1
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Burdo TH, Chen C, Kaminski R, Sariyer IK, Mancuso P, Donadoni M, Smith MD, Sariyer R, Caocci M, Liao S, Liu H, Huo W, Zhao H, Misamore J, Lewis MG, Simonyan V, Thompson EE, Xu EY, Cradick TJ, Gordon J, Khalili K. Preclinical safety and biodistribution of CRISPR targeting SIV in non-human primates. Gene Ther 2024; 31:224-233. [PMID: 37587230 PMCID: PMC11090835 DOI: 10.1038/s41434-023-00410-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/31/2023] [Accepted: 06/28/2023] [Indexed: 08/18/2023]
Abstract
In this study, we demonstrate the safety and utility of CRISPR-Cas9 gene editing technology for in vivo editing of proviral DNA in ART-treated, virally controlled simian immunodeficiency virus (SIV) infected rhesus macaques, an established model for HIV infection. EBT-001 is an AAV9-based vector delivering SaCas9 and dual guide RNAs designed to target multiple regions of the SIV genome: the viral LTRs, and the Gag gene. The results presented here demonstrate that a single IV inoculation of EBT-001 at each of 3 dose levels (1.4 × 1012, 1.4 × 1013 and 1.4 × 1014 genome copies/kg) resulted in broad and functional biodistribution of AAV9-EBT-001 to known tissue reservoirs of SIV. No off-target effects or abnormal pathology were observed, and animals returned to their normal body weight after receiving EBT-001. Importantly, the macaques that received the 2 highest doses of EBT-001 showed improved absolute lymphocyte counts as compared to antiretroviral-treated controls. Taken together, these results demonstrate safety, biodistribution, and in vivo proviral DNA editing following IV administration of EBT-001, supporting the further development of CRISPR-based gene editing as a potential therapeutic approach for HIV in humans.
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Affiliation(s)
- Tricia H Burdo
- Department of Microbiology, Immunology, and Inflammation, Center for NeuroVirology and Gene Editing, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA.
| | - Chen Chen
- Department of Microbiology, Immunology, and Inflammation, Center for NeuroVirology and Gene Editing, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Rafal Kaminski
- Department of Microbiology, Immunology, and Inflammation, Center for NeuroVirology and Gene Editing, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Ilker K Sariyer
- Department of Microbiology, Immunology, and Inflammation, Center for NeuroVirology and Gene Editing, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Pietro Mancuso
- Department of Microbiology, Immunology, and Inflammation, Center for NeuroVirology and Gene Editing, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Martina Donadoni
- Department of Microbiology, Immunology, and Inflammation, Center for NeuroVirology and Gene Editing, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Mandy D Smith
- Department of Microbiology, Immunology, and Inflammation, Center for NeuroVirology and Gene Editing, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Rahsan Sariyer
- Department of Microbiology, Immunology, and Inflammation, Center for NeuroVirology and Gene Editing, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Maurizio Caocci
- Department of Microbiology, Immunology, and Inflammation, Center for NeuroVirology and Gene Editing, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Shuren Liao
- Department of Microbiology, Immunology, and Inflammation, Center for NeuroVirology and Gene Editing, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Hong Liu
- Department of Microbiology, Immunology, and Inflammation, Center for NeuroVirology and Gene Editing, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Wenwen Huo
- Excision BioTherapeutics, Inc., San Francisco, CA, USA
| | - Huaqing Zhao
- Center for Biostatistics and Epidemiology, Department of Biomedical Education and Data Science, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | | | | | | | | | - Ethan Y Xu
- Excision BioTherapeutics, Inc., San Francisco, CA, USA
| | | | | | - Kamel Khalili
- Department of Microbiology, Immunology, and Inflammation, Center for NeuroVirology and Gene Editing, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA.
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Keeney JG, Gulzar N, Baker JB, Klempir O, Hannigan GD, Bitton DA, Maritz JM, King CHS, Patel JA, Duncan P, Mazumder R. Communicating computational workflows in a regulatory environment. Drug Discov Today 2024; 29:103884. [PMID: 38219969 DOI: 10.1016/j.drudis.2024.103884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 12/14/2023] [Accepted: 01/10/2024] [Indexed: 01/16/2024]
Abstract
The volume of nucleic acid sequence data has exploded recently, amplifying the challenge of transforming data into meaningful information. Processing data can require an increasingly complex ecosystem of customized tools, which increases difficulty in communicating analyses in an understandable way yet is of sufficient detail to enable informed decisions or repeats. This can be of particular interest to institutions and companies communicating computations in a regulatory environment. BioCompute Objects (BCOs; an instance of pipeline documentation that conforms to the IEEE 2791-2020 standard) were developed as a standardized mechanism for analysis reporting. A suite of BCOs is presented, representing interconnected elements of a computation modeled after those that might be found in a regulatory submission but are shared publicly - in this case a pipeline designed to identify viral contaminants in biological manufacturing, such as for vaccines.
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Affiliation(s)
- Jonathon G Keeney
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA.
| | - Naila Gulzar
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | | | - Ondrej Klempir
- R&D Informatics Solutions, MSD Czech Republic, Prague, Czech Republic
| | | | - Danny A Bitton
- R&D Informatics Solutions, MSD Czech Republic, Prague, Czech Republic
| | - Julia M Maritz
- Exploratory Science Center, Merck & Co., Cambridge, MA, USA
| | - Charles H S King
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Janisha A Patel
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | | | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
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3
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Patel JA, Dean DA, King CH, Xiao N, Koc S, Minina E, Golikov A, Brooks P, Kahsay R, Navelkar R, Ray M, Roberson D, Armstrong C, Mazumder R, Keeney J. Bioinformatics tools developed to support BioCompute Objects. Database (Oxford) 2021; 2021:baab008. [PMID: 33784373 PMCID: PMC8009203 DOI: 10.1093/database/baab008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/10/2021] [Accepted: 03/06/2021] [Indexed: 11/17/2022]
Abstract
Developments in high-throughput sequencing (HTS) result in an exponential increase in the amount of data generated by sequencing experiments, an increase in the complexity of bioinformatics analysis reporting and an increase in the types of data generated. These increases in volume, diversity and complexity of the data generated and their analysis expose the necessity of a structured and standardized reporting template. BioCompute Objects (BCOs) provide the requisite support for communication of HTS data analysis that includes support for workflow, as well as data, curation, accessibility and reproducibility of communication. BCOs standardize how researchers report provenance and the established verification and validation protocols used in workflows while also being robust enough to convey content integration or curation in knowledge bases. BCOs that encapsulate tools, platforms, datasets and workflows are FAIR (findable, accessible, interoperable and reusable) compliant. Providing operational workflow and data information facilitates interoperability between platforms and incorporation of future dataset within an HTS analysis for use within industrial, academic and regulatory settings. Cloud-based platforms, including High-performance Integrated Virtual Environment (HIVE), Cancer Genomics Cloud (CGC) and Galaxy, support BCO generation for users. Given the 100K+ userbase between these platforms, BioCompute can be leveraged for workflow documentation. In this paper, we report the availability of platform-dependent and platform-independent BCO tools: HIVE BCO App, CGC BCO App, Galaxy BCO API Extension and BCO Portal. Community engagement was utilized to evaluate tool efficacy. We demonstrate that these tools further advance BCO creation from text editing approaches used in earlier releases of the standard. Moreover, we demonstrate that integrating BCO generation within existing analysis platforms greatly streamlines BCO creation while capturing granular workflow details. We also demonstrate that the BCO tools described in the paper provide an approach to solve the long-standing challenge of standardizing workflow descriptions that are both human and machine readable while accommodating manual and automated curation with evidence tagging. Database URL: https://www.biocomputeobject.org/resources.
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Affiliation(s)
- Janisha A Patel
- The Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | | | - Charles Hadley King
- The Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
- The McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Nan Xiao
- Seven Bridges, Charlestown, MA 02129, USA
| | - Soner Koc
- Seven Bridges, Charlestown, MA 02129, USA
| | - Ekaterina Minina
- CBER-HIVE, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Anton Golikov
- CBER-HIVE, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | | | - Robel Kahsay
- The Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Rahi Navelkar
- The Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | | | | | - Chris Armstrong
- The Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Raja Mazumder
- The Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
- The McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Jonathon Keeney
- The Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
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Bozza WP, Takeda K, Alterovitz WL, Chou CK, Shen RF, Zhang B. Anthracycline-Induced Cardiotoxicity: Molecular Insights Obtained from Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes (hiPSC-CMs). AAPS JOURNAL 2021; 23:44. [PMID: 33719006 PMCID: PMC7956936 DOI: 10.1208/s12248-021-00576-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/24/2021] [Indexed: 01/18/2023]
Abstract
Anthracyclines are a class of chemotherapy drugs that are highly effective for the treatment of human cancers, but their clinical use is limited by associated dose-dependent cardiotoxicity. The precise mechanisms by which individual anthracycline induces cardiotoxicity are not fully understood. Human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are emerging as a physiologically relevant model to assess drugs cardiotoxicity. Here, we describe an assay platform by coupling hiPSC-CMs and impedance measurement, which allows real-time monitoring of cardiomyocyte cellular index, beating amplitude, and beating rate. Using this approach, we have performed comparative studies on a panel of four anthracycline drugs (doxorubicin, epirubicin, idarubicin, and daunorubicin) which share a high degree of structural similarity but are associated with distinct cardiotoxicity profiles and maximum cumulative dose limits. Notably, results from our hiPSC-CMs impedance model (dose-dependent responses and EC50 values) agree well with the recommended clinical dose limits for these drugs. Using time-lapse imaging and RNAseq, we found that the differences in anthracycline cardiotoxicity are closely linked to extent of cardiomyocyte uptake and magnitude of activation/inhibition of several cellular pathways such as death receptor signaling, ROS production, and dysregulation of calcium signaling. The results provide molecular insights into anthracycline cardiac interactions and offer a novel assay system to more robustly assess potential cardiotoxicity during drug development.
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Affiliation(s)
- William P Bozza
- Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Kazuyo Takeda
- Microscopy and Imaging Core Facility, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Wei-Lun Alterovitz
- High-performance Integrated Virtual Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Chao-Kai Chou
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Baolin Zhang
- Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA.
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5
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BMT: Bioinformatics mini toolbox for comprehensive DNA and protein analysis. Genomics 2020; 112:4561-4566. [PMID: 32791200 DOI: 10.1016/j.ygeno.2020.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/01/2020] [Accepted: 08/07/2020] [Indexed: 01/05/2023]
Abstract
Background Bioinformatics tools are of great significance and are used in different spheres of life sciences. There are wide variety of tools available to perform primary analysis of DNA and protein but most of them are available on different platforms and many remain undetected. Accessing these tools separately to perform individual task is uneconomical and inefficient. Objective Our aim is to bring different bioinformatics models on a single platform to ameliorate scientific research. Hence, our objective is to make a tool for comprehensive DNA and protein analysis. Methods To develop a reliable, straight-forward and standalone desktop application we used state of the art python packages and libraries. Bioinformatics Mini Toolbox (BMT) is combination of seven tools including FastqTrimmer, Gene Prediction, DNA Analysis, Translation, Protein analysis and Pairwise and Multiple alignment. Results FastqTrimmer assists in quality assurance of NGS data. Gene prediction predicts the genes by homology from novel genome on the basis of reference sequence. Protein analysis and DNA analysis calculates physiochemical properties of nucleotide and protein sequences, respectively. Translation translates the DNA sequence into six open reading frames. Pairwise alignment performs pairwise global and local alignment of DNA and protein sequences on the basis or multiple matrices. Multiple alignment aligns multiple sequences and generates a phylogenetic tree. Conclusion We developed a tool for comprehensive DNA and protein analysis. The link to download BMT is https://github.com/nasiriqbal012/BMT_SETUP.git.
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Ford-Siltz LA, Wales S, Tohma K, Gao Y, Parra GI. Genotype-Specific Neutralization of Norovirus Is Mediated by Antibodies Against the Protruding Domain of the Major Capsid Protein. J Infect Dis 2020; 225:1205-1214. [DOI: 10.1093/infdis/jiaa116] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/24/2020] [Indexed: 01/26/2023] Open
Abstract
Abstract
Human noroviruses are the most common viral agents of acute gastroenteritis. Recently, human intestinal enteroids were shown to be permissive for norovirus infection. We tested their suitability as a system to study norovirus neutralization. Hyperimmune sera raised against virus-like particles (VLPs) representing different genotypes showed highly specific neutralization activity against GII.4 and GII.6 noroviruses. Carbohydrate blocking assays and neutralization exhibited similar patterns in antibody responses. Notably, sera produced against chimeric VLPs that presented swapped structural shell and protruding (P) domains, from different genotypes showed that neutralization is primarily mediated by antibodies mapping to the P domain of the norovirus capsid protein. This study provides empirical information on the antigenic differences among genotypes as measured by neutralization, which could guide vaccine design.
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Affiliation(s)
- Lauren A Ford-Siltz
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Samantha Wales
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, Maryland, USA
| | - Kentaro Tohma
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yamei Gao
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Gabriel I Parra
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
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Komatsu TE, Hodowanec AC, Colberg-Poley AM, Pikis A, Singer ME, O'Rear JJ, Donaldson EF. In-depth genomic analyses identified novel letermovir resistance-associated substitutions in the cytomegalovirus UL56 and UL89 gene products. Antiviral Res 2019; 169:104549. [DOI: 10.1016/j.antiviral.2019.104549] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 01/08/2023]
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8
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Transcriptomic profiling reveals p53 as a key regulator of doxorubicin-induced cardiotoxicity. Cell Death Discov 2019; 5:102. [PMID: 31231550 PMCID: PMC6561911 DOI: 10.1038/s41420-019-0182-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 03/21/2019] [Accepted: 04/29/2019] [Indexed: 01/10/2023] Open
Abstract
Doxorubicin is an important anticancer drug in the clinic. Unfortunately, it causes cumulative and dose-dependent cardiotoxic side effects. As the population of cancer survivors who have been exposed to treatment continues to grow, there is increased interest in assessing the long-term cardiac effects of doxorubicin and understanding the underlying mechanisms at play. In this study, we investigated doxorubicin-induced transcriptomic changes using RNA-sequencing (RNAseq) and a cellular model comprised of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Analyses of predicted upstream regulators identified the p53 protein as a key regulator of transcriptomic changes induced by doxorubicin. Clustering and pathway analyses showed that increased death receptor (DR) expression and enrichment of the extrinsic apoptotic pathway are significantly associated with doxorubicin-induced cardiotoxicity. Increased expression of p53 and DRs were confirmed via immunoblotting. Our data pinpoints increased DR expression as an early transcriptomic indicator of cardiotoxicity, suggesting that DR expression might function as a predictive biomarker for cardiac damage.
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A complete Leishmania donovani reference genome identifies novel genetic variations associated with virulence. Sci Rep 2018; 8:16549. [PMID: 30409989 PMCID: PMC6224596 DOI: 10.1038/s41598-018-34812-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/19/2018] [Indexed: 12/13/2022] Open
Abstract
Leishmania donovani is responsible for visceral leishmaniasis, a neglected and lethal parasitic disease with limited treatment options and no vaccine. The study of L. donovani has been hindered by the lack of a high-quality reference genome and this can impact experimental outcomes including the identification of virulence genes, drug targets and vaccine development. We therefore generated a complete genome assembly by deep sequencing using a combination of second generation (Illumina) and third generation (PacBio) sequencing technologies. Compared to the current L. donovani assembly, the genome assembly reported within resulted in the closure over 2,000 gaps, the extension of several chromosomes up to telomeric repeats and the re-annotation of close to 15% of protein coding genes and the annotation of hundreds of non-coding RNA genes. It was possible to correctly assemble the highly repetitive A2 and Amastin virulence gene clusters. A comparative sequence analysis using the improved reference genome confirmed 70 published and identified 15 novel genomic differences between closely related visceral and atypical cutaneous disease-causing L. donovani strains providing a more complete map of genes associated with virulence and visceral organ tropism. Bioinformatic tools including protein variation effect analyzer and basic local alignment search tool were used to prioritize a list of potential virulence genes based on mutation severity, gene conservation and function. This complete genome assembly and novel information on virulence factors will support the identification of new drug targets and the development of a vaccine for L. donovani.
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10
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Kurtz SL, Voskanian-Kordi A, Simonyan V, Elkins KL. Sequence comparison of Francisella tularensis LVS, LVS-G and LVS-R. Pathog Dis 2018; 76:5078346. [PMID: 30137434 DOI: 10.1093/femspd/fty067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 08/20/2018] [Indexed: 11/14/2022] Open
Abstract
Francisella tularensis is a gram-negative organism found in many regions of the world. F. tularensis can cause a fatal, febrile illness, although these natural tularemia infections are rare in the United States. However, the development of F. tularensis as a potential weapon of bioterrorism during the Cold War spurred the development of a live attenuated vaccine, LVS, from F. tularensis subsp. holarctica in the 1960s. Two colony morphology variants, LVS-G and LVS-R, were generated from parental LVS by plate passage and by acridine orange mutagenesis, respectively. In vaccinated mice, LVS-G and LVS-R exhibit altered immunogenicity and protective capacities. While the exact nature of the mutations in these strains was unknown, previous studies indicated that both had altered lipopolysaccharide structures. To better understand the impact of these mutations on LVS' immunogenicity, we sequenced the genomes of LVS-G and LVS-R as well as our parental laboratory stock of LVS, originally obtained from ATCC, and compared these to the F. tularensis subsp. holarctica LVS genome currently deposited in GenBank. The results indicate that the genomic sequence of ATCC LVS is nearly identical to that of the human LVS vaccine. Furthermore, a limited number of genomic mutations likely account for the phenotypes of LVS-G and LVS-R.
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Affiliation(s)
- Sherry L Kurtz
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration
| | - Alin Voskanian-Kordi
- High Performance Integrated Virtual Environment (HIVE), Center for Biologics Evaluation and Research, Food and Drug Administration
| | - Vahan Simonyan
- High Performance Integrated Virtual Environment (HIVE), Center for Biologics Evaluation and Research, Food and Drug Administration
| | - Karen L Elkins
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration
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Whole genome sequencing of live attenuated Leishmania donovani parasites reveals novel biomarkers of attenuation and enables product characterization. Sci Rep 2017; 7:4718. [PMID: 28680050 PMCID: PMC5498541 DOI: 10.1038/s41598-017-05088-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 06/06/2017] [Indexed: 01/03/2023] Open
Abstract
No licensed human vaccines are currently available against leishmaniasis. Several anti-leishmanial vaccines are currently undergoing testing, including genetically modified live-attenuated parasite vaccines. Studies with live attenuated Leishmania vaccines such as centrin deleted Leishmania donovani parasites (LdCen−/−) showed protective immunity in animal models. Such studies typically examined the biomarkers of protective immunity however the biomarkers of attenuation in the parasite preparations have not received adequate attention. As several candidate vaccines enter clinical trials, a more complete product characterization to enable maintenance of product quality will help meet regulatory requirements. Towards this goal, we have determined the complete genome sequence of LdCen−/− and its parent strain Ld1S-2D (LdWT) and characterized the LdCen−/− vaccine strain using bioinformatics tools. Results showed that the LdCen−/− parasites, in addition to loss of the centrin gene, have additional deletions ranging from 350 bp to 6900 bp in non-contiguous loci on several chromosomes, most commonly in untranslated regions. We have experimentally verified a subset of these adventitious deletions that had no impact on the attenuation of the LdCen−/− parasites. Our results identified hitherto unknown features of attenuation of virulence that could be used as markers of product quality in production lots and highlight the importance of product characterization in parasitic vaccines.
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