacyl moiety and tRNA acceptor stem by human (Homo sapiens, or Hs) ProXp-ala was examined. Enzymatic assays revealed that Hs ProXp-ala requires C72 and C73 in the context of Hs cytosolic tRNAPro for efficient deacylation of mischarged Ala-tRNAPro The strong dependence on these bases prevents cross-species deacylation of bacterial Ala-tRNAPro or of Hs mitochondrial Ala-tRNAPro by the human enzyme. Similar to the bacterial enzyme, Hs ProXp-ala showed strong tRNA acceptor-stem recognition but differed in its amino acid specificity profile relative to bacterial ProXp-ala. Changes at conserved residues in both the Hs and bacterial ProXp-ala substrate-binding pockets modulated this specificity. These results illustrate how the mechanism of substrate selection diverged during the evolution of the ProXp-ala family, providing the first example of a trans-editing domain whose specificity evolved to adapt to changes in its tRNA substrate.
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Affiliation(s)
- Oscar Vargas-Rodriguez
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Daniel McGowan
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Jawad Abid
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.
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Howitz N, Su T, Lazazzera BA. Meta-Tyrosine Induces Cytotoxic Misregulation of Metabolism in Escherichia coli. J Mol Biol 2020; 432:166716. [PMID: 33220263 DOI: 10.1016/j.jmb.2020.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/16/2022]
Abstract
The non-protein amino acid meta-Tyrosine (m-Tyr) is produced in cells under conditions of oxidative stress, and m-Tyr has been shown to be toxic to a broad range of biological systems. However, the mechanism by which m-Tyr damages cells is unclear. In E. coli, the quality control (QC) function of phenyalanyl-tRNA synthetase (PheRS) is required for resistantce to m-Tyr. To determine the mechanism of m-Tyr toxicity, we utilitized a strain of E. coli that expresses a QC-defective PheRS. The global responses of E. coli cells to m-Tyr were assessed by RNA-seq, and >500 genes were differentially expressed after the addition of m-Tyr. The most strongly up-regulated genes are involved in unfolded-protein stress response, and cells exposed to m-Tyr contained large, electron-dense protein aggregates, indicating that m-Tyr destabilized a large fraction of the proteome. Additionally, we observed that amino acid biosynthesis and transport regulons, controlled by ArgR, TrpR, and TyrR, and the stringent-response regulon, controlled by DksA/ppGpp, were differentially expressed. m-Tyr resistant mutants were isolated and found to have altered a promoter to increase expression of the enzymes for Phe production or to have altered transporters, which likely result in less uptake or increased efflux of m-Tyr. These findings indicate that when m-Tyr has passed the QC checkpoint by the PheRS, this toxicity of m-Tyr may result from interfering with amino acid metabolism, destabalizing a large number of proteins, and the formation of protein aggregates.
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Affiliation(s)
- Nathaniel Howitz
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Trent Su
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biology, University of California, Los Angeles, CA 90095, USA
| | - Beth A Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
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Unceta I, Nin J, Pujol O. Environmental Adaptation and Differential Replication in Machine Learning. Entropy (Basel) 2020; 22:e22101122. [PMID: 33286891 PMCID: PMC7597251 DOI: 10.3390/e22101122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/17/2020] [Accepted: 09/29/2020] [Indexed: 11/16/2022]
Abstract
When deployed in the wild, machine learning models are usually confronted with an environment that imposes severe constraints. As this environment evolves, so do these constraints. As a result, the feasible set of solutions for the considered need is prone to change in time. We refer to this problem as that of environmental adaptation. In this paper, we formalize environmental adaptation and discuss how it differs from other problems in the literature. We propose solutions based on differential replication, a technique where the knowledge acquired by the deployed models is reused in specific ways to train more suitable future generations. We discuss different mechanisms to implement differential replications in practice, depending on the considered level of knowledge. Finally, we present seven examples where the problem of environmental adaptation can be solved through differential replication in real-life applications.
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Affiliation(s)
- Irene Unceta
- BBVA Data & Analytics, 28050 Madrid, Spain;
- Department of Mathematics and Computer Science, Universitat de Barcelona, 08007 Barcelona, Spain;
| | - Jordi Nin
- Department of Operations, Innovation and Data Sciences, Universitat Ramon Llull, ESADE, 08172 Sant Cugat del Vallès, Spain
- Correspondence: ; Tel.: +34-932-806162 (ext. 2513)
| | - Oriol Pujol
- Department of Mathematics and Computer Science, Universitat de Barcelona, 08007 Barcelona, Spain;
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31
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Romano G, Saviana M, Le P, Li H, Micalo L, Nigita G, Acunzo M, Nana-Sinkam P. Non-Coding RNA Editing in Cancer Pathogenesis. Cancers (Basel) 2020; 12:E1845. [PMID: 32650588 DOI: 10.3390/cancers12071845] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
In the last two decades, RNA post-transcriptional modifications, including RNA editing, have been the subject of increasing interest among the scientific community. The efforts of the Human Genome Project combined with the development of new sequencing technologies and dedicated bioinformatic approaches created to detect and profile RNA transcripts have served to further our understanding of RNA editing. Investigators have determined that non-coding RNA (ncRNA) A-to-I editing is often deregulated in cancer. This discovery has led to an increased number of published studies in the field. However, the eventual clinical application for these findings remains a work in progress. In this review, we provide an overview of the ncRNA editing phenomenon in cancer. We discuss the bioinformatic strategies for RNA editing detection as well as the potential roles for ncRNA A to I editing in tumor immunity and as clinical biomarkers.
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32
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Best C, Mizrahi R, Ostersetzer-Biran O. Why so Complex? The Intricacy of Genome Structure and Gene Expression, Associated with Angiosperm Mitochondria, May Relate to the Regulation of Embryo Quiescence or Dormancy-Intrinsic Blocks to Early Plant Life. Plants (Basel) 2020; 9:E598. [PMID: 32397140 PMCID: PMC7284508 DOI: 10.3390/plants9050598] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/14/2022]
Abstract
Mitochondria play key roles in cellular-energy metabolism and are vital for plant-life, such as for successful germination and early-seedling establishment. Most mitochondria contain their own genetic system (mtDNA, mitogenome), with an intrinsic protein-synthesis machinery. Although the challenges of maintaining prokaryotic-type structures and functions are common to Eukarya, land plants possess some of the most complex organelle composition of all known organisms. Angiosperms mtDNAs are characteristically the largest and least gene-dense among the eukaryotes. They often contain highly-variable intergenic regions of endogenous or foreign origins and undergo frequent recombination events, which result in different mtDNA configurations, even between closely-related species. The expression of the mitogenome in angiosperms involves extensive mtRNA processing steps, including numerous editing and splicing events. Why do land-plant's mitochondria have to be so complex? The answer to this remains a matter of speculation. We propose that this complexity may have arisen throughout the terrestrialization of plants, as a means to control embryonic mitochondrial functions -a critical adaptive trait to optimize seed germination. The unique characteristics of plant mtDNA may play pivotal roles in the nuclear-regulation of organellar biogenesis and metabolism, possibly to control embryos quiescence or dormancy, essential determinants for the establishment of viable plantlets that can survive post-germination.
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Affiliation(s)
| | | | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus—Givat Ram, Jerusalem 9190401, Israel; (C.B.); (R.M.)
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33
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Gassner FJ, Zaborsky N, Feldbacher D, Greil R, Geisberger R. RNA Editing Alters miRNA Function in Chronic Lymphocytic Leukemia. Cancers (Basel) 2020; 12:cancers12051159. [PMID: 32380696 PMCID: PMC7280959 DOI: 10.3390/cancers12051159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 12/26/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a high incidence B cell leukemia with a highly variable clinical course, leading to survival times ranging from months to several decades. MicroRNAs (miRNAs) are small non-coding RNAs that regulate the expression levels of genes by binding to the untranslated regions of transcripts. Although miRNAs have been previously shown to play a crucial role in CLL development, progression and treatment resistance, their further processing and diversification by RNA editing (specifically adenosine to inosine or cytosine to uracil deamination) has not been addressed so far. In this study, we analyzed next generation sequencing data to provide a detailed map of adenosine to inosine and cytosine to uracil changes in miRNAs from CLL and normal B cells. Our results reveal that in addition to a CLL-specific expression pattern, there is also specific RNA editing of many miRNAs, particularly miR-3157 and miR-6503, in CLL. Our data draw further light on how miRNAs and miRNA editing might be implicated in the pathogenesis of the disease.
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Affiliation(s)
- Franz J. Gassner
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Cancer Cluster Salzburg, Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (F.J.G.); (N.Z.); (D.F.); (R.G.)
| | - Nadja Zaborsky
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Cancer Cluster Salzburg, Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (F.J.G.); (N.Z.); (D.F.); (R.G.)
| | - Daniel Feldbacher
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Cancer Cluster Salzburg, Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (F.J.G.); (N.Z.); (D.F.); (R.G.)
- Department of Biosciences, University of Salzburg, Hellbrunner Strasse, 34, 5020 Salzburg, Austria
| | - Richard Greil
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Cancer Cluster Salzburg, Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (F.J.G.); (N.Z.); (D.F.); (R.G.)
| | - Roland Geisberger
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Cancer Cluster Salzburg, Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (F.J.G.); (N.Z.); (D.F.); (R.G.)
- Correspondence: ; Tel.: +43-57255-25847; Fax: +43-57255-25998
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34
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El Azzouzi H, Vilaça AP, Feyen DAM, Gommans WM, de Weger RA, Doevendans PAF, Sluijter JPG. Cardiomyocyte Specific Deletion of ADAR1 Causes Severe Cardiac Dysfunction and Increased Lethality. Front Cardiovasc Med 2020; 7:30. [PMID: 32258062 PMCID: PMC7093378 DOI: 10.3389/fcvm.2020.00030] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/21/2020] [Indexed: 12/18/2022] Open
Abstract
Background: Adenosine deaminase acting on RNA 1 (ADAR1) is a double-stranded RNA-editing enzyme that is involved in several functions including the deamination of adenosine to inosine, RNA interference (RNAi) mechanisms and microRNA (miRNA) processing, rendering ADAR1 essential for life. Methods and Results: To investigate whether maintenance of ADAR1 expression is required for normal myocardial homeostasis, we bypassed the early embryonic lethality of ADAR1-null mice through the use of a tamoxifen-inducible Cre recombinase under the control of the cardiac-specific α-myosin heavy chain promoter (αMHC). Targeted ADAR1 deletion in adult mice caused a significant increase in lethality accompanied by severe ventricular remodeling and quick and spontaneous cardiac dysfunction, induction of stress markers and overall reduced expression of miRNAs. Administration of a selective inhibitor of the unfolded protein response (UPR) stress significantly blunted the deleterious effects and improved cardiac function thereby prolonging animal survival. In vitro restoring miR-199a-5p levels in cardiomyocytes lacking ADAR1 diminished UPR activation and concomitant apoptosis. Conclusions: Our findings demonstrate an essential role for ADAR1 in cardiomyocyte survival and maintenance of cardiac function through a mechanism that integrates ADAR1 dependent miRNA processing and the suppression of UPR stress.
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Affiliation(s)
- Hamid El Azzouzi
- Laboratory of Experimental Cardiology, Circulatory Health Laboratory, Department of Cardiology, Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Andreia P Vilaça
- Laboratory of Experimental Cardiology, Circulatory Health Laboratory, Department of Cardiology, Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, Netherlands
| | - Dries A M Feyen
- Laboratory of Experimental Cardiology, Circulatory Health Laboratory, Department of Cardiology, Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, Netherlands
| | - Willemijn M Gommans
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, United States
| | - Roel A de Weger
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Pieter A F Doevendans
- Laboratory of Experimental Cardiology, Circulatory Health Laboratory, Department of Cardiology, Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, Netherlands.,Interuniversity Cardiology Institute Netherlands, Royal Netherlands Academy of Sciences, Utrecht, Netherlands.,Utrecht University, Utrecht, Netherlands
| | - Joost P G Sluijter
- Laboratory of Experimental Cardiology, Circulatory Health Laboratory, Department of Cardiology, Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, Netherlands.,Interuniversity Cardiology Institute Netherlands, Royal Netherlands Academy of Sciences, Utrecht, Netherlands.,Utrecht University, Utrecht, Netherlands
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35
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Weitzel CS, Li L, Zhang C, Eilts KK, Bretz NM, Gatten AL, Whitaker RJ, Martinis SA. Duplication of leucyl-tRNA synthetase in an archaeal extremophile may play a role in adaptation to variable environmental conditions. J Biol Chem 2020; 295:4563-4576. [PMID: 32102848 DOI: 10.1074/jbc.ra118.006481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/25/2020] [Indexed: 12/23/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are ancient enzymes that play a fundamental role in protein synthesis. They catalyze the esterification of specific amino acids to the 3'-end of their cognate tRNAs and therefore play a pivotal role in protein synthesis. Although previous studies suggest that aaRS-dependent errors in protein synthesis can be beneficial to some microbial species, evidence that reduced aaRS fidelity can be adaptive is limited. Using bioinformatics analyses, we identified two distinct leucyl-tRNA synthetase (LeuRS) genes within all genomes of the archaeal family Sulfolobaceae. Remarkably, one copy, designated LeuRS-I, had key amino acid substitutions within its editing domain that would be expected to disrupt hydrolytic editing of mischarged tRNALeu and to result in variation within the proteome of these extremophiles. We found that another copy, LeuRS-F, contains canonical active sites for aminoacylation and editing. Biochemical and genetic analyses of the paralogs within Sulfolobus islandicus supported the hypothesis that LeuRS-F, but not LeuRS-I, functions as an essential tRNA synthetase that accurately charges leucine to tRNALeu for protein translation. Although LeuRS-I was not essential, its expression clearly supported optimal S. islandicus growth. We conclude that LeuRS-I may have evolved to confer a selective advantage under the extreme and fluctuating environmental conditions characteristic of the volcanic hot springs in which these archaeal extremophiles reside.
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Affiliation(s)
| | - Li Li
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801
| | - Changyi Zhang
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Kristen K Eilts
- Department of Chemistry, Illinois State University, Normal, Illinois 61761
| | - Nicholas M Bretz
- Department of Chemistry, Illinois State University, Normal, Illinois 61761
| | - Alex L Gatten
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Susan A Martinis
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801
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36
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Tawfik DS, Gruic-Sovulj I. How evolution shapes enzyme selectivity - lessons from aminoacyl-tRNA synthetases and other amino acid utilizing enzymes. FEBS J 2020; 287:1284-1305. [PMID: 31891445 DOI: 10.1111/febs.15199] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 12/08/2019] [Accepted: 12/30/2019] [Indexed: 12/21/2022]
Abstract
Aminoacyl-tRNA synthetases (AARSs) charge tRNA with their cognate amino acids. Many other enzymes use amino acids as substrates, yet discrimination against noncognate amino acids that threaten the accuracy of protein translation is a hallmark of AARSs. Comparing AARSs to these other enzymes allowed us to recognize patterns in molecular recognition and strategies used by evolution for exercising selectivity. Overall, AARSs are 2-3 orders of magnitude more selective than most other amino acid utilizing enzymes. AARSs also reveal the physicochemical limits of molecular discrimination. For example, amino acids smaller by a single methyl moiety present a discrimination ceiling of ~200, while larger ones can be discriminated by up to 105 -fold. In contrast, substrates larger by a hydroxyl group challenge AARS selectivity, due to promiscuous H-bonding with polar active site groups. This 'hydroxyl paradox' is resolved by editing. Indeed, when the physicochemical discrimination limits are reached, post-transfer editing - hydrolysis of tRNAs charged with noncognate amino acids, evolved. The editing site often selectively recognizes the edited noncognate substrate using the very same feature that the synthetic site could not efficiently discriminate against. Finally, the comparison to other enzymes also reveals that the selectivity of AARSs is an explicitly evolved trait, showing some clear examples of how selection acted not only to optimize catalytic efficiency with the target substrate, but also to abolish activity with noncognate threat substrates ('negative selection').
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Affiliation(s)
- Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
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37
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Salonia F, Ciacciulli A, Poles L, Pappalardo HD, La Malfa S, Licciardello C. New Plant Breeding Techniques in Citrus for the Improvement of Important Agronomic Traits. A Review. Front Plant Sci 2020; 11:1234. [PMID: 32922420 PMCID: PMC7456868 DOI: 10.3389/fpls.2020.01234] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/28/2020] [Indexed: 05/18/2023]
Abstract
New plant breeding techniques (NPBTs) aim to overcome traditional breeding limits for fruit tree species, in order to obtain new varieties with improved organoleptic traits and resistance to biotic and abiotic stress, and to maintain fruit quality achieved over centuries by (clonal) selection. Knowledge on the gene(s) controlling a specific trait is essential for the use of NPBTs, such as genome editing and cisgenesis. In the framework of the international scientific community working on fruit tree species, including citrus, NPBTs have mainly been applied to address pathogen threats. Citrus could take advantage of NPBTs because of its complex species biology (seedlessness, apomixis, high heterozygosity, and long juvenility phase) and aptitude for in vitro manipulation. To our knowledge, genome editing in citrus via transgenesis has successful for induced resistance to Citrus bacterial canker in sweet orange and grapefruit using the resistance gene CsLOB1. In the future, NPBTs will also be used to improve fruit traits, making them healthier. The regeneration of plants following the application of NPBTs is a bottleneck, making it necessary to optimize the efficiency of current protocols. The strengths and weaknesses of using explants from young in vitro plantlets, and from mature plants, will be discussed. Other major issues addressed in this review are related to the requirement for marker-free systems and shortening the long juvenility phase. This review aims to summarize methods and approaches available in the literature that are suitable to citrus, focusing on the principles observed before the use of NPBTs.
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Affiliation(s)
- Fabrizio Salonia
- CREA - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Angelo Ciacciulli
- CREA - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
| | - Lara Poles
- CREA - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | | | - Stefano La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
- *Correspondence: Stefano La Malfa, ; Concetta Licciardello,
| | - Concetta Licciardello
- CREA - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
- *Correspondence: Stefano La Malfa, ; Concetta Licciardello,
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38
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Masic I, Jankovic SM, Kurjak A, Donev DM, Zildzic M, Sinanovic O, Hozo I, Milicevic S, Hasukic S, Mujanovic E, Arnautovic K, Trnacevic S, Mesic E, Biscevic M, Sefic M, Gerc V, Kucukalic A, Hrgovic Z, Bergsland J, Grujic M. Guidelines for Editing Biomedical Journals: Recommended by Academy of Medical Sciences of Bosnia and Herzegovina. Acta Inform Med 2020; 28:232-236. [PMID: 33627922 PMCID: PMC7879445 DOI: 10.5455/aim.2020.28.232-236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background: Enormous number of medical journals published around the globe requires standardization of editing practice. Objective: The aim of this article was to enlist main principles of editing biomedical scientific journals adopted at annual meeting of Academy of Medical Sciences of Bosnia & Herzegovina (AMSB&H). Methods: The evidence for writing this Guideline was systematically searched for during September 2020 in the PUBMED and GOOGLE SCHOLAR databases. The inclusion criteria were: original studies, systematic reviews, invited expert opinions, guidelines and editorials. The exclusion criteria were narrative reviews and uninvited opinion articles. The retrieved evidence was analyzed by members of the AMSB&H, then discussed at 2020 annual meeting of the AMSB&H and adopted by nominal group technique. Results: In total 14 recommendations were made, based on A to C class of evidence. The editors should educate potential authors and instruct them how to structure their manuscript, how to write every segment of the manuscript, and take care about correct use of statistical tests. Plagiarism detection softwares should be used regularly, and statistical and technical editing should be rigorous and thorough. International standards of reporting specific types of studies should be followed, and principles of ethical and responsible behavior of editors, reviewers and authors should be published on the journal’s web site. The editors should insist on registration of clinical studies before submission, and check whether non-essential personal information is removed from the articles; when essential personal information has to be included, an article should not be published without signed informed consent by the patient to whom these information relate. Conclusions: Principles of editing biomedical scientific journals recommended in this guideline should serve as one of the means of improving medical journals’ quality.
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Affiliation(s)
- Izet Masic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina.,World Academy of Art and Science, Washington, USA.,International Academy of Health Science Informatics, Geneva, Switzerland
| | - Slobodan M Jankovic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina.,Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Asim Kurjak
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina.,World Academy of Art and Science, Washington, USA.,European Academy of Sciences and Arts, Salzburg, Austria.,International Academy of Perinatal medicine, Zagreb, Croatia.,Sarajevo School of Science and Technology, Sarajevo, Bosnia and Herzegovina
| | - Doncho M Donev
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina.,European Academy of Sciences and Arts, Salzburg, Austria.,Faculty of Medicine, Ss Cyril and Methodius University, Skopje, R.N. Macedonia
| | - Muharem Zildzic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina
| | - Osman Sinanovic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina.,Sarajevo School of Science and Technology, Sarajevo, Bosnia and Herzegovina
| | - Izet Hozo
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina.,Faculty of Medicine, University of Split, Split, Croatia
| | - Snjezana Milicevic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina.,Faculty of Medicine, University of Banja Luka, Banja Luka, Bosnia and Herzegovina
| | - Sefik Hasukic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina.,Department of Surgery, University Clinical Center Tuzla, Tuzla, Bosnia and Herzegovina
| | - Emir Mujanovic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina.,Medical center Bayer, Tuzla, Tuzla, Bosnia and Herzegovina
| | - Kenan Arnautovic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina.,Semmes Murphey Leaders in Brain and Spine Care, Memphis, Tennessee, USA
| | - Senaid Trnacevic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina.,University Clinical Center Tuzla, Tuzla, Bosnia and Herzegovina
| | - Enisa Mesic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina.,University Clinical Center Tuzla, Tuzla, Bosnia and Herzegovina
| | - Mirza Biscevic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina.,General Hospital "Prim. Dr. Abdulah Nakas", Sarajevo, Bosnia and Herzegovina
| | - Mustafa Sefic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina
| | - Vjekoslav Gerc
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina
| | - Abdulah Kucukalic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina
| | - Zlatko Hrgovic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina
| | - Jacob Bergsland
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina.,University Hospital Oslo, Oslo, Norway
| | - Mirko Grujic
- Academy of Medical Sciences of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina
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39
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Brezgin S, Kostyusheva A, Kostyushev D, Chulanov V. Dead Cas Systems: Types, Principles, and Applications. Int J Mol Sci 2019; 20:E6041. [PMID: 31801211 PMCID: PMC6929090 DOI: 10.3390/ijms20236041] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 12/12/2022] Open
Abstract
The gene editing tool CRISPR-Cas has become the foundation for developing numerous molecular systems used in research and, increasingly, in medical practice. In particular, Cas proteins devoid of nucleolytic activity (dead Cas proteins; dCas) can be used to deliver functional cargo to programmed sites in the genome. In this review, we describe current CRISPR systems used for developing different dCas-based molecular approaches and summarize their most significant applications. We conclude with comments on the state-of-art in the CRISPR field and future directions.
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MESH Headings
- CRISPR-Associated Protein 9/genetics
- CRISPR-Associated Protein 9/metabolism
- CRISPR-Cas Systems
- Chromatin/chemistry
- Chromatin/metabolism
- Clustered Regularly Interspaced Short Palindromic Repeats
- Communicable Diseases/genetics
- Communicable Diseases/metabolism
- Communicable Diseases/pathology
- Communicable Diseases/therapy
- DNA Methylation
- Epigenesis, Genetic
- Gene Editing/methods
- Genetic Diseases, Inborn/genetics
- Genetic Diseases, Inborn/metabolism
- Genetic Diseases, Inborn/pathology
- Genetic Diseases, Inborn/therapy
- Genome, Human
- Histones/genetics
- Histones/metabolism
- Humans
- Inflammation/genetics
- Inflammation/metabolism
- Inflammation/pathology
- Inflammation/therapy
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Neoplasms/therapy
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
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Affiliation(s)
- Sergey Brezgin
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow 127994, Russia; (S.B.); (A.K.); (V.C.)
- Institute of Immunology, Federal Medical Biological Agency, Moscow 115522, Russia
| | - Anastasiya Kostyusheva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow 127994, Russia; (S.B.); (A.K.); (V.C.)
| | - Dmitry Kostyushev
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow 127994, Russia; (S.B.); (A.K.); (V.C.)
| | - Vladimir Chulanov
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow 127994, Russia; (S.B.); (A.K.); (V.C.)
- Sechenov First Moscow State Medical University, Moscow 119146, Russia
- Central Research Institute of Epidemiology, Moscow 111123, Russia
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Ziccardi L, Cordeddu V, Gaddini L, Matteucci A, Parravano M, Malchiodi-Albedi F, Varano M. Gene Therapy in Retinal Dystrophies. Int J Mol Sci. 2019;20. [PMID: 31739639 PMCID: PMC6888000 DOI: 10.3390/ijms20225722] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) are a group of clinically and genetically heterogeneous degenerative disorders. To date, mutations have been associated with IRDs in over 270 disease genes, but molecular diagnosis still remains elusive in about a third of cases. The methodologic developments in genome sequencing techniques that we have witnessed in this last decade have represented a turning point not only in diagnosis and prognosis but, above all, in the identification of new therapeutic perspectives. The discovery of new disease genes and pathogenetic mechanisms underlying IRDs has laid the groundwork for gene therapy approaches. Several clinical trials are ongoing, and the recent approval of Luxturna, the first gene therapy product for Leber congenital amaurosis, marks the beginning of a new era. Due to its anatomical and functional characteristics, the retina is the organ of choice for gene therapy, although there are quite a few difficulties in the translational approaches from preclinical models to humans. In the first part of this review, an overview of the current knowledge on methodological issues and future perspectives of gene therapy applied to IRDs is discussed; in the second part, the state of the art of clinical trials on the gene therapy approach in IRDs is illustrated.
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Setz CS, Hug E, Khadour A, Abdelrasoul H, Bilal M, Hobeika E, Jumaa H. PI3K-Mediated Blimp-1 Activation Controls B Cell Selection and Homeostasis. Cell Rep 2019; 24:391-405. [PMID: 29996100 PMCID: PMC6057491 DOI: 10.1016/j.celrep.2018.06.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/07/2018] [Accepted: 06/08/2018] [Indexed: 11/04/2022] Open
Abstract
Activation of phosphoinositide 3-kinase (PI3K) signaling plays a central role in regulating proliferation and survival of B cells. Here, we tested the hypothesis that B cell receptor (BCR)-mediated activation of PI3K induces the terminal differentiation factor Blimp-1 that interferes with proliferation and survival, thereby controlling the expansion of activated B cells. In fact, B-cell-specific inactivation of Pten, the negative regulator of PI3K signaling, leads to deregulated PI3K activity and elevated Blimp-1 expression. Combined deficiency for Pten and Blimp-1 results in abnormal expansion of B-1 B cells and splenomegaly. Interestingly, Blimp-1 also acts at early stages of B cell development to regulate B cell selection, as Blimp-1 deficiency results in an increased proportion of autoreactive B cells. Together, our data suggest that the combined requirement of deregulated PI3K signaling in addition to defective terminal differentiation represents the basis for proper selection and expansion of developing B cells. B cell expansion is normal despite increased PI3K activity after Pten deletion Deregulated PI3K induces Blimp-1 and leads to premature terminal differentiation Premature terminal differentiation prevents expansion of activated B cells Expansion of B-1 B cells by autoreactive BCR and defective terminal differentiation
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Affiliation(s)
- Corinna S Setz
- Institute of Immunology, University Medical Center Ulm, 89081 Ulm, Germany
| | - Eva Hug
- Institute of Immunology, University Medical Center Ulm, 89081 Ulm, Germany
| | - Ahmad Khadour
- Institute of Immunology, University Medical Center Ulm, 89081 Ulm, Germany
| | - Hend Abdelrasoul
- Institute of Immunology, University Medical Center Ulm, 89081 Ulm, Germany; Genetic Engineering and Biotechnology Division, Molecular Biology Department, National Research Centre (NRC), 12622 Giza, Egypt
| | - Mayas Bilal
- Institute of Immunology, University Medical Center Ulm, 89081 Ulm, Germany
| | - Elias Hobeika
- Institute of Immunology, University Medical Center Ulm, 89081 Ulm, Germany
| | - Hassan Jumaa
- Institute of Immunology, University Medical Center Ulm, 89081 Ulm, Germany.
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Urbano A, Smith J, Weeks RJ, Chatterjee A. Gene-Specific Targeting of DNA Methylation in the Mammalian Genome. Cancers (Basel) 2019; 11:cancers11101515. [PMID: 31600992 PMCID: PMC6827012 DOI: 10.3390/cancers11101515] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/02/2019] [Accepted: 10/05/2019] [Indexed: 02/07/2023] Open
Abstract
DNA methylation is the most widely-studied epigenetic modification, playing a critical role in the regulation of gene expression. Dysregulation of DNA methylation is implicated in the pathogenesis of numerous diseases. For example, aberrant DNA methylation in promoter regions of tumor-suppressor genes has been strongly associated with the development and progression of many different tumors. Accordingly, technologies designed to manipulate DNA methylation at specific genomic loci are very important, especially in the context of cancer therapy. Traditionally, epigenomic editing technologies have centered around zinc finger proteins (ZFP)- and transcription activator-like effector protein (TALE)-based targeting. More recently, however, the emergence of clustered regulatory interspaced short palindromic repeats (CRISPR)-deactivated Cas9 (dCas9)-based editing systems have shown to be a more specific and efficient method for the targeted manipulation of DNA methylation. Here, we describe the regulation of the DNA methylome, its significance in cancer and the current state of locus-specific editing technologies for altering DNA methylation.
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Affiliation(s)
- Arthur Urbano
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin 9054, New Zealand.
| | - Jim Smith
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin 9054, New Zealand.
| | - Robert J Weeks
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin 9054, New Zealand.
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin 9054, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, 3A Symonds Street, Private Bag 92019, Auckland, New Zealand.
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van de Wouw M, Stilling RM, Peterson VL, Ryan FJ, Hoban AE, Shanahan F, Clarke G, Claesson MJ, Dinan TG, Cryan JF, Schellekens H. Host Microbiota Regulates Central Nervous System Serotonin Receptor 2C Editing in Rodents. ACS Chem Neurosci 2019; 10:3953-3960. [PMID: 31415146 DOI: 10.1021/acschemneuro.9b00414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Microbial colonization of the gastrointestinal tract plays a crucial role in the development of enteric and central nervous system functionality. The serotonergic system has been heavily implicated in microbiota-gut-brain axis signaling, particularly in proof-of-principle studies in germ-free (GF) animals. One aspect of the serotonergic system that has been left unexplored in relation to the microbiota is the unique ability of the serotonin receptor 2C (5-HT2C) to undergo post-transcriptional editing, which has been implicated in decreased receptor functionality. We investigated whether GF mice, with absent microbiota from birth, have altered 5-HT2C receptor expression and editing in the brain, and if colonization of the microbiota is able to restore editing patterns. Next, we investigated whether microbiota depletion later in life using a chronic antibiotic treatment could affect 5-HT2C receptor editing patterns in rats. We found that GF mice have an increased prevalence of the edited 5-HT2C receptor isoforms in the amygdala, hypothalamus, prefrontal cortex, and striatum, which was partially normalized upon colonization post-weaning. However, no alterations were observed in the hypothalamus after microbiota depletion using an antibiotic treatment in adult rats. This suggests that alterations in the microbiome during development, but not later in life, could influence 5-HT2C receptor editing patterns. Overall, these results demonstrate that the microbiota affects 5-HT2C receptor editing in the brain and may inform novel therapeutic strategies in conditions in which 5-HT2C receptor editing is altered, such as depression.
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Affiliation(s)
- Marcel van de Wouw
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Roman M. Stilling
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Veronica L. Peterson
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
| | - Feargal J. Ryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Alan E. Hoban
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Fergus Shanahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
| | - Marcus J. Claesson
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Timothy G. Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
| | - John F. Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Harriët Schellekens
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
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EauClaire SF, Webb CJ. A CRISPR/Cas9 method to generate heterozygous alleles in Saccharomyces cerevisiae. Yeast 2019; 36:607-615. [PMID: 31301239 DOI: 10.1002/yea.3432] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/08/2019] [Indexed: 12/30/2022] Open
Abstract
Saccharomyces cerevisiae is a genetically facile organism, yet multiple CRISPR/Cas9 techniques are widely used to edit its genome more efficiently and cost effectively than conventional methods. The absence of selective markers makes CRISPR/Cas9 editing particularly useful when making mutations within genes or regulatory sequences. Heterozygous mutations within genes frequently arise in the winners of evolution experiments. The genetic dissection of heterozygous alleles can be important to understanding gene structure and function. Unfortunately, the high efficiency of genome cutting and repair makes the introduction of heterozygous alleles by standard CRISPR/Cas9 technique impossible. To be able to quickly and reliably determine the individual phenotypes of the thousands of heterozygous mutations that can occur during directed evolutions is of particular interest to industrial strain improvement research. In this report, we describe a CRISPR/Cas9 method that introduces specific heterozygous mutations into the S. cerevisiae genome. This method relies upon creating silent point mutations in the protospacer adjacent motif site or removing the protospacer adjacent motif site entirely to stop the multiple rounds of genome editing that prevent heterozygous alleles from being generated. This technique should be able to create heterozygous alleles in other diploid yeasts and different allelic copy numbers in polyploid cells.
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Affiliation(s)
- Steven F EauClaire
- Experimental Station E353/107C, DuPont Nutrition & Biosciences, Wilmington, Delaware
| | - Christopher J Webb
- DuPont Palo Alto Research & Development Center, Dupont Nutrition & Biosciences, Palo Alto, California
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Lau CH, Reeves R, Bolt EL. Adaptation processes that build CRISPR immunity: creative destruction, updated. Essays Biochem 2019; 63:227-35. [PMID: 31186288 DOI: 10.1042/EBC20180073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 01/01/2023]
Abstract
Prokaryotes can defend themselves against invading mobile genetic elements (MGEs) by acquiring immune memory against them. The memory is a DNA database located at specific chromosomal sites called CRISPRs (clustered regularly interspaced short palindromic repeats) that store fragments of MGE DNA. These are utilised to target and destroy returning MGEs, preventing re-infection. The effectiveness of CRISPR-based immune defence depends on 'adaptation' reactions that capture and integrate MGE DNA fragments into CRISPRs. This provides the means for immunity to be delivered against MGEs in 'interference' reactions. Adaptation and interference are catalysed by Cas (CRISPR-associated) proteins, aided by enzymes well known for other roles in cells. We survey the molecular biology of CRISPR adaptation, highlighting entirely new developments that may help us to understand how MGE DNA is captured. We focus on processes in Escherichia coli, punctuated with reference to other prokaryotes that illustrate how common requirements for adaptation, DNA capture and integration, can be achieved in different ways. We also comment on how CRISPR adaptation enzymes, and their antecedents, can be utilised for biotechnology.
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Abstract
Along with my colleagues, I presented a number of sessions at the 2019 Oncology Nursing Society (ONS) Congress on publishing and how it contributes to career advancement and professional fulfillment. Ellen Carr, RN, MSN, AOCN®, editor of the Clinical Journal of Oncology Nursing, Leslie McGee, MA, senior editorial manager at ONS, and I talked about various aspects of the publishing process and answered questions from enthusiastic audience members, many of whom had not published before. As we described the process of writing a manuscript, following the instructions for authors, and eventually finding a home for the work, I thought about the important role that editing plays.
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Branzoli F, Deelchand DK, Sanson M, Lehéricy S, Marjańska M. In vivo 1 H MRS detection of cystathionine in human brain tumors. Magn Reson Med 2019; 82:1259-1265. [PMID: 31131476 DOI: 10.1002/mrm.27810] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/29/2019] [Accepted: 04/22/2019] [Indexed: 11/09/2022]
Abstract
PURPOSE To report the technical aspects of noninvasive detection of cystathionine in human brain glioma with edited MRS, and to investigate possible further acquisition improvements for robust quantification of this metabolite. METHODS In vivo 1 H MR spectra were acquired at 3 T in 15 participants with an isocitrate dehydrogenase-mutated glioma using a MEGA-PRESS (MEscher GArwood point resolved spectroscopy) sequence previously employed for 2-hydroxyglutarate detection (TR = 2 s, TE = 68 ms). The editing pulse was applied at 1.9 ppm for the edit-on condition and at 7.5 ppm for the edit-off condition. To evaluate the editing efficiency, spectra were acquired in 1 participant by placing the editing pulse for the edit-on condition at 1.9, 2.03, and 2.16 ppm. Cystathionine concentration was quantified using LCModel and a simulated basis set. To confirm chemical shifts and J-coupling values of cystathionine, the 1 H NMR cystathionine spectrum was measured using a high-resolution 500 MHz spectrometer. RESULTS In 12 gliomas, cystathionine was observed in the in vivo edited MR spectra at 2.72 and 3.85 ppm and quantified. The signal intensity of the cystathionine resonance at 2.72 ppm increased 1.7 and 2.13 times when the editing pulse was moved to 2.03 and 2.16 ppm, respectively. Cystathionine was not detectable in normal brain tissue. CONCLUSION Cystathionine can be detected in vivo by edited MRS using the same protocol as for 2-hydroxyglutarate detection. This finding may enable a more accurate, noninvasive investigation of cellular metabolism in glioma.
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Affiliation(s)
- Francesca Branzoli
- Institut du Cerveau et de la Moelle épinère-ICM, Centre de NeuroImagerie de Recherche-CENIR, Paris, France.,Sorbonne Université, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, Paris, France
| | - Dinesh K Deelchand
- Center for Magnetic Resonance Research and Department of Radiology, University of Minnesota, Minneapolis, Minnesota
| | - Marc Sanson
- Sorbonne Université, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, Paris, France.,AP-HP, Hôpital de la Pitié-Salpêtrière, Service de Neurologie 2, Paris, France.,Onconeurotek Tumor Bank, Institut du Cerveau et de la Moelle épinère-ICM, Paris, France
| | - Stéphane Lehéricy
- Institut du Cerveau et de la Moelle épinère-ICM, Centre de NeuroImagerie de Recherche-CENIR, Paris, France.,Sorbonne Université, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, Paris, France.,AP-HP, Hôpital de la Pitié-Salpêtrière, Service de Neuroradiologie, Paris, France
| | - Małgorzata Marjańska
- Center for Magnetic Resonance Research and Department of Radiology, University of Minnesota, Minneapolis, Minnesota
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Wasala NB, Hakim CH, Chen SJ, Yang NN, Duan D. Questions Answered and Unanswered by the First CRISPR Editing Study in a Canine Model of Duchenne Muscular Dystrophy. Hum Gene Ther 2019; 30:535-543. [PMID: 30648435 PMCID: PMC6534086 DOI: 10.1089/hum.2018.243] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/11/2019] [Indexed: 12/17/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) editing is being considered as a potential gene repair therapy to treat Duchenne muscular dystrophy, a dystrophin-deficient lethal muscle disease affecting all muscles in the body. A recent preliminary study from the Olson laboratory (Amoasii et al. Science 2018;362:89-91) showed robust dystrophin restoration in a canine Duchenne muscular dystrophy model following intramuscular or intravenous delivery of the CRISPR editing machinery by adeno-associated virus serotype 9. Despite the limitation of the small sample size, short study duration, and the lack of muscle function data, the Olson lab findings have provided important proof of principle for scaling up CRISPR therapy from rodents to large mammals. Future large-scale, long-term, and comprehensive studies are warranted to establish the safety and efficacy of CRISPR editing therapy in large mammals.
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Affiliation(s)
- Nalinda B. Wasala
- Department of Molecular Microbiology, College of Veterinary Medicine, The University of Missouri, Columbia
| | - Chady H. Hakim
- Department of Molecular Microbiology, College of Veterinary Medicine, The University of Missouri, Columbia
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Shi-Jie Chen
- Department of Physics, College of Veterinary Medicine, The University of Missouri, Columbia
- Department of Biochemistry, College of Veterinary Medicine, The University of Missouri, Columbia
| | - N. Nora Yang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Dongsheng Duan
- Department of Molecular Microbiology, College of Veterinary Medicine, The University of Missouri, Columbia
- Department of Neurology, School of Medicine, College of Veterinary Medicine, The University of Missouri, Columbia
- Department of Bioengineering, College of Veterinary Medicine, The University of Missouri, Columbia
- Department of Biomedical Sciences, College of Veterinary Medicine, The University of Missouri, Columbia
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Felden B, Gilot D. Modulation of Bacterial sRNAs Activity by Epigenetic Modifications: Inputs from the Eukaryotic miRNAs. Genes (Basel) 2018; 10:genes10010022. [PMID: 30602712 PMCID: PMC6356536 DOI: 10.3390/genes10010022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/18/2018] [Accepted: 12/21/2018] [Indexed: 12/14/2022] Open
Abstract
Trans-encoded bacterial regulatory RNAs (sRNAs) are functional analogues of eukaryotic microRNAs (miRNAs). These RNA classes act by base-pairing complementarity with their RNA targets to modulate gene expression (transcription, half-life and/or translation). Based on base-pairing, algorithms predict binding and the impact of small RNAs on targeted-RNAs expression and fate. However, other actors are involved such as RNA binding proteins and epigenetic modifications of the targeted and small RNAs. Post-transcriptional base modifications are widespread in all living organisms where they lower undesired RNA folds through conformation adjustments and influence RNA pairing and stability, especially if remodeling their ends. In bacteria, sRNAs possess RNA modifications either internally (methylation, pseudouridinylation) or at their ends. Nicotinamide adenine dinucleotide were detected at 5′-ends, and polyadenylation can occur at 3′-ends. Eukaryotic miRNAs possess N6-methyladenosine (m6A), A editing into I, and non-templated addition of uridines at their 3′-ends. Biological functions and enzymes involved in those sRNA and micro RNA epigenetic modifications, when known, are presented and challenged.
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Affiliation(s)
- Brice Felden
- University of Rennes 1, Inserm, BRM (Bacterial Regulatory RNAs and Medicine), UMR_S 1230, F-35043 Rennes, France.
| | - David Gilot
- CNRS UMR 6290, IGDR, University of Rennes 1, F-35043 Rennes, France.
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Arias-Gonzalez JR. Writing, Proofreading and Editing in Information Theory. Entropy (Basel) 2018; 20:e20050368. [PMID: 33265458 PMCID: PMC7512888 DOI: 10.3390/e20050368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/04/2018] [Accepted: 05/12/2018] [Indexed: 12/30/2022]
Abstract
Information is a physical entity amenable to be described by an abstract theory. The concepts associated with the creation and post-processing of the information have not, however, been mathematically established, despite being broadly used in many fields of knowledge. Here, inspired by how information is managed in biomolecular systems, we introduce writing, entailing any bit string generation, and revision, as comprising proofreading and editing, in information chains. Our formalism expands the thermodynamic analysis of stochastic chains made up of material subunits to abstract strings of symbols. We introduce a non-Markovian treatment of operational rules over the symbols of the chain that parallels the physical interactions responsible for memory effects in material chains. Our theory underlies any communication system, ranging from human languages and computer science to gene evolution.
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Affiliation(s)
- J. Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia, C/Faraday 9, Cantoblanco, 28049 Madrid, Spain; ; Tel.: +34-91-299-8860
- CNB-CSIC-IMDEA Nanociencia Associated Unit “Unidad de Nanobiotecnología”, Cantoblanco, 28049 Madrid, Spain
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