1
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Lin J, Nguyen MA, Lin LY, Zeng J, Verma A, Neri NR, da Silva LF, Mucci A, Wolfe S, Shaw KL, Clement K, Brendel C, Pinello L, Pellin D, Bauer DE. Scalable assessment of genome editing off-targets associated with genetic variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.24.605019. [PMID: 39211178 PMCID: PMC11360989 DOI: 10.1101/2024.07.24.605019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Genome editing with RNA-guided DNA binding factors carries risk of off-target editing at homologous sequences. Genetic variants may introduce sequence changes that increase homology to a genome editing target, thereby increasing risk of off-target editing. Conventional methods to verify candidate off-targets rely on access to cells with genomic DNA carrying these sequences. However, for candidate off-targets associated with genetic variants, appropriate cells for experimental verification may not be available. Here we develop a method, Assessment By Stand-in Off-target LentiViral Ensemble with sequencing (ABSOLVE-seq), to integrate a set of candidate off-target sequences along with unique molecular identifiers (UMIs) in genomes of primary cells followed by clinically relevant gene editor delivery. Gene editing of dozens of candidate off-target sequences may be evaluated in a single experiment with high sensitivity, precision, and power. We provide an open-source pipeline to analyze sequencing data. This approach enables experimental assessment of the influence of human genetic diversity on specificity evaluation during gene editing therapy development.
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2
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Wang D, Liu Y, Zhang Y, Chen Q, Han Y, Hou W, Liu C, Yu Y, Li Z, Li Z, Zhao J, Shi L, Zheng Y, Li J, Zhang R. A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials. Nat Commun 2024; 15:6167. [PMID: 39039053 PMCID: PMC11263697 DOI: 10.1038/s41467-024-50420-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 07/02/2024] [Indexed: 07/24/2024] Open
Abstract
Translating RNA-seq into clinical diagnostics requires ensuring the reliability and cross-laboratory consistency of detecting clinically relevant subtle differential expressions, such as those between different disease subtypes or stages. As part of the Quartet project, we present an RNA-seq benchmarking study across 45 laboratories using the Quartet and MAQC reference samples spiked with ERCC controls. Based on multiple types of 'ground truth', we systematically assess the real-world RNA-seq performance and investigate the influencing factors involved in 26 experimental processes and 140 bioinformatics pipelines. Here we show greater inter-laboratory variations in detecting subtle differential expressions among the Quartet samples. Experimental factors including mRNA enrichment and strandedness, and each bioinformatics step, emerge as primary sources of variations in gene expression. We underscore the profound influence of experimental execution, and provide best practice recommendations for experimental designs, strategies for filtering low-expression genes, and the optimal gene annotation and analysis pipelines. In summary, this study lays the foundation for developing and quality control of RNA-seq for clinical diagnostic purposes.
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Affiliation(s)
- Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yuanfeng Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Cong Liu
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ziyang Li
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Ziqiang Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Jiaxin Zhao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai, China.
- International Human Phenome Institutes, Shanghai, China.
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai, China.
- International Human Phenome Institutes, Shanghai, China.
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China.
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China.
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
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3
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Tito RY, Verbandt S, Aguirre Vazquez M, Lahti L, Verspecht C, Lloréns-Rico V, Vieira-Silva S, Arts J, Falony G, Dekker E, Reumers J, Tejpar S, Raes J. Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development. Nat Med 2024; 30:1339-1348. [PMID: 38689063 PMCID: PMC11108775 DOI: 10.1038/s41591-024-02963-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Despite substantial progress in cancer microbiome research, recognized confounders and advances in absolute microbiome quantification remain underused; this raises concerns regarding potential spurious associations. Here we study the fecal microbiota of 589 patients at different colorectal cancer (CRC) stages and compare observations with up to 15 published studies (4,439 patients and controls total). Using quantitative microbiome profiling based on 16S ribosomal RNA amplicon sequencing, combined with rigorous confounder control, we identified transit time, fecal calprotectin (intestinal inflammation) and body mass index as primary microbial covariates, superseding variance explained by CRC diagnostic groups. Well-established microbiome CRC targets, such as Fusobacterium nucleatum, did not significantly associate with CRC diagnostic groups (healthy, adenoma and carcinoma) when controlling for these covariates. In contrast, the associations of Anaerococcus vaginalis, Dialister pneumosintes, Parvimonas micra, Peptostreptococcus anaerobius, Porphyromonas asaccharolytica and Prevotella intermedia remained robust, highlighting their future target potential. Finally, control individuals (age 22-80 years, mean 57.7 years, standard deviation 11.3) meeting criteria for colonoscopy (for example, through a positive fecal immunochemical test) but without colonic lesions are enriched for the dysbiotic Bacteroides2 enterotype, emphasizing uncertainties in defining healthy controls in cancer microbiome research. Together, these results indicate the importance of quantitative microbiome profiling and covariate control for biomarker identification in CRC microbiome studies.
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Affiliation(s)
- Raúl Y Tito
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Sara Verbandt
- Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Marta Aguirre Vazquez
- Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Leo Lahti
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Computing, University of Turku, Turku, Finland
| | - Chloe Verspecht
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Verónica Lloréns-Rico
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Systems Biology of Host-Microbiome Interactions Laboratory, Principe Felipe Research Center (CIPF), Valencia, Spain
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Janine Arts
- Oncology, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Evelien Dekker
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Joke Reumers
- Therapeutics Discovery, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Sabine Tejpar
- Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium.
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium.
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4
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Gao L, Li L, Fang B, Fang Z, Xiang Y, Zhang M, Zhou J, Song H, Chen L, Li T, Xiao H, Wan R, Jiang Y, Peng H. Carryover Contamination-Controlled Amplicon Sequencing Workflow for Accurate Qualitative and Quantitative Detection of Pathogens: a Case Study on SARS-CoV-2. Microbiol Spectr 2023; 11:e0020623. [PMID: 37098913 PMCID: PMC10269707 DOI: 10.1128/spectrum.00206-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/02/2023] [Indexed: 04/27/2023] Open
Abstract
Carryover contamination during amplicon sequencing workflow (AMP-Seq) put the accuracy of the high-throughput detection for pathogens at risk. The purpose of this study is to develop a carryover contaminations-controlled AMP-Seq (ccAMP-Seq) workflow to enable accurate qualitative and quantitative detection for pathogens. By using the AMP-Seq workflow to detect SARS-CoV-2, Aerosols, reagents and pipettes were identified as potential sources of contaminations and ccAMP-Seq was then developed. ccAMP-Seq used filter tips and physically isolation of experimental steps to avoid cross contamination, synthetic DNA spike-ins to compete with contaminations and quantify SARS-CoV-2, dUTP/uracil DNA glycosylase system to digest the carryover contaminations, and a new data analysis procedure to remove the sequencing reads from contaminations. Compared to AMP-Seq, the contamination level of ccAMP-Seq was at least 22-folds lower and the detection limit was also about an order of magnitude lower-as low as one copy/reaction. By testing the dilution series of SARS-CoV-2 nucleic acid standard, ccAMP-Seq showed 100% sensitivity and specificity. The high sensitivity of ccAMP-Seq was further confirmed by the detection of SARS-CoV-2 from 62 clinical samples. The consistency between qPCR and ccAMP-Seq was 100% for all the 53 qPCR-positive clinical samples. Seven qPCR-negative clinical samples were found to be positive by ccAMP-Seq, which was confirmed by extra qPCR tests on subsequent samples from the same patients. This study presents a carryover contamination-controlled, accurate qualitative and quantitative amplicon sequencing workflow that addresses the critical problem of pathogen detection for infectious diseases. IMPORTANCE Accuracy, a key indicator of pathogen detection technology, is compromised by carryover contamination in the amplicon sequencing workflow. Taking the detection of SARS-CoV-2 as case, this study presents a new carryover contamination-controlled amplicon sequencing workflow. The new workflow significantly reduces the degree of contamination in the workflow, thereby significantly improving the accuracy and sensitivity of the SARS-CoV-2 detection and empowering the ability of quantitative detection. More importantly, the use of the new workflow is simple and economical. Therefore, the results of this study can be easily applied to other microorganism, which has great significance for improving the detection level of microorganism.
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Affiliation(s)
- Lifen Gao
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Lun Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Bin Fang
- Hubei Provincial Centers for Disease Control and Prevention, Wuhan, Hubei, People’s Republic of China
| | - Zhiwei Fang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Yanghai Xiang
- Yueyang Central Hospital, Yueyang, Hunan, People’s Republic of China
| | - Min Zhang
- Yueyang Central Hospital, Yueyang, Hunan, People’s Republic of China
| | - Junfei Zhou
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Huiyin Song
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Lihong Chen
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Tiantian Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Huafeng Xiao
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Renjing Wan
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Yongzhong Jiang
- Hubei Provincial Centers for Disease Control and Prevention, Wuhan, Hubei, People’s Republic of China
| | - Hai Peng
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
- Mingliao Biotechnology Co., Ltd., Wuhan, Hubei, People’s Republic of China
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5
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A modified protocol with less clean-up steps increased efficiency and product yield of sequencing library preparation. 3 Biotech 2022; 12:111. [PMID: 35462954 PMCID: PMC8995211 DOI: 10.1007/s13205-022-03168-5] [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: 11/13/2021] [Accepted: 03/19/2022] [Indexed: 11/01/2022] Open
Abstract
Library preparation is an essential step for the next-generation sequencing, such as whole-genome sequencing, reduced-representation genome sequencing, exome sequencing and transcriptome sequencing. The library preparation often involves many steps, including DNA fragmentation, end repair, ligation and amplification. Each step involves different enzymes and buffer systems, so many washing steps are implemented in between to clean-up the enzymes and solutes from the previous step. Those extra washing steps not only are tedious and costly, but more importantly may introduce cross-contamination and reduce the final library yield. Here, we modified the common protocol of Illumina library prep to reduce the washing steps by deactivating the enzymes with high temperature. The modified protocol has two less washing steps than the original one, which can save more than 40 min of hands-on time and reduce potential risk of cross-contamination. We compared our protocol with the original one by constructing libraries using 200 ng DNA of Tetraodon nigroviridis. The results showed that libraries prepared with the modified protocol had higher yields than that using the original protocol (53.4 ± 16.8 ng/ml vs. 8 ± 0.7 ng/ml), whereas the coverage and PCR duplication rate were similar. Furthermore, we eliminated the very first washing step after DNA shearing to preserve short DNA fragments, which increased proportion of fragments less than 100 bp DNA from 0.82 to 2.99%. In conclusion, using the modified protocols not only can save time and money, but also can generate higher yield and keep more short DNA fragments. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03168-5.
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6
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Wu H, Ma X, Chu Y, Qi X, Zou B, Liu Y, Zhou G. Digital Nucleic Acid Signal Amplification Platform for Highly Sensitive DNA Mutation Analysis. Anal Chem 2022; 94:3858-3864. [PMID: 35212518 DOI: 10.1021/acs.analchem.1c04765] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Digital nucleic acid analysis technology has shown great application potential due to its excellent performance. However, most current digital nucleic acid detection methods are based on PCR or other template amplification strategies. Here, we present an alternative analysis platform based on digital nucleic acid signal amplification in droplets termed dNASA. Using a bead-based controllable extension bridged cascade signal amplification reaction, we achieved an ultralow background, high efficiency, and highly specific nucleic acid signal amplification analysis. As a "proof of concept", we demonstrated the feasibility of the proposed dNASA platform in single-base DNA mutation analysis using artificially synthesized samples. This platform provides innovative ideas for the field of digital nucleic acid analysis.
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Affiliation(s)
- Haiping Wu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Xueping Ma
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Xiemin Qi
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Bingjie Zou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, China Pharmaceutical University, Nanjing 210009, China.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Yunlong Liu
- State Key Laboratory of Natural Medicines, Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Guohua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China
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7
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Yang F, Zhang H, Cai S, Imtiaz K, Li M, Wang M, Liu Y, Xue F, Zhang L, Gu F. Green Fluorescent Protein Tagged Polycistronic Reporter System Reveals Functional Editing Characteristics of CRISPR-Cas. CRISPR J 2022; 5:254-263. [PMID: 35085009 DOI: 10.1089/crispr.2021.0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The green fluorescent protein (GFP)-based reporter system has been widely harnessed as a quick quantitative activity assessment method for characterizing CRISPR-Cas via flow cytometry. However, due to the small size (738 nt) of the GFP coding sequence, the targeting sites for certain CRISPR-Cas are greatly restricted. To address this, here we developed a GFP tagged polycistronic reporter system to determine the activity of CRISPR-Cas in human cells. Specifically, the system contains the herpes simplex virus thymidine kinase (TK) gene, bacterial neomycin phosphotransferase (Neo) gene, and green fluorescent protein (GFP), named TNG gene, with a coding sequence of 2,577 nt. To investigate its performance, we generated a human cell line harboring the TNG expression cassette at the AAVS1 locus, and then we tested it with different Cas orthologs (SaCas9, St1Cas9, and AsCas12a). Our results demonstrated that using the TNG reporter system greatly expands the targeting site selection (3- to 13-fold) with CRISPR-Cas genome editing. The study therefore reports an additional method for the characterization of CRISPR-Cas technology.
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Affiliation(s)
- Fayu Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Hao Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Shuo Cai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Kiran Imtiaz
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Mingchun Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Mi Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Yingchun Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Feiqun Xue
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Lifang Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Feng Gu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
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8
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Marquez S, Babrak L, Greiff V, Hoehn KB, Lees WD, Luning Prak ET, Miho E, Rosenfeld AM, Schramm CA, Stervbo U. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis. Methods Mol Biol 2022; 2453:297-316. [PMID: 35622333 PMCID: PMC9761518 DOI: 10.1007/978-1-0716-2115-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Adaptive immune receptor repertoires (AIRRs) are rich with information that can be mined for insights into the workings of the immune system. Gene usage, CDR3 properties, clonal lineage structure, and sequence diversity are all capable of revealing the dynamic immune response to perturbation by disease, vaccination, or other interventions. Here we focus on a conceptual introduction to the many aspects of repertoire analysis and orient the reader toward the uses and advantages of each. Along the way, we note some of the many software tools that have been developed for these investigations and link the ideas discussed to chapters on methods provided elsewhere in this volume.
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Affiliation(s)
- Susanna Marquez
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Lmar Babrak
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Kenneth B Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - William D Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Enkelejda Miho
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- aiNET GmbH, Basel, Switzerland
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Ulrik Stervbo
- Center for Translational Medicine, Immunology, and Transplantation, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
- Immundiagnostik, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
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9
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Jung E, Romero R, Yoon BH, Theis KR, Gudicha DW, Tarca AL, Diaz-Primera R, Winters AD, Gomez-Lopez N, Yeo L, Hsu CD. Bacteria in the amniotic fluid without inflammation: early colonization vs. contamination. J Perinat Med 2021; 49:1103-1121. [PMID: 34229367 PMCID: PMC8570988 DOI: 10.1515/jpm-2021-0191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Intra-amniotic infection, defined by the presence of microorganisms in the amniotic cavity, is often accompanied by intra-amniotic inflammation. Occasionally, laboratories report the growth of bacteria or the presence of microbial nucleic acids in amniotic fluid in the absence of intra-amniotic inflammation. This study was conducted to determine the clinical significance of the presence of bacteria in amniotic fluid samples in the absence of intra-amniotic inflammation. METHODS A retrospective cross-sectional study included 360 patients with preterm labor and intact membranes who underwent transabdominal amniocentesis for evaluation of the microbial state of the amniotic cavity as well as intra-amniotic inflammation. Cultivation techniques were used to isolate microorganisms, and broad-range polymerase chain reaction coupled with electrospray ionization mass spectrometry (PCR/ESI-MS) was utilized to detect the nucleic acids of bacteria, viruses, and fungi. RESULTS Patients whose amniotic fluid samples evinced microorganisms but did not indicate inflammation had a similar perinatal outcome to those without microorganisms or inflammation [amniocentesis-to-delivery interval (p=0.31), spontaneous preterm birth before 34 weeks (p=0.83), acute placental inflammatory lesions (p=1), and composite neonatal morbidity (p=0.8)]. CONCLUSIONS The isolation of microorganisms from a sample of amniotic fluid in the absence of intra-amniotic inflammation is indicative of a benign condition, which most likely represents contamination of the specimen during the collection procedure or laboratory processing rather than early colonization or infection.
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Affiliation(s)
- Eunjung Jung
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Roberto Romero
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA,Department of Obstetrics and Gynecology, University of Michigan Health System, Ann Arbor, Michigan, USA,Department of Epidemiology and Biostatistics, College of Human Medicine, Michigan State University, East Lansing, Michigan, USA,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA,Detroit Medical Center, Detroit, Michigan, USA,Department of Obstetrics and Gynecology, Florida International University, Miami, Florida, USA
| | - Bo Hyun Yoon
- BioMedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kevin R. Theis
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Dereje W. Gudicha
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Adi L. Tarca
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA,Department of Computer Science, College of Engineering, Wayne State University, Detroit, Michigan, USA
| | - Ramiro Diaz-Primera
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Andrew D. Winters
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Lami Yeo
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Chaur-Dong Hsu
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA,Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
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10
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Roghmann MC, Lydecker AD, Shardell M, DeBoy RT, Johnson JK, Zhao L, Hittle LL, Mongodin EF. Effect of mupirocin for Staphylococcus aureus decolonization on the microbiome of the nose and throat in community and nursing home dwelling adults. PLoS One 2021; 16:e0252004. [PMID: 34101737 PMCID: PMC8186807 DOI: 10.1371/journal.pone.0252004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/28/2021] [Indexed: 12/26/2022] Open
Abstract
Objective To characterize the microbial communities of the anterior nares (nose) and posterior pharynx (throat) of adults dwelling in the community and in nursing homes before and after treatment with intranasal mupirocin. Methods Staphylococcus aureus-colonized adults were recruited from the community (n = 25) and from nursing homes (n = 7). S. aureus colonization was confirmed using cultures. Participants had specimens taken from nose and throat for S. aureus quantitation using quantitative PCR for the nuc gene and bacterial profiling using 16S rRNA gene sequencing over 12 weeks. After two baseline study visits 4 weeks apart, participants received intranasal mupirocin for 5 days with 3 further visits over a 8 week follow-up period. Results We found a decrease in the absolute abundance of S. aureus in the nose for 8 weeks after mupirocin (1693 vs 141 fg/ul, p = 0.047). Mupirocin caused a statistically significant disruption in bacterial communities of the nose and throat after 1 week, which was no longer detected after 8 weeks. Bacterial community profiling demonstrated that there was a decrease in the relative abundance of S. aureus (8% vs 0.3%, p<0.01) 8 weeks after mupirocin and a transient decrease in the relative abundance of Staphylococcus epidermidis in the nose (21% vs 5%, p<0.01) 1 week after mupirocin. Conclusions Decolonization with mupirocin leads to a sustained effect on absolute and relative abundance of S. aureus but not for other bacteria in the nose. This demonstrates that a short course of mupirocin selectively decreases S. aureus in the nose for up to 8 weeks.
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Affiliation(s)
- Mary-Claire Roghmann
- Geriatrics Research Education and Clinical Center, VA Maryland Health Care System, Baltimore, Maryland, United States of America
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
| | - Alison D. Lydecker
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Michelle Shardell
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Robert T. DeBoy
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - J. Kristie Johnson
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - LiCheng Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Lauren L. Hittle
- Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Emmanuel F. Mongodin
- Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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11
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Shen J, McFarland AG, Young VB, Hayden MK, Hartmann EM. Toward Accurate and Robust Environmental Surveillance Using Metagenomics. Front Genet 2021; 12:600111. [PMID: 33747038 PMCID: PMC7973286 DOI: 10.3389/fgene.2021.600111] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/21/2021] [Indexed: 01/23/2023] Open
Abstract
Environmental surveillance is a critical tool for combatting public health threats represented by the global COVID-19 pandemic and the continuous increase of antibiotic resistance in pathogens. With its power to detect entire microbial communities, metagenomics-based methods stand out in addressing the need. However, several hurdles remain to be overcome in order to generate actionable interpretations from metagenomic sequencing data for infection prevention. Conceptually and technically, we focus on viability assessment, taxonomic resolution, and quantitative metagenomics, and discuss their current advancements, necessary precautions and directions to further development. We highlight the importance of building solid conceptual frameworks and identifying rational limits to facilitate the application of techniques. We also propose the usage of internal standards as a promising approach to overcome analytical bottlenecks introduced by low biomass samples and the inherent lack of quantitation in metagenomics. Taken together, we hope this perspective will contribute to bringing accurate and consistent metagenomics-based environmental surveillance to the ground.
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Affiliation(s)
- Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
| | - Alexander G. McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
| | - Vincent B. Young
- Division of Infectious Diseases, Department of Internal Medicine, The University of Michigan Medical School, Ann Arbor, MI, United States
| | - Mary K. Hayden
- Division of Infectious Diseases, Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
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12
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Ni G, Lu J, Maulani N, Tian W, Yang L, Harliwong I, Wang Z, Mueller J, Yang B, Yuan Z, Hu S, Guo J. Novel Multiplexed Amplicon-Based Sequencing to Quantify SARS-CoV-2 RNA from Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2021; 8:683-690. [PMID: 37566375 PMCID: PMC8276671 DOI: 10.1021/acs.estlett.1c00408] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 05/18/2023]
Abstract
The application of wastewater-based epidemiology (WBE) to support the global response to the COVID-19 pandemic has shown encouraging outcomes. The accurate, sensitive, and high-throughput detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in municipal wastewater is critical for WBE. Here, we present a novel approach based on multiplexed amplicon-based sequencing, namely the ATOPlex platform, for detecting SARS-CoV-2. The ATOPlex platform is capable of quantifying SARS-CoV-2 RNA at concentrations that are at least 1 order of magnitude lower than the detection limit of reverse transcription quantitative polymerase chain reaction (RT-qPCR). Robust and accurate phylogenetic placement can be done at viral concentrations 4 times lower than the detection limit of RT-qPCR. We further found that the solid fraction in wastewater harbors a considerable amount of viral RNA, highlighting the need to extract viral RNA from the solid and liquid fractions of wastewater. This study delivers a highly sensitive, phylogenetically informative, and high-throughput analytical workflow that facilitates the application of WBE.
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Affiliation(s)
- Gaofeng Ni
- Advanced Water Management Centre, The
University of Queensland, St. Lucia, Brisbane, QLD 4072,
Australia
| | - Ji Lu
- Advanced Water Management Centre, The
University of Queensland, St. Lucia, Brisbane, QLD 4072,
Australia
| | - Nova Maulani
- Advanced Water Management Centre, The
University of Queensland, St. Lucia, Brisbane, QLD 4072,
Australia
| | - Wei Tian
- BGI Australia, 300 Herston
Road, Herston, Brisbane, QLD 4006, Australia
| | - Lin Yang
- BGI Australia, 300 Herston
Road, Herston, Brisbane, QLD 4006, Australia
| | - Ivon Harliwong
- BGI Australia, 300 Herston
Road, Herston, Brisbane, QLD 4006, Australia
| | - Zhiyao Wang
- Advanced Water Management Centre, The
University of Queensland, St. Lucia, Brisbane, QLD 4072,
Australia
| | - Jochen Mueller
- Queensland Alliance for Environmental Health Sciences
(QAEHS), The University of Queensland, 20 Cornwall Street,
Woolloongabba, QLD 4103, Australia
| | - Bicheng Yang
- BGI Australia, 300 Herston
Road, Herston, Brisbane, QLD 4006, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The
University of Queensland, St. Lucia, Brisbane, QLD 4072,
Australia
| | - Shihu Hu
- Advanced Water Management Centre, The
University of Queensland, St. Lucia, Brisbane, QLD 4072,
Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The
University of Queensland, St. Lucia, Brisbane, QLD 4072,
Australia
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13
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Manso CF, Bibby DF, Lythgow K, Mohamed H, Myers R, Williams D, Piorkowska R, Chan YT, Bowden R, Ansari MA, Ip CLC, Barnes E, Bradshaw D, Mbisa JL. Technical Validation of a Hepatitis C Virus Whole Genome Sequencing Assay for Detection of Genotype and Antiviral Resistance in the Clinical Pathway. Front Microbiol 2020; 11:576572. [PMID: 33162957 PMCID: PMC7583327 DOI: 10.3389/fmicb.2020.576572] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/14/2020] [Indexed: 01/05/2023] Open
Abstract
Choice of direct acting antiviral (DAA) therapy for Hepatitis C Virus (HCV) in the United Kingdom and similar settings usually requires knowledge of the genotype and, in some cases, antiviral resistance (AVR) profile of the infecting virus. To determine these, most laboratories currently use Sanger technology, but next-generation sequencing (NGS) offers potential advantages in throughput and accuracy. However, NGS poses unique technical challenges, which require idiosyncratic development and technical validation approaches. This applies particularly to virology, where sequence diversity is high and the amount of starting genetic material is low, making it difficult to distinguish real data from artifacts. We describe the development and technical validation of a sequence capture-based HCV whole genome sequencing (WGS) assay to determine viral genotype and AVR profile. We use clinical samples of known subtypes and viral loads, and simulated FASTQ datasets to validate the analytical performances of both the wet laboratory and bioinformatic pipeline procedures. We show high concordance of the WGS assay compared to current "gold standard" Sanger assays. Specificity was 92.3 and 96.1% for AVR and genotyping, respectively. Discordances were due to the inability of Sanger assays to assign the correct subtype or accurately call mixed drug-resistant variants. We show high repeatability and reproducibility with >99.8% sequence similarity between sequence runs as well as high precision for variant frequency detection at >98.8% in the 95th percentile. Post-sequencing bioinformatics quality control workflows allow the accurate distinction between mixed infections, cross-contaminants and recombinant viruses at a threshold of >5% for the minority population. The sequence capture-based HCV WGS assay is more accurate than legacy AVR and genotyping assays. The assay has now been implemented in the clinical pathway of England's National Health Service HCV treatment programs, representing the first validated HCV WGS pipeline in clinical service. The data generated will additionally provide granular national-level genomic information for public health policy making and support the WHO HCV elimination strategy.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Rory Bowden
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - M. Azim Ansari
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Camilla L. C. Ip
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | | | - Jean L. Mbisa
- Public Health England, London, United Kingdom
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
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14
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Noble AS, Noe S, Clearwater MJ, Lee CK. A core phyllosphere microbiome exists across distant populations of a tree species indigenous to New Zealand. PLoS One 2020; 15:e0237079. [PMID: 32790769 PMCID: PMC7425925 DOI: 10.1371/journal.pone.0237079] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/19/2020] [Indexed: 12/30/2022] Open
Abstract
The phyllosphere microbiome is increasingly recognised as an influential component of plant physiology, yet it remains unclear whether stable host-microbe associations generally exist in the phyllosphere. Leptospermum scoparium (mānuka) is a tea tree indigenous to New Zealand, and honey derived from mānuka is widely known to possess unique antimicrobial properties. However, the host physiological traits associated with these antimicrobial properties vary widely, and the specific cause of such variation has eluded scientists despite decades of research. Notably, the mānuka phyllosphere microbiome remains uncharacterised, and its potential role in mediating host physiology has not been considered. Working within the prevailing core microbiome conceptual framework, we hypothesise that the phyllosphere microbiome of mānuka exhibits specific host association patterns congruent with those of a microbial community under host selective pressure (null hypothesis: the mānuka phyllosphere microbiome is recruited stochastically from the surrounding environment). To examine our hypothesis, we characterised the phyllosphere and associated soil microbiomes of five distinct and geographically distant mānuka populations across the North Island of New Zealand. We identified a habitat-specific and relatively abundant core microbiome in the mānuka phyllosphere, which was persistent across all samples. In contrast, non-core phyllosphere microorganisms exhibited significant variation across individual host trees and populations that was strongly driven by environmental and spatial factors. Our results demonstrate the existence of a dominant and ubiquitous core microbiome in the phyllosphere of mānuka, supporting our hypothesis that phyllosphere microorganisms of mānuka exhibit specific host association and potentially mediate physiological traits of this nationally and culturally treasured indigenous plant. In addition, our results illustrate biogeographical patterns in mānuka phyllosphere microbiomes and offer insight into factors contributing to phyllosphere microbiome assembly.
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Affiliation(s)
- Anya S. Noble
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Stevie Noe
- School of Science, University of Waikato, Hamilton, New Zealand
| | | | - Charles K. Lee
- School of Science, University of Waikato, Hamilton, New Zealand
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15
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Seitz V, Kleo K, Dröge A, Schaper S, Elezkurtaj S, Bedjaoui N, Dimitrova L, Sommerfeld A, Berg E, von der Wall E, Müller U, Joosten M, Lenze D, Heimesaat MM, Baldus C, Zinser C, Cieslak A, Macintyre E, Stocking C, Hennig S, Hummel M. Evidence for a role of RUNX1 as recombinase cofactor for TCRβ rearrangements and pathological deletions in ETV6-RUNX1 ALL. Sci Rep 2020; 10:10024. [PMID: 32572036 PMCID: PMC7308335 DOI: 10.1038/s41598-020-65744-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 05/06/2020] [Indexed: 11/08/2022] Open
Abstract
T-cell receptor gene beta (TCRβ) gene rearrangement represents a complex, tightly regulated molecular mechanism involving excision, deletion and recombination of DNA during T-cell development. RUNX1, a well-known transcription factor for T-cell differentiation, has recently been described to act in addition as a recombinase cofactor for TCRδ gene rearrangements. In this work we employed a RUNX1 knock-out mouse model and demonstrate by deep TCRβ sequencing, immunostaining and chromatin immunoprecipitation that RUNX1 binds to the initiation site of TCRβ rearrangement and its homozygous inactivation induces severe structural changes of the rearranged TCRβ gene, whereas heterozygous inactivation has almost no impact. To compare the mouse model results to the situation in Acute Lymphoblastic Leukemia (ALL) we analyzed TCRβ gene rearrangements in T-ALL samples harboring heterozygous Runx1 mutations. Comparable to the Runx1+/- mouse model, heterozygous Runx1 mutations in T-ALL patients displayed no detectable impact on TCRβ rearrangements. Furthermore, we reanalyzed published sequence data from recurrent deletion borders of ALL patients carrying an ETV6-RUNX1 translocation. RUNX1 motifs were significantly overrepresented at the deletion ends arguing for a role of RUNX1 in the deletion mechanism. Collectively, our data imply a role of RUNX1 as recombinase cofactor for both physiological and aberrant deletions.
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Affiliation(s)
- V Seitz
- Charité University Medicine Berlin, Institute of Pathology, Berlin, Germany
- HS Diagnomics GmbH, Berlin, Germany
| | - K Kleo
- Charité University Medicine Berlin, Institute of Pathology, Berlin, Germany
| | - A Dröge
- HS Diagnomics GmbH, Berlin, Germany
| | | | - S Elezkurtaj
- Charité University Medicine Berlin, Institute of Pathology, Berlin, Germany
| | - N Bedjaoui
- University of Paris, Institute Necker-Enfants Malades (INEM), INSERM U1151, Laboratoire d'Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - L Dimitrova
- Charité University Medicine Berlin, Institute of Pathology, Berlin, Germany
| | - A Sommerfeld
- Charité University Medicine Berlin, Institute of Pathology, Berlin, Germany
| | - E Berg
- Charité University Medicine Berlin, Institute of Pathology, Berlin, Germany
| | - E von der Wall
- Charité University Medicine Berlin, Institute of Pathology, Berlin, Germany
| | - U Müller
- Heinrich-Pette-Institute, Leibniz-Institute for Experimental Virology, Hamburg, Germany
| | - M Joosten
- Charité University Medicine Berlin, Institute of Pathology, Berlin, Germany
| | - D Lenze
- Charité University Medicine Berlin, Institute of Pathology, Berlin, Germany
| | - M M Heimesaat
- Charité University Medicine Berlin, Institute of Microbiology, Infectious Diseases and Immunology, Berlin, Germany
| | - C Baldus
- University Medical Center Schleswig-Holstein, Department of Internal Medicine II, Kiel, Germany
| | - C Zinser
- Precigen Bioinformatics Germany GmbH, Munich, Germany
| | - A Cieslak
- University of Paris, Institute Necker-Enfants Malades (INEM), INSERM U1151, Laboratoire d'Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - E Macintyre
- University of Paris, Institute Necker-Enfants Malades (INEM), INSERM U1151, Laboratoire d'Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - C Stocking
- University Medical Center Eppendorf, Department of Stem Cell Transplantation, Hamburg, Germany
| | - S Hennig
- HS Diagnomics GmbH, Berlin, Germany
| | - M Hummel
- Charité University Medicine Berlin, Institute of Pathology, Berlin, Germany.
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16
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Proof of concept: used malaria rapid diagnostic tests applied for parallel sequencing for surveillance of molecular markers of anti-malarial resistance in Bissau, Guinea-Bissau during 2014-2017. Malar J 2019; 18:252. [PMID: 31349834 PMCID: PMC6660714 DOI: 10.1186/s12936-019-2894-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/23/2019] [Indexed: 01/17/2023] Open
Abstract
Background Large-scale surveillance of molecular markers of anti-malarial drug resistance is an attractive method of resistance monitoring, to complement therapeutic efficacy studies in settings where the latter are logistically challenging. Methods Between 2014 and 2017, this study sampled malaria rapid diagnostic tests (RDTs), used in routine clinical care, from two health centres in Bissau, Guinea-Bissau. In order to obtain epidemiological insights, RDTs were collected together with patient data on age and sex. A subset of positive RDTs from one of the two sites (n = 2184) were tested for Plasmodium DNA content. Those testing positive for Plasmodium DNA by PCR (n = 1390) were used for library preparation, custom designed dual indexing and next generation Miseq targeted sequencing of Plasmodium falciparum genes pfcrt, pfmdr1, pfdhfr, pfdhps and pfk13. Results The study found a high frequency of the pfmdr1 codon 86N at 88–97%, a significant decrease of the pfcrt wildtype CVMNK haplotype and elevated levels of the pfdhfr/pfdhps quadruple mutant ranging from 33 to 51% between 2014 and 2017. No polymorphisms indicating artemisinin tolerance were discovered. The demographic data indicate a large proportion of young adults (66%, interquartile range 11–28 years) presenting with P. falciparum infections. While a total of 5532 gene fragments were successfully analysed on a single Illumina Miseq flow cell, PCR-positivity from the library preparation varied considerably from 13 to 87% for different amplicons. Furthermore, pre-screening of samples for Plasmodium DNA content proved necessary prior to library preparation. Conclusions This study serves as a proof of concept for using leftover clinical material (used RDTs) for large-scale molecular surveillance, encompassing the inherent complications regarding to methodology and analysis when doing so. Factors such as RDT storage prior to DNA extraction and parasitaemia of the infection are likely to have an effect on whether or not parasite DNA can be successfully analysed, and are considered part of the reason the data yield is suboptimal. However, given the necessity of molecular surveillance of anti-malarial resistance in settings where poor infrastructure, poor economy, lack of educated staff and even surges of political instability remain major obstacles to performing clinical studies, obtaining the necessary data from used RDTs, despite suboptimal output, becomes a feasible, affordable and hence a justifiable method. Electronic supplementary material The online version of this article (10.1186/s12936-019-2894-8) contains supplementary material, which is available to authorized users.
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17
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Gueidan C, Elix JA, McCarthy PM, Roux C, Mallen-Cooper M, Kantvilas G. PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens. MycoKeys 2019; 53:73-91. [PMID: 31205446 PMCID: PMC6557899 DOI: 10.3897/mycokeys.53.34761] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/10/2019] [Indexed: 12/12/2022] Open
Abstract
The detection and identification of species of fungi in the environment using molecular methods heavily depends on reliable reference sequence databases. However, these databases are largely incomplete in terms of taxon coverage, and a significant effort is required from herbaria and living fungal collections for the mass-barcoding of well-identified and well-curated fungal specimens or strains. Here, a PacBio amplicon sequencing approach is applied to recent lichen herbarium specimens for the sequencing of the fungal ITS barcode, allowing a higher throughput sample processing than Sanger sequencing, which often required the use of cloning. Out of 96 multiplexed samples, a full-length ITS sequence of the target lichenised fungal species was recovered for 85 specimens. In addition, sequences obtained for co-amplified fungi gave an interesting insight into the diversity of endolichenic fungi. Challenges encountered at both the laboratory and bioinformatic stages are discussed, and cost and quality are compared with Sanger sequencing. With increasing data output and reducing sequencing cost, PacBio amplicon sequencing is seen as a promising approach for the generation of reference sequences for lichenised fungi as well as the characterisation of lichen-associated fungal communities.
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Affiliation(s)
- Cécile Gueidan
- Australian National Herbarium, National Research Collections Australia, CSIRO-NCMI, Canberra, ACT, 2601, Australia Australian National Herbarium Canberra Australia
| | - John A Elix
- Research School of Chemistry, Building 137, Australian National University, Canberra, ACT, 2601, Australia Australian National University Canberra Australia
| | - Patrick M McCarthy
- 64 Broadsmith St, Scullin, ACT, 2614, Australia Unaffilaited Canberra Australia
| | - Claude Roux
- 390 chemin des Vignes vieilles, 84120 Mirabeau, France Unaffilaited Mirabeau France
| | - Max Mallen-Cooper
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, NSW, 2052, Australia University of New South Wales Sydney Sydney Australia
| | - Gintaras Kantvilas
- 64 Broadsmith St, Scullin, ACT, 2614, Australia Unaffilaited Canberra Australia
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18
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Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls. Sci Rep 2018; 8:9095. [PMID: 29904073 PMCID: PMC6002373 DOI: 10.1038/s41598-018-27314-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/29/2018] [Indexed: 11/12/2022] Open
Abstract
Workflows for microbiome community profiling by high-throughput sequencing are prone to sample mix-ups and cross-contamination due to the complexity of the procedures and large number of samples typically analyzed in parallel. We employed synthetic 16S rRNA gene spike-in controls to establish a method for tracking of sample identity and detection of cross-contamination in microbiome community profiling assays based on 16S rRNA gene amplicon sequencing (16S-seq). Results demonstrated that combinatorial sample tracking mixes (STMs) can be reliably resolved by Illumina sequencing and faithfully represent their sample of origin. In a single-blinded experiment, addition of STMs at low levels was shown to be sufficient to unambiguously identify and resolve swapped samples. Using artificial admixtures of individually SMT-tagged samples, we further established the ability to detect and quantify cross-contamination down to a level of approximately 1%. The utility of our technique was underscored through detection of an unplanned case of cross-contamination that occurred during this study. By enabling detection of sample mix-ups and cross-contamination throughout 16S-seq workflows, the present technique thus assures provenance of sequence data on a per-sample basis. The method can be readily implemented in standard 16S-seq workflows and its routine application is expected to enhance the reliability of 16S-seq data.
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19
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Izraelson M, Nakonechnaya TO, Moltedo B, Egorov ES, Kasatskaya SA, Putintseva EV, Mamedov IZ, Staroverov DB, Shemiakina II, Zakharova MY, Davydov AN, Bolotin DA, Shugay M, Chudakov DM, Rudensky AY, Britanova OV. Comparative analysis of murine T-cell receptor repertoires. Immunology 2017; 153:133-144. [PMID: 29080364 DOI: 10.1111/imm.12857] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/06/2017] [Accepted: 10/06/2017] [Indexed: 12/21/2022] Open
Abstract
For understanding the rules and laws of adaptive immunity, high-throughput profiling of T-cell receptor (TCR) repertoires becomes a powerful tool. The structure of TCR repertoires is instructive even before the antigen specificity of each particular receptor becomes available. It embodies information about the thymic and peripheral selection of T cells; the readiness of an adaptive immunity to withstand new challenges; the character, magnitude and memory of immune responses; and the aetiological and functional proximity of T-cell subsets. Here, we describe our current analytical approaches for the comparative analysis of murine TCR repertoires, and show several examples of how these approaches can be applied for particular experimental settings. We analyse the efficiency of different metrics used for estimation of repertoire diversity, repertoire overlap, V-gene and J-gene segments usage similarity, and amino acid composition of CDR3. We discuss basic differences of these metrics and their advantages and limitations in different experimental models, and we provide guidelines for choosing an efficient way to lead a comparative analysis of TCR repertoires. Applied to the various known and newly developed mouse models, such analysis should allow us to disentangle multiple sophisticated puzzles in adaptive immunity.
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Affiliation(s)
- Mark Izraelson
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Tatiana O Nakonechnaya
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Bruno Moltedo
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Evgeniy S Egorov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Sofya A Kasatskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Ilgar Z Mamedov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy B Staroverov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Irina I Shemiakina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Maria Y Zakharova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Dmitriy A Bolotin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,MiLaboratory LLC, Skolkovo Innovation Centre, Moscow, Russia
| | - Mikhail Shugay
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,Central European Institute of Technology, Brno, Czech Republic.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Dmitriy M Chudakov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,Central European Institute of Technology, Brno, Czech Republic.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olga V Britanova
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
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20
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Ostmeyer J, Christley S, Rounds WH, Toby I, Greenberg BM, Monson NL, Cowell LG. Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis. BMC Bioinformatics 2017; 18:401. [PMID: 28882107 PMCID: PMC5588725 DOI: 10.1186/s12859-017-1814-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/29/2017] [Indexed: 12/29/2022] Open
Abstract
Background Deep sequencing of lymphocyte receptor repertoires has made it possible to comprehensively profile the clonal composition of lymphocyte populations. This opens the door for novel approaches to diagnose and prognosticate diseases with a driving immune component by identifying repertoire sequence patterns associated with clinical phenotypes. Indeed, recent studies support the feasibility of this, demonstrating an association between repertoire-level summary statistics (e.g., diversity) and patient outcomes for several diseases. In our own prior work, we have shown that six codons in VH4-containing genes in B cells from the cerebrospinal fluid of patients with relapsing remitting multiple sclerosis (RRMS) have higher replacement mutation frequencies than observed in healthy controls or patients with other neurological diseases. However, prior methods to date have been limited to focusing on repertoire-level summary statistics, ignoring the vast amounts of information in the millions of individual immune receptors comprising a repertoire. We have developed a novel method that addresses this limitation by using innovative approaches for accommodating the extraordinary sequence diversity of immune receptors and widely used machine learning approaches. We applied our method to RRMS, an autoimmune disease that is notoriously difficult to diagnose. Results We use the biochemical features encoded by the complementarity determining region 3 of each B cell receptor heavy chain in every patient repertoire as input to a detector function, which is fit to give the correct diagnosis for each patient using maximum likelihood optimization methods. The resulting statistical classifier assigns patients to one of two diagnosis categories, RRMS or other neurological disease, with 87% accuracy by leave-one-out cross-validation on training data (N = 23) and 72% accuracy on unused data from a separate study (N = 102). Conclusions Our method is the first to apply statistical learning to immune repertoires to aid disease diagnosis, learning repertoire-level labels from the set of individual immune repertoire sequences. This method produced a repertoire-based statistical classifier for diagnosing RRMS that provides a high degree of diagnostic capability, rivaling the accuracy of diagnosis by a clinical expert. Additionally, this method points to a diagnostic biochemical motif in the antibodies of RRMS patients, which may offer insight into the disease process. Electronic supplementary material The online version of this article (10.1186/s12859-017-1814-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jared Ostmeyer
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9066, USA
| | - Scott Christley
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9066, USA
| | - William H Rounds
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9066, USA
| | - Inimary Toby
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9066, USA
| | - Benjamin M Greenberg
- Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9036, USA
| | - Nancy L Monson
- Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9036, USA
| | - Lindsay G Cowell
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9066, USA.
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21
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Roghmann MC, Lydecker AD, Hittle L, DeBoy RT, Nowak RG, Johnson JK, Mongodin EF. Comparison of the Microbiota of Older Adults Living in Nursing Homes and the Community. mSphere 2017; 2:e00210-17. [PMID: 28932812 PMCID: PMC5597966 DOI: 10.1128/msphere.00210-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/12/2017] [Indexed: 12/26/2022] Open
Abstract
Our objective for this study was to characterize the microbial communities of the anterior nares (nose), posterior pharynx (throat), and skin of the femoral and subclavian areas in older adults from nursing homes and the community. Older adults (≥65 years) without antibiotic use for the past 3 months were recruited from nursing homes (NH; n = 16) and from the community (CB; n = 51). Specimens were taken from nose, throat, and skin sites for culture and bacterial profiling using 16S rRNA gene sequencing. We found that pathogenic Gram-negative rod (GNR) colonization on the femoral skin was higher in NH participants than CB participants; otherwise, there were no differences in GNR colonization at other body sites or in Staphylococcus aureus colonization at any body site. Bacterial community profiling demonstrated that the operational taxonomic unit compositions of the different body sites were similar between NH and CB participants, but the analysis identified differences in relative abundance levels. Streptococcus spp. were more abundant and Prevotella spp. were less abundant in the throats of NH participants than in throats of CB participants. Proteus, Escherichia coli, and Enterococcus were more abundant in NH participants on the femoral skin. We found a pattern of decreased abundance of specific Proteobacteria in NH participants at the anterior nares and at both skin sites. We concluded that bacterial communities were largely similar in diversity and composition within body sites between older adults without recent antibiotic use from NH compared to those from the community. Our findings support the rationale for improved hygiene in NH residents to reduce the transmission risk of antibiotic-resistant bacteria, such as Enterococcus spp. or Enterobacteriaceae. IMPORTANCE The nose, throat, and skin over the subclavian and femoral veins are the body sites which harbor the bacteria which most commonly cause health care-associated infection. We assessed the effect of nursing home residence on the microbiota of these body sites in older adults. We found that the microbiota composition of the different body sites was similar between nursing home and community participants, but we identified differences in relative abundance levels. We found remarkable similarities in the bacterial communities of different body sites in older adults who lived in nursing homes compared to those in the community among people who had not been on antibiotics for the past 3 months. We also found that the femoral skin microbiota had evidence of stool contamination in the nursing home residents, providing a rationale for improved skin hygiene. Taken together, it appears that the health care environment does not alter the microbiota to the extent that antibiotics do.
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Affiliation(s)
- Mary-Claire Roghmann
- Geriatrics Research Education and Clinical Center, VA Maryland Health Care System, Baltimore, Maryland, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Alison D. Lydecker
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lauren Hittle
- Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Robert T. DeBoy
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Rebecca G. Nowak
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - J. Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Emmanuel F. Mongodin
- Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
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22
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Zhu QG, Zhang SM, Ding XX, He B, Zhang HQ. Driver genes in non-small cell lung cancer: Characteristics, detection methods, and targeted therapies. Oncotarget 2017; 8:57680-57692. [PMID: 28915704 PMCID: PMC5593676 DOI: 10.18632/oncotarget.17016] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 03/30/2017] [Indexed: 12/11/2022] Open
Abstract
Lung cancer is one of the most common causes of cancer-related death in the world. The large number of lung cancer cases is non-small cell lung cancer (NSCLC), which approximately accounting for 75% of lung cancer. Over the past years, our comprehensive knowledge about the molecular biology of NSCLC has been rapidly enriching, which has promoted the discovery of driver genes in NSCLC and directed FDA-approved targeted therapies. Of course, the targeted therapies based on driver genes provide a more exact option for advanced non-small cell lung cancer, improving the survival rate of patients. Now, we will review the landscape of driver genes in NSCLC including the characteristics, detection methods, the application of target therapy and challenges.
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Affiliation(s)
- Qing-Ge Zhu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Shi-Ming Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Xiao-Xiao Ding
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Bing He
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Hu-Qin Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China
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23
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Cruaud P, Rasplus JY, Rodriguez LJ, Cruaud A. High-throughput sequencing of multiple amplicons for barcoding and integrative taxonomy. Sci Rep 2017; 7:41948. [PMID: 28165046 PMCID: PMC5292727 DOI: 10.1038/srep41948] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 01/03/2017] [Indexed: 11/09/2022] Open
Abstract
Until now, the potential of NGS for the construction of barcode libraries or integrative taxonomy has been seldom realised. Here, we amplified (two-step PCR) and simultaneously sequenced (MiSeq) multiple markers from hundreds of fig wasp specimens. We also developed a workflow for quality control of the data. Illumina and Sanger sequences accumulated in the past years were compared. Interestingly, primers and PCR conditions used for the Sanger approach did not require optimisation to construct the MiSeq library. After quality controls, 87% of the species (76% of the specimens) had a valid MiSeq sequence for each marker. Importantly, major clusters did not always correspond to the targeted loci. Nine specimens exhibited two divergent sequences (up to 10%). In 95% of the species, MiSeq and Sanger sequences obtained from the same sampling were similar. For the remaining 5%, species were paraphyletic or the sequences clustered into divergent groups on the Sanger + MiSeq trees (>7%). These problematic cases may represent coding NUMTS or heteroplasms. Our results illustrate that Illumina approaches are not artefact-free and confirm that Sanger databases can contain non-target genes. This highlights the importance of quality controls, working with taxonomists and using multiple markers for DNA-taxonomy or species diversity assessment.
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Affiliation(s)
| | | | - Lillian Jennifer Rodriguez
- INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France
- Institute of Biology, University of the Philippines Diliman, Quezon City, Philippines
| | - Astrid Cruaud
- INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France
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24
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Lee HK, Lee CK, Tang JWT, Loh TP, Koay ESC. Contamination-controlled high-throughput whole genome sequencing for influenza A viruses using the MiSeq sequencer. Sci Rep 2016; 6:33318. [PMID: 27624998 PMCID: PMC5022032 DOI: 10.1038/srep33318] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/24/2016] [Indexed: 12/04/2022] Open
Abstract
Accurate full-length genomic sequences are important for viral phylogenetic studies. We developed a targeted high-throughput whole genome sequencing (HT-WGS) method for influenza A viruses, which utilized an enzymatic cleavage-based approach, the Nextera XT DNA library preparation kit, for library preparation. The entire library preparation workflow was adapted for the Sentosa SX101, a liquid handling platform, to automate this labor-intensive step. As the enzymatic cleavage-based approach generates low coverage reads at both ends of the cleaved products, we corrected this loss of sequencing coverage at the termini by introducing modified primers during the targeted amplification step to generate full-length influenza A sequences with even coverage across the whole genome. Another challenge of targeted HTS is the risk of specimen-to-specimen cross-contamination during the library preparation step that results in the calling of false-positive minority variants. We included an in-run, negative system control to capture contamination reads that may be generated during the liquid handling procedures. The upper limits of 99.99% prediction intervals of the contamination rate were adopted as cut-off values of contamination reads. Here, 148 influenza A/H3N2 samples were sequenced using the HTS protocol and were compared against a Sanger-based sequencing method. Our data showed that the rate of specimen-to-specimen cross-contamination was highly significant in HTS.
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Affiliation(s)
- Hong Kai Lee
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Chun Kiat Lee
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Julian Wei-Tze Tang
- Department of Infection, Immunity, Inflammation, University of Leicester, Leicester, UK.,Clinical Microbiology, Leicester Royal Infirmary, Leicester, UK
| | - Tze Ping Loh
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Evelyn Siew-Chuan Koay
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore.,Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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