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Schwarz PM, Freisleben B. Data recovery methods for DNA storage based on fountain codes. Comput Struct Biotechnol J 2024; 23:1808-1823. [PMID: 38707543 PMCID: PMC11066528 DOI: 10.1016/j.csbj.2024.04.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024] Open
Abstract
Today's digital data storage systems typically offer advanced data recovery solutions to address the problem of catastrophic data loss, such as software-based disk sector analysis or physical-level data retrieval methods for conventional hard disk drives. However, DNA-based data storage currently relies solely on the inherent error correction properties of the methods used to encode digital data into strands of DNA. Any error that cannot be corrected utilizing the redundancy added by DNA encoding methods results in permanent data loss. To provide data recovery for DNA storage systems, we present a method to automatically reconstruct corrupted or missing data stored in DNA using fountain codes. Our method exploits the relationships between packets encoded with fountain codes to identify and rectify corrupted or lost data. Furthermore, we present file type-specific and content-based data recovery methods for three file types, illustrating how a fusion of fountain encoding-specific redundancy and knowledge about the data can effectively recover information in a corrupted DNA storage system, both in an automatic and in a guided manual manner. To demonstrate our approach, we introduce DR4DNA, a software toolkit that contains all methods presented. We evaluate DR4DNA using both in-silico and in-vitro experiments.
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Affiliation(s)
- Peter Michael Schwarz
- Department of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Straße 6, Marburg, D-35043, Germany
| | - Bernd Freisleben
- Department of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Straße 6, Marburg, D-35043, Germany
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2
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Poyatos-García J, Soblechero-Martín P, Liquori A, López-Martínez A, Maestre P, González-Romero E, Vázquez-Manrique RP, Muelas N, García-García G, Ohana J, Arechavala-Gomeza V, Vílchez JJ. Deletion of exons 45 to 55 in the DMD gene: from the therapeutic perspective to the in vitro model. Skelet Muscle 2024; 14:21. [PMID: 39354597 PMCID: PMC11443720 DOI: 10.1186/s13395-024-00353-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 09/13/2024] [Indexed: 10/03/2024] Open
Abstract
BACKGROUND Gene editing therapies in development for correcting out-of-frame DMD mutations in Duchenne muscular dystrophy aim to replicate benign spontaneous deletions. Deletion of 45-55 DMD exons (del45-55) was described in asymptomatic subjects, but recently serious skeletal and cardiac complications have been reported. Uncovering why a single mutation like del45-55 is able to induce diverse phenotypes and grades of severity may impact the strategies of emerging therapies. Cellular models are essential for this purpose, but their availability is compromised by scarce muscle biopsies. METHODS We introduced, as a proof-of-concept, using CRISPR-Cas9 edition, a del45-55 mimicking the intronic breakpoints harboured by a subset of patients of this form of dystrophinopathy (designing specific gRNAs), into a Duchenne patient's cell line. The edited cell line was characterized evaluating the dystrophin expression and the myogenic status. RESULTS Dystrophin expression was restored, and the myogenic defects were ameliorated in the edited myoblasts harbouring a specific del45-55. Besides confirming the potential of CRISPR-Cas9 to create tailored mutations (despite the low cleavage efficiency of our gRNAs) as a useful approach to generate in vitro models, we also generated an immortalized myoblast line derived from a patient with a specific del45-55. CONCLUSIONS Overall, we provide helpful resources to deepen into unknown factors responsible for DMD-pathophysiology.
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Affiliation(s)
- Javier Poyatos-García
- Neuromuscular and Ataxias Research Group, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain.
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), CB23/07/00005, Madrid, Spain.
- University of Valencia, Valencia, Spain.
| | - Patricia Soblechero-Martín
- Nucleic Acid Therapeutics for Rare Disorders (NAT-RD), Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Alessandro Liquori
- Hematology Research Group, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
- Centre for Biomedical Network Research on Cancer (CIBERONC), CB16/12/00284, Madrid, Spain
| | - Andrea López-Martínez
- Nucleic Acid Therapeutics for Rare Disorders (NAT-RD), Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Pilar Maestre
- Neuromuscular and Ataxias Research Group, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
| | - Elisa González-Romero
- Hematology Research Group, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
| | - Rafael P Vázquez-Manrique
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Health Research Institute Hospital La Fe, Valencia, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), U755, CB06/07/1030, Madrid, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, Valencia, Spain
| | - Nuria Muelas
- Neuromuscular and Ataxias Research Group, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
- Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO- NMD), Hospital Universitari I Politècnic La Fe, Valencia, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), U763, CB06/05/0091, Madrid, Spain
| | - Gema García-García
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Health Research Institute Hospital La Fe, Valencia, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), U755, CB06/07/1030, Madrid, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, Valencia, Spain
| | - Jessica Ohana
- Centre de Recherche en Myologie, Sorbonne Université, INSERM, Institut de Myologie, Paris, 75013, France
| | - Virginia Arechavala-Gomeza
- Nucleic Acid Therapeutics for Rare Disorders (NAT-RD), Biobizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Juan J Vílchez
- Neuromuscular and Ataxias Research Group, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain.
- University of Valencia, Valencia, Spain.
- Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO- NMD), Hospital Universitari I Politècnic La Fe, Valencia, Spain.
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), U763, CB06/05/0091, Madrid, Spain.
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3
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Hadi MI, Laksmi FA, Helbert, Amalia AR, Muhammad AD, Violando WA. An efficient approach for overproduction of DNA polymerase from Pyrococcus furiosus using an optimized autoinduction system in Escherichia coli. World J Microbiol Biotechnol 2024; 40:324. [PMID: 39294482 DOI: 10.1007/s11274-024-04127-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 08/31/2024] [Indexed: 09/20/2024]
Abstract
High fidelity DNA polymerase from Pyrococcus furiosus (Pfupol) is an attractive alternative to the highly popular DNA polymerase from Thermus aquaticus. Because this enzyme is in great demand for biotechnological applications, optimizing Pfupol production is essential to supplying the industry's expanding demand. T7-induced promoter expression in Escherichia coli expression systems is used to express recombinant Pfupol; however, this method is not cost-effective. Here, we have effectively developed an optimized process for the autoinduction approach of Pfupol expression in a defined medium. To better examine Pfupol's activities, its purified fraction was used. A 71 mg/L of pure Pfupol was effectively produced, resulting in a 2.6-fold increase in protein yield when glucose, glycerol, and lactose were added in a defined medium at concentrations of 0.05%, 1%, and 0.6%, respectively, and the condition for production in a 5 L bioreactor was as follow: 200 rpm, 3 vvm, and 10% inoculant. Furthermore, the protein exhibited 1445 U/mg of specific activity when synthesized in its active state. This work presents a high level of Pfupol production, which makes it an economically viable and practically useful approach.
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Affiliation(s)
- Moch Irfan Hadi
- Faculty of Science and Technology, UIN Sunan Ampel, Surabaya, Indonesia
| | - Fina Amreta Laksmi
- Research Center for Applied Microbiology, National Research and Innovation Agency, Jalan Raya Bogor KM 46, Cibinong, Bogor, 16911, West Java, Indonesia.
| | - Helbert
- Research Center for Ecology and Ethnobiology, National Research and Innovation Agency, Jalan Raya Bogor KM 46, Cibinong, Bogor, 16911, West Java, Indonesia
| | - Arfena Rizqi Amalia
- Research Center for Applied Microbiology, National Research and Innovation Agency, Jalan Raya Bogor KM 46, Cibinong, Bogor, 16911, West Java, Indonesia
| | - Azriel Dafa Muhammad
- Research Center for Applied Microbiology, National Research and Innovation Agency, Jalan Raya Bogor KM 46, Cibinong, Bogor, 16911, West Java, Indonesia
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Luescher AM, Gimpel AL, Stark WJ, Heckel R, Grass RN. Chemical unclonable functions based on operable random DNA pools. Nat Commun 2024; 15:2955. [PMID: 38580696 PMCID: PMC10997750 DOI: 10.1038/s41467-024-47187-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/25/2024] [Indexed: 04/07/2024] Open
Abstract
Physical unclonable functions (PUFs) based on unique tokens generated by random manufacturing processes have been proposed as an alternative to mathematical one-way algorithms. However, these tokens are not distributable, which is a disadvantage for decentralized applications. Finding unclonable, yet distributable functions would help bridge this gap and expand the applications of object-bound cryptography. Here we show that large random DNA pools with a segmented structure of alternating constant and randomly generated portions are able to calculate distinct outputs from millions of inputs in a specific and reproducible manner, in analogy to physical unclonable functions. Our experimental data with pools comprising up to >1010 unique sequences and encompassing >750 comparisons of resulting outputs demonstrate that the proposed chemical unclonable function (CUF) system is robust, distributable, and scalable. Based on this proof of concept, CUF-based anti-counterfeiting systems, non-fungible objects and decentralized multi-user authentication are conceivable.
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Affiliation(s)
- Anne M Luescher
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Andreas L Gimpel
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Wendelin J Stark
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Reinhard Heckel
- Department of Computer Engineering, Technical University of Munich, Arcisstrasse 21, 80333, Munich, Germany
| | - Robert N Grass
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland.
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5
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Zhuang X, Ye R, Zhou Y, Cheng MY, Cui H, Wang L, Zhang S, Wang S, Cui Y, Zhang W. Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma. Genome Med 2024; 16:50. [PMID: 38566210 PMCID: PMC10985887 DOI: 10.1186/s13073-024-01319-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Mitochondria play essential roles in tumorigenesis; however, little is known about the contribution of mitochondrial DNA (mtDNA) to esophageal squamous cell carcinoma (ESCC). Whole-genome sequencing (WGS) is by far the most efficient technology to fully characterize the molecular features of mtDNA; however, due to the high redundancy and heterogeneity of mtDNA in regular WGS data, methods for mtDNA analysis are far from satisfactory. METHODS Here, we developed a likelihood-based method dMTLV to identify low-heteroplasmic mtDNA variants. In addition, we described fNUMT, which can simultaneously detect non-reference nuclear sequences of mitochondrial origin (non-ref NUMTs) and their derived artifacts. Using these new methods, we explored the contribution of mtDNA to ESCC utilizing the multi-omics data of 663 paired tumor-normal samples. RESULTS dMTLV outperformed the existing methods in sensitivity without sacrificing specificity. The verification using Nanopore long-read sequencing data showed that fNUMT has superior specificity and more accurate breakpoint identification than the current methods. Leveraging the new method, we identified a significant association between the ESCC overall survival and the ratio of mtDNA copy number of paired tumor-normal samples, which could be potentially explained by the differential expression of genes enriched in pathways related to metabolism, DNA damage repair, and cell cycle checkpoint. Additionally, we observed that the expression of CBWD1 was downregulated by the non-ref NUMTs inserted into its intron region, which might provide precursor conditions for the tumor cells to adapt to a hypoxic environment. Moreover, we identified a strong positive relationship between the number of mtDNA truncating mutations and the contribution of signatures linked to tumorigenesis and treatment response. CONCLUSIONS Our new frameworks promote the characterization of mtDNA features, which enables the elucidation of the landscapes and roles of mtDNA in ESCC essential for extending the current understanding of ESCC etiology. dMTLV and fNUMT are freely available from https://github.com/sunnyzxh/dMTLV and https://github.com/sunnyzxh/fNUMT , respectively.
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Affiliation(s)
- Xuehan Zhuang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Rui Ye
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yong Zhou
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Matthew Yibo Cheng
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Heyang Cui
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Longlong Wang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Shuangping Zhang
- The Department of Thoracic Surgery, Shanxi Cancer Hospital; Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Shubin Wang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Yongping Cui
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China.
- The Department of Thoracic Surgery, Shanxi Cancer Hospital; Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, China.
| | - Weimin Zhang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China.
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute; Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, 100142, China.
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Wang H, Liu K, He Z, Chen Y, Hu Z, Chen W, Leaw CP, Chen N. Extensive intragenomic variations of the 18S rDNA V4 region in the toxigenic diatom species Pseudo-nitzschia multistriata revealed through high-throughput sequencing. MARINE POLLUTION BULLETIN 2024; 201:116198. [PMID: 38428045 DOI: 10.1016/j.marpolbul.2024.116198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
Metabarcoding analysis is an effective technique for monitoring the domoic acid-producing Pseudo-nitzschia species in marine environments, uncovering high-levels of molecular diversity. However, such efforts may result in the overinterpretation of Pseudo-nitzschia species diversity, as molecular diversity not only encompasses interspecies and intraspecies diversities but also exhibits extensive intragenomic variations (IGVs). In this study, we analyzed the V4 region of the 18S rDNA of 30 strains of Pseudo-nitzschia multistriata collected from the coasts of China. The results showed that each P. multistriata strain harbored about a hundred of unique 18S rDNA V4 sequence varieties, of which each represented by a unique amplicon sequence variant (ASV). This study demonstrated the extensive degree of IGVs in P. multistriata strains, suggesting that IGVs may also present in other Pseudo-nitzschia species and other phytoplankton species. Understanding the scope and levels of IGVs is crucial for accurately interpreting the results of metabarcoding analysis.
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Affiliation(s)
- Hui Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Kuiyan Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ziyan He
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhangxi Hu
- Department of Aquaculture, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Weizhou Chen
- Institution of Marine Biology, Shantou University, Shantou, Guangdong 515063, China
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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Huang X, Cui J, Qiang W, Ye J, Wang Y, Xie X, Li Y, Dai J. Storage-D: A user-friendly platform that enables practical and personalized DNA data storage. IMETA 2024; 3:e168. [PMID: 38882485 PMCID: PMC11170965 DOI: 10.1002/imt2.168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/30/2023] [Accepted: 11/14/2023] [Indexed: 06/18/2024]
Abstract
Deoxyribonucleic acid (DNA) has been suggested as a very promising medium for data storage in recent years. Although numerous studies have advocated for DNA data storage, its practical application remains obscure and there is a lack of a user-oriented platform. Here, we developed a DNA data storage platform, named Storage-D, which allows users to convert their data into DNA sequences of any length and vice versa by selecting algorithms, error-correction, random-access, and codec pin strategies in terms of their own choice. It incorporates a newly designed "Wukong" algorithm, which provides over 20 trillion codec pins for data privacy use. This algorithm can also control GC content to the selected standard, as well as adjust the homopolymer run length to a defined level, while maintaining a high coding potential of ~1.98 bis/nt, allowing it to outperform previous algorithms. By connecting to a commercial DNA synthesis and sequencing platform with "Storage-D," we successfully stored "Diagnosis and treatment protocol for COVID-19 patients" into 200 nt oligo pools in vitro, and 500 bp genes in vivo which replicated in both normal and extreme bacteria. Together, this platform allows for practical and personalized DNA data storage, potentially with a wide range of applications.
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Affiliation(s)
- Xiaoluo Huang
- Shenzhen Key Laboratory of Synthetic Genomics Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences Shenzhen China
| | - Junting Cui
- Shenzhen Key Laboratory of Synthetic Genomics Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences Shenzhen China
| | - Wei Qiang
- Shenzhen Key Laboratory of Synthetic Genomics Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences Shenzhen China
| | - Jianwen Ye
- School of Biology and Biological Engineering South China University of Technology Guangzhou China
| | - Yu Wang
- Shenzhen Key Laboratory of Synthetic Genomics Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences Shenzhen China
| | - Xinying Xie
- School of Biology and Biological Engineering South China University of Technology Guangzhou China
| | - Yuanzhen Li
- Shenzhen Key Laboratory of Synthetic Genomics Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences Shenzhen China
| | - Junbiao Dai
- Shenzhen Key Laboratory of Synthetic Genomics Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences Shenzhen China
- Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen China
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García-López R, Taboada B, Zárate S, Muñoz-Medina JE, Salas-Lais AG, Herrera-Estrella A, Boukadida C, Vazquez-Perez JA, Gómez-Gil B, Sanchez-Flores A, Arias CF. Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover. Microb Genom 2024; 10:001220. [PMID: 38512312 PMCID: PMC11004493 DOI: 10.1099/mgen.0.001220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
A total of 14 973 alleles in 29 661 sequenced samples collected between March 2021 and January 2023 by the Mexican Consortium for Genomic Surveillance (CoViGen-Mex) and collaborators were used to construct a thorough map of mutations of the Mexican SARS-CoV-2 genomic landscape containing Intra-Patient Minor Allelic Variants (IPMAVs), which are low-frequency alleles not ordinarily present in a genomic consensus sequence. This additional information proved critical in identifying putative coinfecting variants included alongside the most common variants, B.1.1.222, B.1.1.519, and variants of concern (VOCs) Alpha, Gamma, Delta, and Omicron. A total of 379 coinfection events were recorded in the dataset (a rate of 1.28 %), resulting in the first such catalogue in Mexico. The most common putative coinfections occurred during the spread of Delta or after the introduction of Omicron BA.2 and its descendants. Coinfections occurred constantly during periods of variant turnover when more than one variant shared the same niche and high infection rate was observed, which was dependent on the local variants and time. Coinfections might occur at a higher frequency than customarily reported, but they are often ignored as only the consensus sequence is reported for lineage identification.
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Affiliation(s)
- Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Angel Gustavo Salas-Lais
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Joel Armando Vazquez-Perez
- Laboratorio de Biología Molecular de Enfermedades Emergentes y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Unidad Mazatlán, Mazatlán, Sinaloa, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Sun W, Perkins M, Huyghe M, Faraldo MM, Fre S, Perié L, Lyne AM. Extracting, filtering and simulating cellular barcodes using CellBarcode tools. NATURE COMPUTATIONAL SCIENCE 2024; 4:128-143. [PMID: 38374363 PMCID: PMC10899113 DOI: 10.1038/s43588-024-00595-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024]
Abstract
Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of barcode types supported or the analysis strategies implemented. As such, there is a need for more versatile and efficient tools for barcode extraction, as well as for tools to investigate which factors impact barcode detection and which filtering strategies to best apply. Here we introduce the package CellBarcode and its barcode simulation kit, CellBarcodeSim, that allows efficient and versatile barcode extraction and filtering for a range of barcode types from bulk or single-cell sequencing data using a variety of filtering strategies. Using the barcode simulation kit and biological data, we explore the technical and biological factors influencing barcode identification and provide a decision tree on how to optimize barcode identification for different barcode settings. We believe that CellBarcode and CellBarcodeSim have the capability to enhance the reproducibility and interpretation of barcode results across studies.
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Affiliation(s)
- Wenjie Sun
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France.
| | - Meghan Perkins
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Mathilde Huyghe
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Marisa M Faraldo
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Silvia Fre
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France.
| | - Anne-Marie Lyne
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France.
- INSERM U900, Paris, France.
- MINES ParisTech, CBIO-Centre for Computational Biology, PSL Research University, Paris, France.
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10
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Usman S, Bushaala A, Teh MT, Waseem A. Site-Directed Mutagenesis to Mutate Multiple Residues in a Single Reaction. Methods Mol Biol 2024; 2849:123-133. [PMID: 38180689 DOI: 10.1007/7651_2023_511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Site-directed mutagenesis (SDM) is a technique that allows mutation of specific nucleotide(s) in a codon to study its functional implications in a protein. Commercial kits are available, which require high-performance liquid chromatography purified oligos for this purpose. These kits are expensive, and they are not very efficient, so one has to sequence several clones to get a desired one. We present here a simple method that requires only crude oligos, commercially available high-fidelity enzymes, and the success rate is close to 100%. In addition, up to 6 different mutations can be introduced in one reaction without causing any fortuitous change in the vector backbone. Using this strategy, we have introduced 32 S/T➔A substitutions in the N-terminus head and 13 changes in the C-terminus tail domain of vimentin.
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Affiliation(s)
- Saima Usman
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Antesar Bushaala
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Muy Teck Teh
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ahmad Waseem
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
- Centre for Oral Immunobiology and Regenerative Medicine, Blizard Institute, London, UK.
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11
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Nuryana I, Laksmi FA, Dewi KS, Akbar FR, Nurhayati, Harmoko R. Codon optimization of a gene encoding DNA polymerase from Pyrococcus furiosus and its expression in Escherichia coli. J Genet Eng Biotechnol 2023; 21:129. [PMID: 37987973 PMCID: PMC10663413 DOI: 10.1186/s43141-023-00605-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND DNA polymerase is an essential component in PCR assay for DNA synthesis. Improving DNA polymerase with characteristics indispensable for a powerful assay is crucial because it can be used in wide-range applications. Derived from Pyrococcus furiosus, Pfu DNA polymerase (Pfu pol) is one of the excellent polymerases due to its high fidelity. Therefore, we aimed to develop Pfu pol from a synthetic gene with codon optimization to increase its protein yield in Escherichia coli. RESULTS Recombinant Pfu pol was successfully expressed and purified with a two-step purification process using nickel affinity chromatography, followed by anion exchange chromatography. Subsequently, the purified Pfu pol was confirmed by Western blot analysis, resulting in a molecular weight of approximately 90 kDa. In the final purification process, we successfully obtained a large amount of purified enzyme (26.8 mg/L). Furthermore, the purified Pfu pol showed its functionality and efficiency when tested for DNA amplification using the standard PCR. CONCLUSIONS Overall, a high-level expression of recombinant Pfu pol was achieved by employing our approach in the present study. In the future, our findings will be useful for studies on synthesizing recombinant DNA polymerase in E. coli expression system.
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Affiliation(s)
- Isa Nuryana
- Research Center for Applied Microbiology, National Research and Innovation Agency, Jalan Raya Bogor Km 46, Cibinong, Bogor, 16911, Indonesia
| | - Fina Amreta Laksmi
- Research Center for Applied Microbiology, National Research and Innovation Agency, Jalan Raya Bogor Km 46, Cibinong, Bogor, 16911, Indonesia.
| | - Kartika Sari Dewi
- Research Center for Genetic Engineering, National Research and Innovation Agency, Jalan Raya Bogor Km 46, Cibinong, Bogor, 16911, Indonesia
| | - Faiz Raihan Akbar
- Department of Biology, Faculty of Sciences and Mathematics, Universitas Diponegoro, Jalan Prof Soedarto, SH, Kampus UNDIP Tembalang, Semarang, 50275, Indonesia
| | - Nurhayati
- Department of Biology, Faculty of Sciences and Mathematics, Universitas Diponegoro, Jalan Prof Soedarto, SH, Kampus UNDIP Tembalang, Semarang, 50275, Indonesia
| | - Rikno Harmoko
- Research Center for Genetic Engineering, National Research and Innovation Agency, Jalan Raya Bogor Km 46, Cibinong, Bogor, 16911, Indonesia
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12
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Gimpel AL, Stark WJ, Heckel R, Grass RN. A digital twin for DNA data storage based on comprehensive quantification of errors and biases. Nat Commun 2023; 14:6026. [PMID: 37758710 PMCID: PMC10533828 DOI: 10.1038/s41467-023-41729-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Archiving data in synthetic DNA offers unprecedented storage density and longevity. Handling and storage introduce errors and biases into DNA-based storage systems, necessitating the use of Error Correction Coding (ECC) which comes at the cost of added redundancy. However, insufficient data on these errors and biases, as well as a lack of modeling tools, limit data-driven ECC development and experimental design. In this study, we present a comprehensive characterisation of the error sources and biases present in the most common DNA data storage workflows, including commercial DNA synthesis, PCR, decay by accelerated aging, and sequencing-by-synthesis. Using the data from 40 sequencing experiments, we build a digital twin of the DNA data storage process, capable of simulating state-of-the-art workflows and reproducing their experimental results. We showcase the digital twin's ability to replace experiments and rationalize the design of redundancy in two case studies, highlighting opportunities for tangible cost savings and data-driven ECC development.
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Affiliation(s)
- Andreas L Gimpel
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Wendelin J Stark
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Reinhard Heckel
- Department of Computer Engineering, Technical University of Munich, Arcistrasse 21, 80333, Munich, Germany
| | - Robert N Grass
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland.
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13
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Light K, Brooks J, Choi YS. Manipulative-based Activity Using Pop Beads for Demonstration of Sanger Sequencing. JOURNAL OF CHEMICAL EDUCATION 2023; 100:3138-3143. [PMID: 37577455 PMCID: PMC10414030 DOI: 10.1021/acs.jchemed.3c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 06/28/2023] [Indexed: 08/15/2023]
Abstract
Sanger sequencing, also known as dideoxy sequencing, is a widely used method for DNA sequencing, particularly for cloned plasmids and clinical samples. This technique requires a combination of essential biochemistry skills, such as a chain-termination reaction, gel electrophoresis, and fluorescence detection. Unfortunately, there is a lack of activities that replicate the Sanger sequencing process for students to learn and practice these skills. To address this issue, a manipulative-based Sanger sequencing activity was developed that incorporates colorful pop beads to demonstrate a chain-termination reaction, separation of products, and fluorescence detection. The beads represent deoxynucleotides and dideoxynucleotides, allowing for a visual representation of DNA fragment generation. This kinesthetic learning activity offers a high visual impact for students, aiding in their understanding of the Sanger sequencing process, and can also be used to illustrate polymerase chain reaction (PCR)-based techniques.
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Affiliation(s)
- Kylie Light
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
| | - Jordan Brooks
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
| | - Yun-Seok Choi
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
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14
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Khumela R, Kabue JP, de Moraes MTB, Traore AN, Potgieter N. Prevalence of Human Norovirus GII.4 Sydney 2012 [P31] between 2019 and 2021 among Young Children from Rural Communities in South Africa. Viruses 2023; 15:1682. [PMID: 37632024 PMCID: PMC10458076 DOI: 10.3390/v15081682] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/31/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Acute gastroenteritis (AGE) accounts for considerable morbidity and mortality in the paediatric population worldwide, especially in low-income countries. Human norovirus (HNoV), particularly GII.4 strains, are important agents of AGE. This study aimed to detect and characterise HNoV in children with and without AGE. Between 2019 and 2021, 300 stool samples (200 AGE and 100 without AGE) were collected from children below 5 years of age referred to the healthcare facilities of the rural communities of Vhembe District, South Africa. After detection using real-time RT-PCR, HNoV positive samples were subjected to RT-PCR and Sanger sequencing. Partial nucleotide sequences (capsid/RdRp) were aligned using the Muscle tool, and phylogenetic analysis was performed using MEGA 11. The nucleotides' percent identity among HNoV strains was compared using ClustalW software. A significant difference in HNoV prevalence between AGE children (37%; 74/200) and non-AGE (14%; 14/100) was confirmed (p < 0.0001). Genogroup II (GII) HNoV was predominant in AGE children (80%; 59/74), whereas most non-AGE children were infected by the GI norovirus genogroup (64%; 9/14). GII.4 Sydney 2012 [P31] strains were dominant (59%; 19/32) during the study period. A phylogenetic analysis revealed a close relationship between the HNoV strains identified in this study and those circulating worldwide; however, ClustalW showed less than 50% nucleotide similarity between strains from this study and those from previously reported norovirus studies in the same region. Our findings indicate significant changes over time in the circulation of HNoV strains, as well as the association between high HNoV prevalence and AGE symptoms within the study area. The monitoring of HuNoV epidemiology, along with stringent preventive measures to mitigate the viral spread and the burden of AGE, are warranted.
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Affiliation(s)
- Ronewa Khumela
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa; (J.-P.K.); (A.N.T.); (N.P.)
| | - Jean-Pierre Kabue
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa; (J.-P.K.); (A.N.T.); (N.P.)
| | - Marcia Terezinha Baroni de Moraes
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Avenida Brazil, 4365-Manguinhos, Rio de Janeiro 21040-360, RJ, Brazil;
| | - Afsatou Ndama Traore
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa; (J.-P.K.); (A.N.T.); (N.P.)
| | - Natasha Potgieter
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa; (J.-P.K.); (A.N.T.); (N.P.)
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15
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Ordóñez CD, Redrejo-Rodríguez M. DNA Polymerases for Whole Genome Amplification: Considerations and Future Directions. Int J Mol Sci 2023; 24:9331. [PMID: 37298280 PMCID: PMC10253169 DOI: 10.3390/ijms24119331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
In the same way that specialized DNA polymerases (DNAPs) replicate cellular and viral genomes, only a handful of dedicated proteins from various natural origins as well as engineered versions are appropriate for competent exponential amplification of whole genomes and metagenomes (WGA). Different applications have led to the development of diverse protocols, based on various DNAPs. Isothermal WGA is currently widely used due to the high performance of Φ29 DNA polymerase, but PCR-based methods are also available and can provide competent amplification of certain samples. Replication fidelity and processivity must be considered when selecting a suitable enzyme for WGA. However, other properties, such as thermostability, capacity to couple replication, and double helix unwinding, or the ability to maintain DNA replication opposite to damaged bases, are also very relevant for some applications. In this review, we provide an overview of the different properties of DNAPs widely used in WGA and discuss their limitations and future research directions.
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Affiliation(s)
- Carlos D. Ordóñez
- CIC bioGUNE, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain
| | - Modesto Redrejo-Rodríguez
- Department of Biochemistry, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas “Alberto Sols”, CSIC-UAM, 28029 Madrid, Spain
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16
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Ceylan HK. Enhanced Biomass Production of Recombinant Pfu DNA Polymerase Producer Escherichia coli BL21(DE3) by Optimization of Induction Variables Using Response Surface Methodology. Protein J 2023:10.1007/s10930-023-10122-8. [PMID: 37199865 DOI: 10.1007/s10930-023-10122-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2023] [Indexed: 05/19/2023]
Abstract
Pfu DNA polymerase is one of the most preferred molecular enzymes that is isolated from the hyperthermophilic Pyrococcus furiosus and used for high-throughput DNA synthesis by the polymerase chain reaction. Therefore, an efficient Pfu DNA polymerase production method is necessary for molecular techniques. In the present study, Pfu DNA polymerase was expressed in recombinant Escherichia coli BL21(DE3) and significant parameters for the biomass production were optimized using the central composite design which is the most popular method of response surface methodology. Induction conditions including cell density prior induction (OD600nm), post-induction temperature, IPTG concentration, and post-induction time and their interactions on biomass production were investigated. The maximum biomass production (14.1 g/L) in shake flasks was achieved using the following predicted optimal conditions: OD600nm before induction of 0.4 and the induction at 32 °C for 7.7 h, with 0.6 mM IPTG. Optimized culture conditions were implemented to scale up experiments. 22% and 70% increase in biomass production was achieved in 3 L and 10 L bioreactors, respectively as compared to initial biomass production observed in unoptimized conditions. Similary, a 30% increase of Pfu DNA polymerase production was obtained after the optimization. The polymerase activity of the purifed Pfu DNA polymerase was assessed by PCR amplification and determined as 2.9 U/μl by comparison with commercial Pfu DNA polymerase. The findings of this study indicated that the proposed fermentation conditions will contribute to further scale‑up studies to enhance the biomass for the production of other recombinant proteins.
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Affiliation(s)
- Hülya Kuduğ Ceylan
- Department of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Tokat Gaziosmanpaşa University, 60250, Tokat, Turkey.
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17
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Sun F, Dong Y, Ni M, Ping Z, Sun Y, Ouyang Q, Qian L. Mobile and Self-Sustained Data Storage in an Extremophile Genomic DNA. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206201. [PMID: 36737843 PMCID: PMC10074078 DOI: 10.1002/advs.202206201] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/11/2023] [Indexed: 06/18/2023]
Abstract
DNA has been pursued as a novel biomaterial for digital data storage. While large-scale data storage and random access have been achieved in DNA oligonucleotide pools, repeated data accessing requires constant data replenishment, and these implementations are confined in professional facilities. Here, a mobile data storage system in the genome of the extremophile Halomonas bluephagenesis, which enables dual-mode storage, dynamic data maintenance, rapid readout, and robust recovery. The system relies on two key components: A versatile genetic toolbox for the integration of 10-100 kb scale synthetic DNA into H. bluephagenesis genome and an efficient error correction coding scheme targeting noisy nanopore sequencing reads. The storage and repeated retrieval of 5 KB data under non-laboratory conditions are demonstrated. The work highlights the potential of DNA data storage in domestic and field scenarios, and expands its application domain from archival data to frequently accessed data.
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Affiliation(s)
- Fajia Sun
- Center for Quantitative BiologyPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
| | - Yiming Dong
- Center for Quantitative BiologyPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
| | - Ming Ni
- Academician Workstation of BGI Synthetic GenomicsBGI‐ShenzhenHuada Comprehensive ParkYantian DistrictShenzhen518083P. R. China
| | - Zhi Ping
- Academician Workstation of BGI Synthetic GenomicsBGI‐ShenzhenHuada Comprehensive ParkYantian DistrictShenzhen518083P. R. China
| | - Yuhui Sun
- Academician Workstation of BGI Synthetic GenomicsBGI‐ShenzhenHuada Comprehensive ParkYantian DistrictShenzhen518083P. R. China
| | - Qi Ouyang
- Center for Quantitative BiologyPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic PhysicsPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
| | - Long Qian
- Center for Quantitative BiologyPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
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18
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Nor Nazli NA, Muthuraju S, Ahmad F, Mohamed Yusoff AA, Jaafar H, Shamsuddin S, Abdullah JM. Characterisation of Primary Human Hippocampal Astrocyte Cell Culture Following Exposure to Hypoxia. Malays J Med Sci 2023; 30:92-106. [PMID: 36875187 PMCID: PMC9984107 DOI: 10.21315/mjms2023.30.1.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/01/2022] [Indexed: 03/05/2023] Open
Abstract
Background The present study aimed to understand the characterisation of human hippocampal astrocyte following hypoxia exposure. Based on the preliminary screening, 15 min was chosen as the time point and the cells were exposed to different oxygen percentages. Methods The Trypan blue viability assay used to examine cell death. Immunofluorescence assay, glial fibrillary acidic protein (GFAP) was used to portray the morphology of astrocytes. The hypoxia-inducible factor 1 (HIF-1) staining was performed to confirm hypoxia induced cell death and there was a dramatic expression of HIF-1α displayed in exposed astrocyte cells compared to the control. In molecular level, genes were chosen, such as glyceraldehyde 3-phosphate dehydrogenase (GAPDH), GFAP, HIF-1α and B-cell lymphoma 2 (Bcl-2) and ran the reverse transcription-polymerase chain reaction (RT-PCR). Results Microscope revealed a filamentous and clear nucleus appearance in a control whereas the rupture nuclei with no rigid structure of the cell were found in the 3% oxygen. The control and hypoxia cells were also stained with the annexin V-fluorescein isothiocyanate (annexin V-FITC). Fluorescence microscope reveals astrocyte cells after hypoxia showed higher expression of nuclei but not in control. Merging PI and FITC showed the differences of nuclei expression between the control and hypoxia. In the molecular analysis, there were significant changes of GFAP, HIF-1α and Bcl-2 in hypoxia exposed cells when compared to the control group. Conclusion Cells that were exposed to hypoxia (3% oxygen for 15 min) clearly showed damage. General view of human hippocampal astrocyte genomic response to hypoxia was obtained.
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Affiliation(s)
- Nurul Atikah Nor Nazli
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.,Brain and Behaviour Cluster, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Sangu Muthuraju
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.,Brain and Behaviour Cluster, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Farizan Ahmad
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.,Brain and Behaviour Cluster, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Abdul Aziz Mohamed Yusoff
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.,Brain and Behaviour Cluster, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Hasnan Jaafar
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Shaharum Shamsuddin
- Department of Biomedicine, School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Jafri Malin Abdullah
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.,Brain and Behaviour Cluster, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
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19
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Cepleanu-Pascu IA, Stan M, Cocioba S, Stoica I. Easy method for six-fragment Golden Gate Assembly of modular vectors. Biotechniques 2023; 74:85-99. [PMID: 36691899 DOI: 10.2144/btn-2022-0041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Efficient cloning techniques are a requirement for synthetic biology. This study provides a simplified cloning method based on Golden Gate Assembly that can be used for rapid vector construction. The building of multiple expression vectors with customizable modules is achieved in a timely manner with minimal hands-on time by removing unnecessary steps in the workflow. The authors constructed a total of 21 mammalian episomal expression vectors and conducted a fluorescence expression comparison for different regulatory region combinations post-transfection in HEK293T and HEPG2 cells. Screening revealed that using the EF-1α promoter in combination with the bovine growth hormone polyadenylation sequence seemed to perform best in the types of cells tested compared with other variants.
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Affiliation(s)
| | - Miruna Stan
- Department of Biochemistry & Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | | | - Ileana Stoica
- Department of Genetics, Faculty of Biology, University of Bucharest, Bucharest, Romania
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20
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Schjeide BMM, Püschel GP. Determining On-Target, Off-Target, and Copy Number Status of Transgenic Events After CRISPR/Cas9 Targeted AAVS1 Safe-Harbor Modification of iPSCs Using Double-Control Quantitative Copy Number PCR. Curr Protoc 2023; 3:e635. [PMID: 36598341 DOI: 10.1002/cpz1.635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Double-control quantitative copy number PCR (dc-qcnPCR) is a recently described tool that can be used to quantify donor DNA insertions in genetically modified monoclonal cell lines. In conjunction with an insert-confirmation PCR, the technique can quickly and easily identify clones containing on-target heterozygous or homozygous donor DNA integrations and exclude off-target insertions. The genetic manipulation of immortal cell lines is a versatile tool to elucidate cellular signaling pathways and protein functions. Despite recent advances in the precision of genetic engineering tools such as CRISPR/Cas9, transcription-activator-like effector nucleases (TALENs), and zinc-finger nucleases (ZFNs), it is still essential to verify the accurate insertion of the sequence of interest (donor DNA) into the targeted genomic DNA (gDNA) locus. This precise integration into a genetic safe harbor, and exclusion of the donor DNA from functionally relevant genes, can ensure normal cellular functionality. Current methods to analyze the specificity of donor DNA insertions either are cost-prohibitive or create dependency on manufacturers for assay design and production. The dc-qcnPCR method is a simple, yet powerful, approach that can be prepared and carried out in any laboratory equipped with standard molecular biology supplies. Here we provide step-by-step instructions to prepare and perform the dc-qcnPCR, and its companion insert-confirmation PCR, to determine donor DNA insertion numbers in monoclonal cell lines genetically modified through CRISPR/Cas9. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Genetic modification at AAVS1 safe harbor in induced pluripotent stem cells (IMR90-4) using CRISPR/Cas9: from plasmid design to monoclonal expansion Support Protocol 1: Measurement of Gaussia luciferase activity to verify reporter protein functionality Support Protocol 2: Verification of monoclonal expansion using immunofluorescence. Basic Protocol 2: Insert-confirmation PCR Basic Protocol 3: Design and preparation of double-control quantitative copy number PCR reagents and quantification of donor DNA integrations in genetically modified monoclonal cells.
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Affiliation(s)
- Brit-Maren Michaud Schjeide
- Department of Nutritional Biochemistry, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,Department of Nutritional Biochemistry, Faculty of Life Sciences: Food, Nutrition and Health, University of Bayreuth, Kulmbach, Germany
| | - Gerhard Paul Püschel
- Department of Nutritional Biochemistry, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
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21
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Skonieczna K, Ciesielka M, Teresiński G, Grzybowski T. Low-level point heteroplasmy detection in human mitogenomes amplified with different polymerases and sequenced on MiSeq FGx platform. ARCHIVES OF FORENSIC MEDICINE AND CRIMINOLOGY 2023; 73:131-138. [PMID: 38186038 DOI: 10.4467/16891716amsik.23.011.18686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
Introduction Massively parallel sequencing of mitogenomes usually requires prior amplification. The PCR step may influence the quality of the data obtained, especially when low-level heteroplasmy detection is applied. Aim The aim of this study was to compare the reliability of two different DNA polymerases in detecting homoplasmic and heteroplasmic substitutions in human mitogenomes. Material and methods Mitogenomes of five samples were amplified with Long PCR Enzyme Mix from Fermentas or TaKaRa LA Taq DNA Polymerase from TaKaRa. Then, NexteraTM XT DNA libraries were sequenced on MiSeq FGx platform (Illumina). mtDNA substitutions were called for alternative variants above the 1% level. Results All homoplasmic substitutions detected in amplicons generated with polymerases studied here and sequenced on MiSeq FGx system were consistently identified as homoplasmies with alternative sequencing methods. TaKaRa LA Taq DNA Polymerase was found to be less accurate in low-level heteroplasmy detection than Long PCR Enzyme Mix enzyme as more false negative and false positive results were observed for minority variants called above the 1% level. Nevertheless, both PCR systems studied can be successfully used to detect authentic mtDNA substitutions, for which minority variants exceed the 3.61% level assuming at least 10,000x coverage and sequencing Nextera XT DNA libraries on MiSeq FGx machine. Conclusions The accuracy and sensitivity of point heteroplasmy detection with the MiSeq FGx instrument varies on polymerase used for mtDNA amplification. Therefore, it is recommended to validate the laboratory protocols used for mtDNA substitution detection prior to their implementation for the forensic or medical genetics purposes.
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Affiliation(s)
- Katarzyna Skonieczna
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | | | - Grzegorz Teresiński
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Tomasz Grzybowski
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
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22
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Amugune BL, Matharu AK, Ouma P, Mutebi F, Elson L, Fillinger U, Krücken J. Cost-Effective PCR-Based Identification of Tunga penetrans (Siphonaptera) Larvae Extracted from Soil Samples Containing PCR Inhibitor-Rich Material. INSECTS 2022; 14:5. [PMID: 36661934 PMCID: PMC9865934 DOI: 10.3390/insects14010005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Tungiasis is a neglected tropical disease caused by skin-penetrating female Tunga penetrans fleas. Although tungiasis causes severe health problems, its ecology is poorly understood and morphological descriptions of the larvae are unavailable. To identify T. penetrans immature stages and sites where they develop, diagnostic PCRs are required. However, flea larvae feed on soil organic matter rich in PCR inhibitors. Here, three DNA preparation methods, including a soil DNA kit that removes inhibitors, a simple ammonium acetate precipitation approach (AmAcet) and a crude lysate of larvae (CL), were combined with amplification by the highly processive FIREPol® Taq or the inhibitor-resistant Phusion® polymerase. Independent of the polymerase used, the frequency of successful amplification, Cq values and PCR efficacies for the low-cost CL and AmAcet methods were superior to the commercial kit for amplification of a 278 bp partial internal transcribed spacer-2 (ITS-2) and a 730 bp pan-Siphonaptera cytochrome oxidase II PCR. For the CL method combined with Phusion® polymerase, the costs were approximately 20-fold lower than for the methods based on the soil DNA kit, which is a considerable advantage in resource-poor settings. The ITS-2 PCR did not amplify Ctenocephalides felis genomic or Tunga trimammilata ITS-2 plasmid DNA, meaning it can be used to specifically identify T. penetrans.
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Affiliation(s)
- Billy L. Amugune
- International Centre of Insect Physiology and Ecology, Human Health Theme, Nairobi 00100, Kenya
| | - Abneel K. Matharu
- International Centre of Insect Physiology and Ecology, Human Health Theme, Nairobi 00100, Kenya
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Paul Ouma
- International Centre of Insect Physiology and Ecology, Human Health Theme, Nairobi 00100, Kenya
| | - Francis Mutebi
- School of Veterinary Medicine and Animal Resources, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala 10218, Uganda
| | - Lynne Elson
- KEMRI-Wellcome Trust Research Programme, Kilifi 80108, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Ulrike Fillinger
- International Centre of Insect Physiology and Ecology, Human Health Theme, Nairobi 00100, Kenya
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
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23
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Guo Q, Lakatos E, Bakir IA, Curtius K, Graham TA, Mustonen V. The mutational signatures of formalin fixation on the human genome. Nat Commun 2022; 13:4487. [PMID: 36068219 PMCID: PMC9448750 DOI: 10.1038/s41467-022-32041-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/14/2022] [Indexed: 12/02/2022] Open
Abstract
Clinical archives of patient material near-exclusively consist of formalin-fixed and paraffin-embedded (FFPE) blocks. The ability to precisely characterise mutational signatures from FFPE-derived DNA has tremendous translational potential. However, sequencing of DNA derived from FFPE material is known to be riddled with artefacts. Here we derive genome-wide mutational signatures caused by formalin fixation. We show that the FFPE-signature is highly similar to signature 30 (the signature of Base Excision Repair deficiency due to NTHL1 mutations), and chemical repair of DNA lesions leads to a signature highly similar to signature 1 (clock-like signature due to spontaneous deamination of methylcytosine). We demonstrate that using uncorrected mutational catalogues of FFPE samples leads to major mis-assignment of signature activities. To correct for this, we introduce FFPEsig, a computational algorithm to rectify the formalin-induced artefacts in the mutational catalogue. We demonstrate that FFPEsig enables accurate mutational signature analysis both in simulated and whole-genome sequenced FFPE cancer samples. FFPEsig thus provides an opportunity to unlock additional clinical potential of archival patient tissues.
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Affiliation(s)
- Qingli Guo
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Eszter Lakatos
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Genomics and Evolutionary Dynamics Laboratory, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Ibrahim Al Bakir
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Kit Curtius
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
- Genomics and Evolutionary Dynamics Laboratory, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland.
- Institute of Biotechnology, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland.
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24
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Wittmann BJ, Johnston KE, Almhjell PJ, Arnold FH. evSeq: Cost-Effective Amplicon Sequencing of Every Variant in a Protein Library. ACS Synth Biol 2022; 11:1313-1324. [PMID: 35172576 DOI: 10.1021/acssynbio.1c00592] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Widespread availability of protein sequence-fitness data would revolutionize both our biochemical understanding of proteins and our ability to engineer them. Unfortunately, even though thousands of protein variants are generated and evaluated for fitness during a typical protein engineering campaign, most are never sequenced, leaving a wealth of potential sequence-fitness information untapped. Primarily, this is because sequencing is unnecessary for many protein engineering strategies; the added cost and effort of sequencing are thus unjustified. It also results from the fact that, even though many lower-cost sequencing strategies have been developed, they often require at least some access to and experience with sequencing or computational resources, both of which can be barriers to access. Here, we present every variant sequencing (evSeq), a method and collection of tools/standardized components for sequencing a variable region within every variant gene produced during a protein engineering campaign at a cost of cents per variant. evSeq was designed to democratize low-cost sequencing for protein engineers and, indeed, anyone interested in engineering biological systems. Execution of its wet-lab component is simple, requires no sequencing experience to perform, relies only on resources and services typically available to biology labs, and slots neatly into existing protein engineering workflows. Analysis of evSeq data is likewise made simple by its accompanying software (found at github.com/fhalab/evSeq, documentation at fhalab.github.io/evSeq), which can be run on a personal laptop and was designed to be accessible to users with no computational experience. Low-cost and easy-to-use, evSeq makes the collection of extensive protein variant sequence-fitness data practical.
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Affiliation(s)
- Bruce J. Wittmann
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, California 91125, United States
| | - Kadina E. Johnston
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, California 91125, United States
| | - Patrick J. Almhjell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, California 91125, United States
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, California 91125, United States
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25
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Henriksen TV, Drue SO, Frydendahl A, Demuth C, Rasmussen MH, Reinert T, Pedersen JS, Andersen CL. Error Characterization and Statistical Modeling Improves Circulating Tumor DNA Detection by Droplet Digital PCR. Clin Chem 2022; 68:657-667. [PMID: 35030248 DOI: 10.1093/clinchem/hvab274] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/03/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Droplet digital PCR (ddPCR) is a widely used and sensitive application for circulating tumor DNA (ctDNA) detection. As ctDNA is often found in low abundance, methods to separate low-signal readouts from noise are necessary. We aimed to characterize the ddPCR-generated noise and, informed by this, create a sensitive and specific ctDNA caller. METHODS We built 2 novel complimentary ctDNA calling methods: dynamic limit of blank and concentration and assay-specific tumor load estimator (CASTLE). Both methods are informed by empirically established assay-specific noise profiles. Here, we characterized noise for 70 mutation-detecting ddPCR assays by applying each assay to 95 nonmutated samples. Using these profiles, the performance of the 2 new methods was assessed in a total of 9447 negative/positive reference samples and in 1311 real-life plasma samples from colorectal cancer patients. Lastly, performances were compared to 7 literature-established calling methods. RESULTS For many assays, noise increased proportionally with the DNA input amount. Assays targeting transition base changes were more error-prone than transversion-targeting assays. Both our calling methods successfully accounted for the additional noise in transition assays and showed consistently high performance regardless of DNA input amount. Calling methods that were not noise-informed performed less well than noise-informed methods. CASTLE was the only calling method providing a statistical estimate of the noise-corrected mutation level and call certainty. CONCLUSIONS Accurate error modeling is necessary for sensitive and specific ctDNA detection by ddPCR. Accounting for DNA input amounts ensures specific detection regardless of the sample-specific DNA concentration. Our results demonstrate CASTLE as a powerful tool for ctDNA calling using ddPCR.
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Affiliation(s)
- Tenna V Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Simon O Drue
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Amanda Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Christina Demuth
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mads H Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jakob S Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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26
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Gao M, Qi Z, Feng W, Huang H, Xu Z, Dong Z, Xu M, Han J, Kloeber JA, Huang J, Lou Z, Liu S. m6A demethylation of cytidine deaminase APOBEC3B mRNA orchestrates arsenic-induced mutagenesis. J Biol Chem 2022; 298:101563. [PMID: 34998823 PMCID: PMC8814665 DOI: 10.1016/j.jbc.2022.101563] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 12/14/2022] Open
Abstract
The cytidine deaminase APOBEC3B (A3B) is an endogenous inducer of somatic mutations and causes chromosomal instability by converting cytosine to uracil in single-stranded DNA. Therefore, identification of factors and mechanisms that mediate A3B expression will be helpful for developing therapeutic approaches to decrease DNA mutagenesis. Arsenic (As) is one well-known mutagen and carcinogen, but the mechanisms by which it induces mutations have not been fully elucidated. Herein, we show that A3B is upregulated and required for As-induced DNA damage and mutagenesis. We found that As treatment causes a decrease of N6-methyladenosine (m6A) modification near the stop codon of A3B, consequently increasing the stability of A3B mRNA. We further reveal that the demethylase FTO is responsible for As-reduced m6A modification of A3B, leading to increased A3B expression and DNA mutation rates in a manner dependent on the m6A reader YTHDF2. Our in vivo data also confirm that A3B is a downstream target of FTO in As-exposed lung tissues. In addition, FTO protein is highly expressed and positively correlates with the protein levels of A3B in tumor samples from human non-small cell lung cancer patients. These findings indicate a previously unrecognized role of A3B in As-triggered somatic mutation and might open new avenues to reduce DNA mutagenesis by targeting the FTO/m6A axis.
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Affiliation(s)
- Ming Gao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zijuan Qi
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University, Ji'nan, Shandong, China
| | - Wenya Feng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Hongyang Huang
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Zhijie Xu
- Department of Pathology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zheng Dong
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ming Xu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jinxiang Han
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University, Ji'nan, Shandong, China
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, Minnesota, USA
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA.
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA.
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.
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27
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AlJanahi AA, Lazzarotto CR, Chen S, Shin TH, Cordes S, Fan X, Jabara I, Zhou Y, Young DJ, Lee BC, Yu KR, Li Y, Toms B, Tunc I, Hong SG, Truitt LL, Klermund J, Andrieux G, Kim MY, Cathomen T, Gill S, Tsai SQ, Dunbar CE. Prediction and validation of hematopoietic stem and progenitor cell off-target editing in transplanted rhesus macaques. Mol Ther 2022; 30:209-222. [PMID: 34174439 PMCID: PMC8753565 DOI: 10.1016/j.ymthe.2021.06.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/18/2021] [Accepted: 06/21/2021] [Indexed: 01/07/2023] Open
Abstract
The programmable nuclease technology CRISPR-Cas9 has revolutionized gene editing in the last decade. Due to the risk of off-target editing, accurate and sensitive methods for off-target characterization are crucial prior to applying CRISPR-Cas9 therapeutically. Here, we utilized a rhesus macaque model to compare the predictive values of CIRCLE-seq, an in vitro off-target prediction method, with in silico prediction (ISP) based solely on genomic sequence comparisons. We use AmpliSeq HD error-corrected sequencing to validate off-target sites predicted by CIRCLE-seq and ISP for a CD33 guide RNA (gRNA) with thousands of off-target sites predicted by ISP and CIRCLE-seq. We found poor correlation between the sites predicted by the two methods. When almost 500 sites predicted by each method were analyzed by error-corrected sequencing of hematopoietic cells following transplantation, 19 off-target sites revealed insertion or deletion mutations. Of these sites, 8 were predicted by both methods, 8 by CIRCLE-seq only, and 3 by ISP only. The levels of cells with these off-target edits exhibited no expansion or abnormal behavior in vivo in animals followed for up to 2 years. In addition, we utilized an unbiased method termed CAST-seq to search for translocations between the on-target site and off-target sites present in animals following transplantation, detecting one specific translocation that persisted in blood cells for at least 1 year following transplantation. In conclusion, neither CIRCLE-seq or ISP predicted all sites, and a combination of careful gRNA design, followed by screening for predicted off-target sites in target cells by multiple methods, may be required for optimizing safety of clinical development.
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Affiliation(s)
- Aisha A AlJanahi
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biology, Georgetown University, Washington, DC 20057, USA
| | - Cicera R Lazzarotto
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shirley Chen
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Tae-Hoon Shin
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Stefan Cordes
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Xing Fan
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Isabel Jabara
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Yifan Zhou
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - David J Young
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Byung-Chul Lee
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Kyung-Rok Yu
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA; Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yuesheng Li
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | | | - Ilker Tunc
- Bioinformatics and Computational Biology Laboratory, NHLBI, NIH, Bethesda, MD 20892, USA
| | - So Gun Hong
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Lauren L Truitt
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Julia Klermund
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Geoffroy Andrieux
- Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
| | - Miriam Y Kim
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Saar Gill
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shengdar Q Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cynthia E Dunbar
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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28
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Detecting MUC1 Variants in Patients Clinicopathologically Diagnosed With Having Autosomal Dominant Tubulointerstitial Kidney Disease. Kidney Int Rep 2022; 7:857-866. [PMID: 35497811 PMCID: PMC9039432 DOI: 10.1016/j.ekir.2021.12.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/15/2021] [Accepted: 12/28/2021] [Indexed: 11/24/2022] Open
Abstract
Introduction Autosomal dominant tubulointerstitial kidney disease (ADTKD)-MUC1 is predominantly caused by frameshift mutations owing to a single-base insertion into the variable number tandem repeat (VNTR) region in MUC1. Because of the complexity of the variant hotspot, identification using short-read sequencers (SRSs) is challenging. Although recent studies have revealed the usefulness of long-read sequencers (LRSs), the prevalence of MUC1 variants in patients with clinically suspected ADTKD remains unknown. We aimed to clarify this prevalence and the genetic characteristics and clinical manifestations of ADTKD-MUC1 in a Japanese population using an SRS and an LRS. Methods From January 2015 to December 2019, genetic analysis was performed using an SRS in 48 patients with clinically suspected ADTKD. Additional analyses were conducted using an LRS in patients with negative SRS results. Results Short-read sequencing results revealed MUC1 variants in 1 patient harboring a cytosine insertion in the second repeat unit of the VNTR region; however, deeper VNTR regions could not be read by the SRS. Therefore, we conducted long-read sequencing analysis of 39 cases and detected MUC1 VNTR variants in 8 patients (in total, 9 patients from unrelated families). With the inclusion of family-affected patients (n = 31), the median age at the development of end-stage kidney disease (ESKD) was 45 years (95% CI: 40–40 years). Conclusion In Japan, the detection rate of MUC1 variants in patients with clinically suspected ADTKD was 18.8%. More than 20% of patients with negative SRS results had MUC1 variants detected by an LRS.
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29
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Lee SO, Xie Q, Fried SD. Optimized Loopable Translation as a Platform for the Synthesis of Repetitive Proteins. ACS CENTRAL SCIENCE 2021; 7:1736-1750. [PMID: 34729417 PMCID: PMC8554844 DOI: 10.1021/acscentsci.1c00574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Indexed: 06/13/2023]
Abstract
The expression of long proteins with repetitive amino acid sequences often presents a challenge in recombinant systems. To overcome this obstacle, we report a genetic construct that circularizes mRNA in vivo by rearranging the topology of a group I self-splicing intron from T4 bacteriophage, thereby enabling "loopable" translation. Using a fluorescence-based assay to probe the translational efficiency of circularized mRNAs, we identify several conditions that optimize protein expression from this system. Our data suggested that translation of circularized mRNAs could be limited primarily by the rate of ribosomal initiation; therefore, using a modified error-prone PCR method, we generated a library that concentrated mutations into the initiation region of circularized mRNA and discovered mutants that generated markedly higher expression levels. Combining our rational improvements with those discovered through directed evolution, we report a loopable translator that achieves protein expression levels within 1.5-fold of the levels of standard vectorial translation. In summary, our work demonstrates loopable translation as a promising platform for the creation of large peptide chains, with potential utility in the development of novel protein materials.
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30
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Mielinis P, Sukackaitė R, Serapinaitė A, Samoilovas F, Alzbutas G, Matjošaitis K, Lubys A. MuA-based Molecular Indexing for Rare Mutation Detection by Next-Generation Sequencing. J Mol Biol 2021; 433:167209. [PMID: 34419430 DOI: 10.1016/j.jmb.2021.167209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022]
Abstract
Detection of low-frequency mutations in cancer genomes or other heterogeneous cell populations requires high-fidelity sequencing. Molecular barcoding is one of the key technologies that enables the differentiation of true mutations from errors, which can be caused by sequencing or library preparation processes. However, current approaches where barcodes are introduced via primer extension or adaptor ligation do not utilize the full power of barcoding, due to complicated library preparation workflows and biases. Here we demonstrate the remarkable tolerance of MuA transposase to the presence of multiple replacements in transposon sequence, and explore this unique feature to engineer the MuA transposome complex with randomised nucleotides in 12 transposon positions, which can be introduced as a barcode into the target molecule after transposition event. We applied the approach of Unique MuA-based Molecular Indexing (UMAMI) to assess the power of rare mutation detection by shortgun sequencing on the Illumina platform. Our results show that UMAMI allows detection of rare mutations readily and reliably, and in this paper we report error rate values for the number of thermophilic DNA polymerases measured by using UMAMI.
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Affiliation(s)
- Paulius Mielinis
- Thermo Fisher Scientific Baltics UAB, V. A. Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Rasa Sukackaitė
- Thermo Fisher Scientific Baltics UAB, V. A. Graičiūno 8, Vilnius LT-02241, Lithuania.
| | - Aistė Serapinaitė
- Thermo Fisher Scientific Baltics UAB, V. A. Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Faustas Samoilovas
- Thermo Fisher Scientific Baltics UAB, V. A. Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Gediminas Alzbutas
- Thermo Fisher Scientific Baltics UAB, V. A. Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Karolis Matjošaitis
- Thermo Fisher Scientific Baltics UAB, V. A. Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Arvydas Lubys
- Thermo Fisher Scientific Baltics UAB, V. A. Graičiūno 8, Vilnius LT-02241, Lithuania
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Wilson A, Shakhtour L, Ward A, Ren Y, Recarey M, Stevenson E, Korom M, Kovacs C, Benko E, Jones RB, Lynch RM. Characterizing the Relationship Between Neutralization Sensitivity and env Gene Diversity During ART Suppression. Front Immunol 2021; 12:710327. [PMID: 34603284 PMCID: PMC8479156 DOI: 10.3389/fimmu.2021.710327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 08/18/2021] [Indexed: 11/30/2022] Open
Abstract
Although antiretroviral therapy (ART) successfully suppresses HIV-1 replication, ART-treated individuals must maintain therapy to avoid rebound from an integrated viral reservoir. Strategies to limit or clear this reservoir are urgently needed. Individuals infected for longer periods prior to ART appear to harbor more genetically diverse virus, but the roles of duration of infection and viral diversity in the humoral immune response remain to be studied. We aim to clarify a role, if any, for autologous and heterologous antibodies in multi-pronged approaches to clearing infection. To that end, we have characterized the breadths and potencies of antibody responses in individuals with varying durations of infection and HIV-1 envelope (env) gene diversity as well as the sensitivity of their inducible virus reservoir to broadly neutralizing antibodies (bNAbs). Plasma was collected from 8 well-characterized HIV-1+ males on ART with varied durations of active infection. HIV envs from reservoir-derived outgrowth viruses were amplified and single genome sequenced in order to measure genetic diversity in each participant. IgG from plasma was analyzed for binding titers against gp41 and gp120 proteins, and for neutralizing titers against a global HIV-1 reference panel as well as autologous outgrowth viruses. The sensitivity to bNAbs of these same autologous viruses was measured. Overall, we observed that greater env diversity was associated with higher neutralizing titers against the global panel and also increased resistance to certain bNAbs. Despite the presence of robust anti-HIV-1 antibody titers, we did not observe potent neutralization against autologous viruses. In fact, 3 of 8 participants harbored viruses that were completely resistant to the highest tested concentration of autologous IgG. That this lack of neutralization was observed regardless of ART duration or viral diversity suggests that the inducible reservoir harbors 'escaped' viruses (that co-evolved with autologous antibody responses), rather than proviruses archived from earlier in infection. Finally, we observed that viruses resistant to autologous neutralization remained sensitive to bNAbs, especially CD4bs and MPER bNAbs. Overall, our data suggest that the inducible reservoir is relatively resistant to autologous antibodies and that individuals with limited virus variation in the env gene, such as those who start ART early in infection, are more likely to be sensitive to bNAb treatment.
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Affiliation(s)
- Andrew Wilson
- Lynch Lab, Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Leyn Shakhtour
- Lynch Lab, Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Adam Ward
- Jones Lab, Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, United States
- PhD Program in Epidemiology, The George Washington University Milken Institute School of Public Health, Washington, DC, United States
| | - Yanqin Ren
- Jones Lab, Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, United States
| | - Melina Recarey
- Lynch Lab, Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Eva Stevenson
- Jones Lab, Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, United States
| | - Maria Korom
- Lynch Lab, Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Colin Kovacs
- Department of Internal Medicine, Maple Leaf Medical Clinic, Toronto, ON, Canada
| | - Erika Benko
- Department of Internal Medicine, Maple Leaf Medical Clinic, Toronto, ON, Canada
| | - R. Brad Jones
- Jones Lab, Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, United States
| | - Rebecca M. Lynch
- Lynch Lab, Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
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32
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Yenerall P, Kollipara RK, Avila K, Peyton M, Eide CA, Bottomly D, McWeeney SK, Liu Y, Westover KD, Druker BJ, Minna JD, Kittler R. Lentiviral-Driven Discovery of Cancer Drug Resistance Mutations. Cancer Res 2021; 81:4685-4695. [PMID: 34301758 PMCID: PMC8448967 DOI: 10.1158/0008-5472.can-21-1153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/08/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022]
Abstract
Identifying resistance mutations in a drug target provides crucial information. Lentiviral transduction creates multiple types of mutations due to the error-prone nature of the HIV-1 reverse transcriptase (RT). Here we optimized and leveraged this property to identify drug resistance mutations, developing a technique we term LentiMutate. This technique was validated by identifying clinically relevant EGFR resistance mutations, then applied to two additional clinical anticancer drugs: imatinib, a BCR-ABL inhibitor, and AMG 510, a KRAS G12C inhibitor. Novel deletions in BCR-ABL1 conferred resistance to imatinib. In KRAS-G12C or wild-type KRAS, point mutations in the AMG 510 binding pocket or oncogenic non-G12C mutations conferred resistance to AMG 510. LentiMutate should prove highly valuable for clinical and preclinical cancer-drug development. SIGNIFICANCE: LentiMutate can evaluate a drug's on-target activity and can nominate resistance mutations before they occur in patients, which could accelerate and refine drug development to increase the survival of patients with cancer.
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Affiliation(s)
- Paul Yenerall
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, Texas
| | - Rahul K Kollipara
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas
| | - Kimberley Avila
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, Texas
| | - Michael Peyton
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, Texas
| | - Christopher A Eide
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Daniel Bottomly
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Divison of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science Center, Portland, Oregon
| | - Shannon K McWeeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Divison of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science Center, Portland, Oregon
| | - Yan Liu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas
| | - Kenneth D Westover
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, Texas.
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Ralf Kittler
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas.
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
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The Importance of Quality Control of LSDV Live Attenuated Vaccines for Its Safe Application in the Field. Vaccines (Basel) 2021; 9:vaccines9091019. [PMID: 34579256 PMCID: PMC8472990 DOI: 10.3390/vaccines9091019] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 01/25/2023] Open
Abstract
Vaccination is an effective approach to prevent, control and eradicate diseases, including lumpy skin disease (LSD). One of the measures to address farmer hesitation to vaccinate is guaranteeing the quality of vaccine batches. The purpose of this study was to demonstrate the importance of a quality procedure via the evaluation of the LSD vaccine, Lumpivax (Kevevapi). The initial PCR screening revealed the presence of wild type LSD virus (LSDV) and goatpox virus (GTPV), in addition to vaccine LSDV. New phylogenetic PCRs were developed to characterize in detail the genomic content and a vaccination/challenge trial was conducted to evaluate the impact on efficacy and diagnostics. The characterization confirmed the presence of LSDV wild-, vaccine- and GTPV-like sequences in the vaccine vial and also in samples taken from the vaccinated animals. The analysis was also suggestive for the presence of GTPV-LSDV (vaccine/wild) recombinants. In addition, the LSDV status of some of the animal samples was greatly influenced by the differentiating real-PCR used and could result in misinterpretation. Although the vaccine was clinically protective, the viral genomic content of the vaccine (being it multiple Capripox viruses and/or recombinants) and the impact on the diagnostics casts serious doubts of its use in the field.
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Duveau F, Vande Zande P, Metzger BP, Diaz CJ, Walker EA, Tryban S, Siddiq MA, Yang B, Wittkopp PJ. Mutational sources of trans-regulatory variation affecting gene expression in Saccharomyces cerevisiae. eLife 2021; 10:67806. [PMID: 34463616 PMCID: PMC8456550 DOI: 10.7554/elife.67806] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/03/2021] [Indexed: 12/15/2022] Open
Abstract
Heritable variation in a gene’s expression arises from mutations impacting cis- and trans-acting components of its regulatory network. Here, we investigate how trans-regulatory mutations are distributed within the genome and within a gene regulatory network by identifying and characterizing 69 mutations with trans-regulatory effects on expression of the same focal gene in Saccharomyces cerevisiae. Relative to 1766 mutations without effects on expression of this focal gene, we found that these trans-regulatory mutations were enriched in coding sequences of transcription factors previously predicted to regulate expression of the focal gene. However, over 90% of the trans-regulatory mutations identified mapped to other types of genes involved in diverse biological processes including chromatin state, metabolism, and signal transduction. These data show how genetic changes in diverse types of genes can impact a gene’s expression in trans, revealing properties of trans-regulatory mutations that provide the raw material for trans-regulatory variation segregating within natural populations.
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Affiliation(s)
- Fabien Duveau
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States.,Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon, Université de Lyon, Lyon, France
| | - Petra Vande Zande
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Brian Ph Metzger
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Crisandra J Diaz
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Elizabeth A Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Stephen Tryban
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Mohammad A Siddiq
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Bing Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Patricia J Wittkopp
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
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35
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Lee SO, Fried SD. An error prone PCR method for small amplicons. Anal Biochem 2021; 628:114266. [PMID: 34081928 DOI: 10.1016/j.ab.2021.114266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022]
Abstract
Error-prone PCR (epPCR) is a commonly employed approach in molecular biology, especially in directed evolution, to generate libraries of DNA molecules with broad mutational spectrums. Though commonly applied to mutagenize protein coding sequences of several hundreds or thousands of basepairs, we found that commonly used protocols were not suitable for small (<100 bp) amplicons. Here we report a modified error-prone PCR protocol utilizing a Touchdown approach and employing only commercially available components, that should be broadly useful for the researcher interested in concentrating mutations into a small region of plasmid DNA. It will also be useful for achieving very high mutational loads on a standard-sized amplicon.
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Affiliation(s)
- Sea On Lee
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
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36
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Jaroenram W, Hayakijkosol O, Owens L, Elliman J. Establishing a gold standard method for the detection of Cherax reovirus using reverse transcriptase, quantitative, polymerase chain reaction. J Virol Methods 2021; 293:114169. [PMID: 33887279 DOI: 10.1016/j.jviromet.2021.114169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 10/21/2022]
Abstract
Cherax reovirus infects redclaw crayfish (Cherax quadricarinatus) and it may be involved in mortalities between 5-20 % and stunting of up to 40 % of survivors. The sequence of the RNA-dependent RNA polymerase was used to develop a reverse transcription, quantitative, PCR (RT-qPCR) which was specific against seven other crustacean viruses (Athtab bunyavirus, Chequa iflavirus, Macrobrachium rosenbergii nodavirus, Gill-associated virus, Taura syndrome virus, White spot syndrome virus, and Penaeus stylirostris Penstylhamaparvovirus) although GAV produced a reaction that was easily separated by melt curve analysis. A strong linear correlation (r2 = 0.9965) was obtained between viral quantities ranging from 107 to 10 viral copies/reaction with an amplification efficiency of 0.92. This RT-qPCR is 2-times faster and 100 times more sensitive than a standard RT-PCR using agarose gel electrophoresis with the potential to detect the virus down to 7.64 copies/reaction in clinical samples. In clinical crayfish samples, it was able to detect Cherax reovirus in crayfish when the traditional RT-PCR was negative. Its' measurement of uncertainty was less than 2% (0.02-1.9), similar to PCRs for other crustacean viruses. This RT-qPCR is proposed as the gold standard and should be used for the screening of populations of C. quadricarinatus for broodstock before being used in hatcheries or on farms.
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Affiliation(s)
- Wansadaj Jaroenram
- College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 Solander Road, Townsville, QLD, 4811, Australia.
| | - Orachun Hayakijkosol
- College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 Solander Road, Townsville, QLD, 4811, Australia.
| | - Leigh Owens
- College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 Solander Road, Townsville, QLD, 4811, Australia.
| | - Jennifer Elliman
- College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 Solander Road, Townsville, QLD, 4811, Australia.
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37
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Vessies DCL, Linders TC, Lanfermeijer M, Ramkisoensing KL, van der Noort V, Schouten RD, Meijer GA, van den Heuvel MM, Monkhorst K, van den Broek D. An Automated Correction Algorithm (ALPACA) for ddPCR Data Using Adaptive Limit of Blank and Correction of False Positive Events Improves Specificity of Mutation Detection. Clin Chem 2021; 67:959-967. [PMID: 33842952 DOI: 10.1093/clinchem/hvab040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/17/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Bio-Rad droplet-digital PCR is a highly sensitive method that can be used to detect tumor mutations in circulating cell-free DNA (cfDNA) of patients with cancer. Correct interpretation of ddPCR results is important for optimal sensitivity and specificity. Despite its widespread use, no standardized method to interpret ddPCR data is available, nor have technical artifacts affecting ddPCR results been widely studied. METHODS False positive rates were determined for 6 ddPCR assays at variable amounts of input DNA, revealing polymerase induced false positive events (PIFs) and other false positives. An in silico correction algorithm, known as the adaptive LoB and PIFs: an automated correction algorithm (ALPACA), was developed to remove PIFs and apply an adaptive limit of blank (LoB) to individual samples. Performance of ALPACA was compared to a standard strategy (no PIF correction and static LoB = 3) using data from commercial reference DNA, healthy volunteer cfDNA, and cfDNA from a real-life cohort of 209 patients with stage IV nonsmall cell lung cancer (NSCLC) whose tumor and cfDNA had been molecularly profiled. RESULTS Applying ALPACA reduced false positive results in healthy cfDNA compared to the standard strategy (specificity 98 vs 88%, P = 10-5) and stage IV NSCLC patient cfDNA (99 vs 93%, P = 10-11), while not affecting sensitivity in commercial reference DNA (70 vs 68% P = 0.77) or patient cfDNA (82 vs 88%, P = 0.13). Overall accuracy in patient samples was improved (98 vs 92%, P = 10-7). CONCLUSIONS Correction of PIFs and application of an adaptive LoB increases specificity without a loss of sensitivity in ddPCR, leading to a higher accuracy in a real-life cohort of patients with stage IV NSCLC.
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Affiliation(s)
- Daan C L Vessies
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Theodora C Linders
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mirthe Lanfermeijer
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | | | - Robert D Schouten
- Department of Pulmonology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, the Netherlands
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38
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Chen F, Li YY, Yu YL, Dai J, Huang JL, Lin J. Simplified plasmid cloning with a universal MCS design and bacterial in vivo assembly. BMC Biotechnol 2021; 21:24. [PMID: 33722223 PMCID: PMC7962268 DOI: 10.1186/s12896-021-00679-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ability to clone DNA sequences quickly and precisely into plasmids is essential for molecular biology studies. The recent development of seamless cloning technologies has made significant improvements in plasmid construction, but simple and reliable tools are always desirable for time- and labor-saving purposes. RESULTS We developed and standardized a plasmid cloning protocol based on a universal MCS (Multiple Cloning Site) design and bacterial in vivo assembly. With this method, the vector is linearized first by PCR (Polymerase Chain Reaction) or restriction digestion. Then a small amount (10 ~ 20 ng) of this linear vector can be mixed with a PCR-amplified insert (5× molar ratio against vector) and transformed directly into competent E. coli cells to obtain the desired clones through in vivo assembly. Since we used a 36-bp universal MCS as the homologous linker, any PCR-amplified insert with ~ 15 bp compatible termini can be cloned into the vector with high fidelity and efficiency. Thus, the need for redesigning insert-amplifying primers according to various vector sequences and the following PCR procedures was eliminated. CONCLUSIONS Our protocol significantly reduced hands-on time for preparing transformation reactions, had excellent reliability, and was confirmed to be a rapid and versatile plasmid cloning technique. The protocol contains mostly mixing steps, making it an extremely automation-friendly and promising tool in modern biology studies.
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Affiliation(s)
- Fan Chen
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China.
| | - Yi-Ya Li
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
| | - Yan-Li Yu
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
| | - Jie Dai
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
| | - Jin-Ling Huang
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
| | - Jie Lin
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
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39
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Moriarty RV, Fesser N, Sutton MS, Venturi V, Davenport MP, Schlub T, O'Connor SL. Validation of multiplex PCR sequencing assay of SIV. Virol J 2021; 18:21. [PMID: 33451356 PMCID: PMC7810186 DOI: 10.1186/s12985-020-01473-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 12/21/2020] [Indexed: 11/24/2022] Open
Abstract
Background The generation of accurate and reproducible viral sequence data is necessary to understand the diversity present in populations of RNA viruses isolated from clinical samples. While various sequencing methods are available, they often require high quality templates and high viral titer to ensure reliable data. Methods We modified a multiplex PCR and sequencing approach to characterize populations of simian immunodeficiency virus (SIV) isolated from nonhuman primates. We chose this approach with the aim of reducing the number of required input templates while maintaining fidelity and sensitivity. We conducted replicate sequencing experiments using different numbers of quantified viral RNA (vRNA) or viral cDNA as input material. We performed assays with clonal SIVmac239 to detect false positives, and we mixed SIVmac239 and a variant with 24 point mutations (SIVmac239-24X) to measure variant detection sensitivity. Results We found that utilizing a starting material of quantified viral cDNA templates had a lower rate of false positives and increased reproducibility when compared to that of quantified vRNA templates. This study identifies the importance of rigorously validating deep sequencing methods and including replicate samples when using a new method to characterize low frequency variants in a population with a small number of templates. Conclusions Because the need to generate reproducible and accurate sequencing data from diverse viruses from low titer samples, we modified a multiplex PCR and sequencing approach to characterize SIV from populations from non-human primates. We found that increasing starting template numbers increased the reproducibility and decreased the number of false positives identified, and this was further seen when cDNA was used as a starting material. Ultimately, we highlight the importance of vigorously validating methods to prevent overinterpretation of low frequency variants in a sample.
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Affiliation(s)
- Ryan V Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Dr, Madison, WI, 53711, USA
| | - Nicolas Fesser
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Dr, Madison, WI, 53711, USA
| | - Matthew S Sutton
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Dr, Madison, WI, 53711, USA
| | - Vanessa Venturi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Miles P Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Timothy Schlub
- Faculty of Medicine and Health, Sydney School of Public Health, University of Sydney, Sydney, NSW, 2000, Australia
| | - Shelby L O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Dr, Madison, WI, 53711, USA.
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40
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D'Ercole J, Prosser SWJ, Hebert PDN. A SMRT approach for targeted amplicon sequencing of museum specimens (Lepidoptera)-patterns of nucleotide misincorporation. PeerJ 2021; 9:e10420. [PMID: 33520432 PMCID: PMC7811786 DOI: 10.7717/peerj.10420] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 11/02/2020] [Indexed: 12/28/2022] Open
Abstract
Natural history collections are a valuable resource for molecular taxonomic studies and for examining patterns of evolutionary diversification, particularly in the case of rare or extinct species. However, the recovery of sequence information is often complicated by DNA degradation. This article describes use of the Sequel platform (Pacific Biosciences) to recover the 658 bp barcode region of the mitochondrial cytochrome c oxidase I (COI) gene from 380 butterflies with an average age of 50 years. Nested multiplex PCR was employed for library preparation to facilitate sequence recovery from extracts with low concentrations of highly degraded DNA. By employing circular consensus sequencing (CCS) of short amplicons (circa 150 bp), full-length barcodes could be assembled without a reference sequence, an important advance from earlier protocols which required reference sequences to guide contig assembly. The Sequel protocol recovered COI sequences (499 bp on average) from 318 of 380 specimens (84%), much higher than for Sanger sequencing (26%). Because each read derives from a single molecule, it was also possible to quantify the incidence of substitutions arising from DNA damage. In agreement with past work on sequence changes induced by DNA degradation, the transition C/G → T/A was the most prevalent category of change, but its rate of occurrence (4.58E−4) was so low that it did not impede the recovery of reliable sequences. Because the current protocol recovers COI sequence from most museum specimens, and because sequence fidelity is unaffected by nucleotide misincorporations, large-scale sequence characterization of museum specimens is feasible.
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Affiliation(s)
- Jacopo D'Ercole
- Centre for Biodiversity Genomics, Guelph, ON, Canada.,Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | | | - Paul D N Hebert
- Centre for Biodiversity Genomics, Guelph, ON, Canada.,Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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41
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Ji J, Day A. Construction of a highly error-prone DNA polymerase for developing organelle mutation systems. Nucleic Acids Res 2020; 48:11868-11879. [PMID: 33135056 PMCID: PMC7708058 DOI: 10.1093/nar/gkaa929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/30/2020] [Accepted: 10/06/2020] [Indexed: 12/21/2022] Open
Abstract
A novel family of DNA polymerases replicates organelle genomes in a wide distribution of taxa encompassing plants and protozoans. Making error-prone mutator versions of gamma DNA polymerases revolutionised our understanding of animal mitochondrial genomes but similar advances have not been made for the organelle DNA polymerases present in plant mitochondria and chloroplasts. We tested the fidelities of error prone tobacco organelle DNA polymerases using a novel positive selection method involving replication of the phage lambda cI repressor gene. Unlike gamma DNA polymerases, ablation of 3'-5' exonuclease function resulted in a modest 5-8-fold error rate increase. Combining exonuclease deficiency with a polymerisation domain substitution raised the organelle DNA polymerase error rate by 140-fold relative to the wild type enzyme. This high error rate compares favourably with error-rates of mutator versions of animal gamma DNA polymerases. The error prone organelle DNA polymerase introduced mutations at multiple locations ranging from two to seven sites in half of the mutant cI genes studied. Single base substitutions predominated including frequent A:A (template: dNMP) mispairings. High error rate and semi-dominance to the wild type enzyme in vitro make the error prone organelle DNA polymerase suitable for elevating mutation rates in chloroplasts and mitochondria.
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MESH Headings
- Amino Acid Sequence
- Bacterial Outer Membrane Proteins/chemistry
- Bacterial Outer Membrane Proteins/genetics
- Bacterial Outer Membrane Proteins/metabolism
- Binding Sites
- Chloroplasts/genetics
- Chloroplasts/metabolism
- Cloning, Molecular
- DNA Polymerase gamma/chemistry
- DNA Polymerase gamma/genetics
- DNA Polymerase gamma/metabolism
- DNA Replication
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Mitochondria/genetics
- Mitochondria/metabolism
- Models, Molecular
- Mutation
- Phylogeny
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Polymorphism, Single Nucleotide
- Porins/chemistry
- Porins/genetics
- Porins/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Selection, Genetic
- Sequence Alignment
- Sequence Homology, Amino Acid
- Nicotiana/classification
- Nicotiana/genetics
- Nicotiana/metabolism
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Affiliation(s)
- Junwei Ji
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Anil Day
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
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42
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Crossley BM, Bai J, Glaser A, Maes R, Porter E, Killian ML, Clement T, Toohey-Kurth K. Guidelines for Sanger sequencing and molecular assay monitoring. J Vet Diagn Invest 2020; 32:767-775. [PMID: 32070230 PMCID: PMC7649556 DOI: 10.1177/1040638720905833] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Genetic sequencing, or DNA sequencing, using the Sanger technique has become widely used in the veterinary diagnostic community. This technology plays a role in verification of PCR results and is used to provide the genetic sequence data needed for phylogenetic analysis, epidemiologic studies, and forensic investigations. The Laboratory Technology Committee of the American Association of Veterinary Laboratory Diagnosticians has prepared guidelines for sample preparation, submission to sequencing facilities or instrumentation, quality assessment of nucleic acid sequence data performed, and for generating basic sequencing data and phylogenetic analysis for diagnostic applications. This guidance is aimed at assisting laboratories in providing consistent, high-quality, and reliable sequence data when using Sanger-based genetic sequencing as a component of their laboratory services.
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Affiliation(s)
- Beate M. Crossley
- Beate M. Crossley, California Animal Health and Food Safety Laboratory, University of California, Davis, PO Box 1770, Davis, CA 95616.
| | - Jianfa Bai
- California Animal Health and Food Safety Laboratory, University of California–Davis, Davis, CA (Crossley, Toohey-Kurth)
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser)
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai, Porter)
- National Veterinary Services Laboratories, Ames, IA (Killian)
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD (Clement)
- Veterinary Diagnostic Laboratory, Michigan State University, Lansing, MI (Maes)
| | - Amy Glaser
- California Animal Health and Food Safety Laboratory, University of California–Davis, Davis, CA (Crossley, Toohey-Kurth)
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser)
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai, Porter)
- National Veterinary Services Laboratories, Ames, IA (Killian)
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD (Clement)
- Veterinary Diagnostic Laboratory, Michigan State University, Lansing, MI (Maes)
| | - Roger Maes
- California Animal Health and Food Safety Laboratory, University of California–Davis, Davis, CA (Crossley, Toohey-Kurth)
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser)
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai, Porter)
- National Veterinary Services Laboratories, Ames, IA (Killian)
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD (Clement)
- Veterinary Diagnostic Laboratory, Michigan State University, Lansing, MI (Maes)
| | - Elizabeth Porter
- California Animal Health and Food Safety Laboratory, University of California–Davis, Davis, CA (Crossley, Toohey-Kurth)
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser)
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai, Porter)
- National Veterinary Services Laboratories, Ames, IA (Killian)
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD (Clement)
- Veterinary Diagnostic Laboratory, Michigan State University, Lansing, MI (Maes)
| | - Mary Lea Killian
- California Animal Health and Food Safety Laboratory, University of California–Davis, Davis, CA (Crossley, Toohey-Kurth)
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser)
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai, Porter)
- National Veterinary Services Laboratories, Ames, IA (Killian)
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD (Clement)
- Veterinary Diagnostic Laboratory, Michigan State University, Lansing, MI (Maes)
| | - Travis Clement
- California Animal Health and Food Safety Laboratory, University of California–Davis, Davis, CA (Crossley, Toohey-Kurth)
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser)
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai, Porter)
- National Veterinary Services Laboratories, Ames, IA (Killian)
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD (Clement)
- Veterinary Diagnostic Laboratory, Michigan State University, Lansing, MI (Maes)
| | - Kathy Toohey-Kurth
- California Animal Health and Food Safety Laboratory, University of California–Davis, Davis, CA (Crossley, Toohey-Kurth)
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser)
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai, Porter)
- National Veterinary Services Laboratories, Ames, IA (Killian)
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD (Clement)
- Veterinary Diagnostic Laboratory, Michigan State University, Lansing, MI (Maes)
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43
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Schwarz M, Welzel M, Kabdullayeva T, Becker A, Freisleben B, Heider D. MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors. Bioinformatics 2020; 36:3322-3326. [PMID: 32129840 PMCID: PMC7267826 DOI: 10.1093/bioinformatics/btaa140] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/30/2020] [Accepted: 02/27/2020] [Indexed: 11/18/2022] Open
Abstract
Summary The development of de novo DNA synthesis, polymerase chain reaction (PCR), DNA sequencing and molecular cloning gave researchers unprecedented control over DNA and DNA-mediated processes. To reduce the error probabilities of these techniques, DNA composition has to adhere to method-dependent restrictions. To comply with such restrictions, a synthetic DNA fragment is often adjusted manually or by using custom-made scripts. In this article, we present MESA (Mosla Error Simulator), a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplification, cloning, sequencing methods and biological restrictions of host organisms. Furthermore, MESA can be used to simulate errors during synthesis, PCR, storage and sequencing processes. Availability and implementation MESA is available at mesa.mosla.de, with the source code available at github.com/umr-ds/mesa_dna_sim. Contact dominik.heider@uni-marburg.de Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | | | - Anke Becker
- Department of Biology, SYNMIKRO, University of Marburg, Marburg D-35032, Germany
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44
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King DJ, Freimanis G, Lasecka-Dykes L, Asfor A, Ribeca P, Waters R, King DP, Laing E. A Systematic Evaluation of High-Throughput Sequencing Approaches to Identify Low-Frequency Single Nucleotide Variants in Viral Populations. Viruses 2020; 12:E1187. [PMID: 33092085 PMCID: PMC7594041 DOI: 10.3390/v12101187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/01/2020] [Accepted: 10/12/2020] [Indexed: 12/28/2022] Open
Abstract
High-throughput sequencing such as those provided by Illumina are an efficient way to understand sequence variation within viral populations. However, challenges exist in distinguishing process-introduced error from biological variance, which significantly impacts our ability to identify sub-consensus single-nucleotide variants (SNVs). Here we have taken a systematic approach to evaluate laboratory and bioinformatic pipelines to accurately identify low-frequency SNVs in viral populations. Artificial DNA and RNA "populations" were created by introducing known SNVs at predetermined frequencies into template nucleic acid before being sequenced on an Illumina MiSeq platform. These were used to assess the effects of abundance and starting input material type, technical replicates, read length and quality, short-read aligner, and percentage frequency thresholds on the ability to accurately call variants. Analyses revealed that the abundance and type of input nucleic acid had the greatest impact on the accuracy of SNV calling as measured by a micro-averaged Matthews correlation coefficient score, with DNA and high RNA inputs (107 copies) allowing for variants to be called at a 0.2% frequency. Reduced input RNA (105 copies) required more technical replicates to maintain accuracy, while low RNA inputs (103 copies) suffered from consensus-level errors. Base errors identified at specific motifs identified in all technical replicates were also identified which can be excluded to further increase SNV calling accuracy. These findings indicate that samples with low RNA inputs should be excluded for SNV calling and reinforce the importance of optimising the technical and bioinformatics steps in pipelines that are used to accurately identify sequence variants.
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Affiliation(s)
- David J. King
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Graham Freimanis
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
| | - Lidia Lasecka-Dykes
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
| | - Amin Asfor
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
- Department of Pathology and Infectious Diseases, Faculty of Health and Medical sciences, School of Veterinary Medicine, University of Surrey, Guilford GU2 7XH, UK
| | - Paolo Ribeca
- Biomathematics and Statistics Scotland, Edinburgh, Midlothian EH9 3FD, UK;
| | - Ryan Waters
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
| | - Donald P. King
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
| | - Emma Laing
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
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45
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Wu H, Zhang K, Chen Y, Li J, Strout MP, Gu X. Optimized high-fidelity 3DPCR to assess potential mitochondrial targeting by activation-induced cytidine deaminase. FEBS Open Bio 2020; 10:1782-1792. [PMID: 32633086 PMCID: PMC7459399 DOI: 10.1002/2211-5463.12927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/10/2020] [Accepted: 06/03/2020] [Indexed: 11/09/2022] Open
Abstract
Activation‐induced cytidine deaminase (AID) initiates somatic hypermutation and class switch recombination of immunoglobulin genes in B cells, whereas off‐targeted AID activity contributes to oncogenic mutations and chromosomal translocations associated with B cell malignancies. Paradoxically, only a minority of AID is allowed to access the nuclear genome, but the majority of AID is retained in the cytoplasm. It is unknown whether cytoplasmic AID can access and target the mitochondrial genome [mitochondrial DNA (mtDNA)]. To address this issue, we developed high‐fidelity differential DNA denaturation PCR, which allowed the enrichment of genuine mtDNA mutations and therefore the identification of endogenous mtDNA mutation signatures in vitro. With this approach, we showed that AID targeting to mtDNA is a rare event in AID‐expressing lymphoma lines. Further biochemical and microscopic analysis revealed that a fraction of cytosol AID is associated with the outer membrane of mitochondria but unable to access the mitochondrial matrix. Together, our data suggested that the mitochondrial genome is protected from AID‐mediated mutagenesis by physical segregation of AID from accessing mtDNA within the mitochondrial matrix.
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Affiliation(s)
- Haiyan Wu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, Research Center of Stomatology, Xi'an Jiaotong University College of Stomatology, Xi'an, China.,Department of Oral and Maxillofacial Surgery, Xi'an Jiaotong University College of Stomatology, Xi'an, China
| | - Kaili Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, Research Center of Stomatology, Xi'an Jiaotong University College of Stomatology, Xi'an, China.,Department of Periodontology and Oral Medicine, Xi'an Jiaotong University College of Stomatology, Xi'an, China
| | - Yue Chen
- Department of Periodontology and Oral Medicine, Xi'an Jiaotong University College of Stomatology, Xi'an, China
| | - Jinfeng Li
- Department of Oral and Maxillofacial Surgery, Xi'an Jiaotong University College of Stomatology, Xi'an, China
| | - Matthew P Strout
- Section of Hematology, Yale University School of Medicine, New Haven, CT, USA
| | - Xiwen Gu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, Research Center of Stomatology, Xi'an Jiaotong University College of Stomatology, Xi'an, China
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46
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Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, Öpik M, Robert V, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 2020; 11:14. [PMID: 32714773 PMCID: PMC7353689 DOI: 10.1186/s43008-020-00033-z] [Citation(s) in RCA: 185] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
| | - M. Catherine Aime
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
| | - Andrew N. Miller
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820-6970 USA
| | - Hiran A. Ariyawansa
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipe City, Taiwan
| | - Takayuki Aoki
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Agriculture and Food Research Organization, Genetic Resources Center, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Gianluigi Cardinali
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
| | - Pedro W. Crous
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Irina S. Druzhinina
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - David M. Geiser
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802 USA
| | - David L. Hawksworth
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UK
- Geography and Environment, University of Southampton, Southampton, SO17 1BJ UK
- Jilin Agricultural University, Changchun, 130118 Jilin Province China
| | - Kevin D. Hyde
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- World Agroforestry Centre, East and Central Asia, Kunming, 650201 Yunnan China
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Rai, 50150 Thailand
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius
| | - Peter R. Johnston
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Manaaki Whenua – Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | | | - Elaine Malosso
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Micologia, Laboratório de Hifomicetos de Folhedo, Avenida da Engenharia, s/n Cidade Universitária, Recife, PE 50.740-600 Brazil
| | - Tom W. May
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004 Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Maarja Öpik
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- University of Tartu, 40 Lai Street, 51 005 Tartu, Estonia
| | - Vincent Robert
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marc Stadler
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Marco Thines
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60439 Frankfurt (Main); Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Andrey M. Yurkov
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ning Zhang
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USA
| | - Conrad L. Schoch
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
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47
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Mukolwe LD, Odongo DO, Byaruhanga C, Snyman LP, Sibeko-Matjila KP. Analysis of p67 allelic sequences reveals a subtype of allele type 1 unique to buffalo-derived Theileria parva parasites from southern Africa. PLoS One 2020; 15:e0231434. [PMID: 32598384 PMCID: PMC7323972 DOI: 10.1371/journal.pone.0231434] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/13/2020] [Indexed: 11/18/2022] Open
Abstract
East Coast fever (ECF) and Corridor disease (CD) caused by cattle- and buffalo-derived T. parva respectively are the most economically important tick-borne diseases of cattle in the affected African countries. The p67 gene has been evaluated as a recombinant subunit vaccine against ECF, and for discrimination of T. parva parasites causing ECF and Corridor disease. The p67 allele type 1 was first identified in cattle-derived T. parva parasites from East Africa, where parasites possessing this allele type have been associated with ECF. Subsequent characterization of buffalo-derived T. parva parasites from South Africa where ECF was eradicated, revealed the presence of a similar allele type, raising concerns as to whether or not allele type 1 from parasites from the two regions is identical. A 900 bp central fragment of the gene encoding p67 was PCR amplified from T. parva DNA extracted from blood collected from cattle and buffalo in South Africa, Mozambique, Kenya, Tanzania and Uganda, followed by DNA sequence analysis. Four p67 allele types previously described were identified. A subtype of p67 allele type 1 was identified in parasites from clinical cases of CD and buffalo from southern Africa. Notably, p67 allele type 1 sequences from parasites associated with ECF in East Africa and CD in Kenya were identical. Analysis of two p67 B-cell epitopes (TpM12 and AR22.7) revealed amino acid substitutions in allele type 1 from buffalo-derived T. parva parasites from southern Africa. However, both epitopes were conserved in allele type 1 from cattle- and buffalo-derived T. parva parasites from East Africa. These findings reveal detection of a subtype of p67 allele type 1 associated with T. parva parasites transmissible from buffalo to cattle in southern Africa.
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Affiliation(s)
- Lubembe D. Mukolwe
- Vectors and Vector-borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
- Department of Veterinary Pathology, Microbiology & Parasitology, Faculty of Veterinary Medicine and Surgery, Egerton University, Egerton, Kenya
- * E-mail:
| | - David O. Odongo
- School of Biological Sciences, University of Nairobi, Nairobi, Kenya
| | - Charles Byaruhanga
- Vectors and Vector-borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
- National Agricultural Research Organization, Entebbe, Uganda
| | - Louwtjie P. Snyman
- Vectors and Vector-borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
- Durban Natural Science Museum, Durban, South Africa
| | - Kgomotso P. Sibeko-Matjila
- Vectors and Vector-borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
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48
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Tang Y, Zheng X, Liu H, Sunxie F. Population genetics and comparative mitogenomic analyses reveal cryptic diversity of Amphioctopus neglectus (Cephalopoda: Octopodidae). Genomics 2020; 112:3893-3902. [PMID: 32603760 DOI: 10.1016/j.ygeno.2020.06.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/14/2020] [Accepted: 06/22/2020] [Indexed: 12/28/2022]
Abstract
This study presented 96 cox1 and 76 cox3 genes of Amphioctopus neglectus populations. Three distinct lineages were formed from phylogenetic trees and networks constructed using haplotypes. Mitogenomes of A. neglectus-a and A. neglectus-b as the representatives of two lineages separated from population genetics were sequenced to compare with A. neglectus at the genome-level. Amphioctopus neglectus-a showed significant differences with A. neglectus, mainly reflected in gene length, intergenic regions and the secondary structure of tandem repeat motifs. Notably, two sequence deletions in mitogenomes of the two representative species were detected in different positions of major non-coding regions, which were the most distinct differences with A. neglectus. Pairwise genetic distances and the phylogenetic analysis supported the relationship of (A. neglectus-a + (A. neglectus + A. neglectus-b)). This study suggested that A. neglectus-a should be considered as a potential cryptic species of this complex, while A. neglectus-b needed further verification to be defined.
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Affiliation(s)
- Yan Tang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, China
| | - Xiaodong Zheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, China.
| | - Haijuan Liu
- Guangxi Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai 536000, China
| | - Feige Sunxie
- Dongshan Boguangtianxing Foods Co., Ltd., Zhangzhou 363000, China
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49
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CRISPR-sub: Analysis of DNA substitution mutations caused by CRISPR-Cas9 in human cells. Comput Struct Biotechnol J 2020; 18:1686-1694. [PMID: 32670508 PMCID: PMC7338987 DOI: 10.1016/j.csbj.2020.06.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 12/18/2022] Open
Abstract
CRISPR-Cas9 induces DNA cleavages at desired target sites in a guide RNA-dependent manner; DNA editing occurs through the resulting activity of DNA repair processes including non-homologous end joining (NHEJ), which is dominant in mammalian cells. NHEJ repair frequently causes small insertions and deletions (indels) near DNA cleavage sites but only rarely causes nucleotide substitutions. High-throughput sequencing is the primary means of assessing indel and substitution frequencies in bulk populations of cells in the gene editing field. However, it is difficult to detect bona fide substitutions, which are embedded among experimentally-induced substitution errors, in high-throughput sequencing data. Here, we developed a novel analysis method, named CRISPR-Sub, to statistically detect Cas9-mediated substitutions in high-throughput sequencing data by comparing Mock- and CRISPR-treated samples. We first pinpointed ‘hotspot positions’ in target sequences at which substitution mutations were quantitatively observed much more often (p > 0.001) in CRISPR- versus Mock-treated samples. We refer to the substitution mutations in defined hotspot positions as ‘apparent substitutions’ and ultimately calculated ‘apparent substitution frequencies’ for each target. By examining 51 endogenous target sites in HeLa cells, we found that the average apparent substitution frequency was 0.8% in all queries, that apparent substitutions frequently occur near CRISPR-Cas9 cleavage sites, and that nucleotide conversion showed no meaningful nucleotide preference patterns. Furthermore, we generated NHEJ-inhibited cell lines (LIG4−/−) by knockout of the gene encoding ligase IV and found that the apparent substitution frequencies were significantly decreased in LIG4−/− cells, strongly suggesting that DNA substitutions are generated by the NHEJ pathway.
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50
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Branton SA, Ghorbani A, Bolt BN, Fifield H, Berghuis LM, Larijani M. Activation-induced cytidine deaminase can target multiple topologies of double-stranded DNA in a transcription-independent manner. FASEB J 2020; 34:9245-9268. [PMID: 32437054 DOI: 10.1096/fj.201903036rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 12/30/2022]
Abstract
Activation-induced cytidine deaminase (AID) mutates immunoglobulin genes and acts genome-wide. AID targets robustly transcribed genes, and purified AID acts on single-stranded (ss) but not double-stranded (ds) DNA oligonucleotides. Thus, it is believed that transcription is the generator of ssDNA for AID. Previous cell-free studies examining the relationship between transcription and AID targeting have employed a bacterial colony count assay wherein AID reverts an antibiotic resistance stop codon in plasmid substrates, leading to colony formation. Here, we established a novel assay where kb-long dsDNA of varying topologies is incubated with AID, with or without transcription, followed by direct sequencing. This assay allows for an unselected and in-depth comparison of mutation frequency and pattern of AID targeting in the absence of transcription or across a range of transcription dynamics. We found that without transcription, AID targets breathing ssDNA in supercoiled and, to a lesser extent, in relaxed dsDNA. The most optimal transcription only modestly enhanced AID action on supercoiled dsDNA in a manner dependent on RNA polymerase speed. These data suggest that the correlation between transcription and AID targeting may reflect transcription leading to AID-accessible breathing ssDNA patches naturally occurring in de-chromatinized dsDNA, as much as being due to transcription directly generating ssDNA.
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Affiliation(s)
- Sarah A Branton
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Atefeh Ghorbani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Brittany N Bolt
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Heather Fifield
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Lesley M Berghuis
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Mani Larijani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
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