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Qiao L, Li C, Lin W, He X, Mi J, Tong Y, Gao J. ViroISDC: a method for calling integration sites of hepatitis B virus based on feature encoding. BMC Bioinformatics 2024; 25:177. [PMID: 38704528 PMCID: PMC11070082 DOI: 10.1186/s12859-024-05763-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/26/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) integrates into human chromosomes and can lead to genomic instability and hepatocarcinogenesis. Current tools for HBV integration site detection lack accuracy and stability. RESULTS This study proposes a deep learning-based method, named ViroISDC, for detecting integration sites. ViroISDC generates corresponding grammar rules and encodes the characteristics of the language data to predict integration sites accurately. Compared with Lumpy, Pindel, Seeksv, and SurVirus, ViroISDC exhibits better overall performance and is less sensitive to sequencing depth and integration sequence length, displaying good reliability, stability, and generality. Further downstream analysis of integrated sites detected by ViroISDC reveals the integration patterns and features of HBV. It is observed that HBV integration exhibits specific chromosomal preferences and tends to integrate into cancerous tissue. Moreover, HBV integration frequency was higher in males than females, and high-frequency integration sites were more likely to be present on hepatocarcinogenesis- and anti-cancer-related genes, validating the reliability of the ViroISDC. CONCLUSIONS ViroISDC pipeline exhibits superior precision, stability, and reliability across various datasets when compared to similar software. It is invaluable in exploring HBV infection in the human body, holding significant implications for the diagnosis, treatment, and prognosis assessment of HCC.
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Affiliation(s)
- Lei Qiao
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Chang Li
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Wei Lin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xiaoqi He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jia Mi
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Jingyang Gao
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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Bryant WB, Yang A, Griffin SH, Zhang W, Rafiq AM, Han W, Deak F, Mills MK, Long X, Miano JM. CRISPR-Cas9 Long-Read Sequencing for Mapping Transgenes in the Mouse Genome. CRISPR J 2023; 6:163-175. [PMID: 37071672 PMCID: PMC10123806 DOI: 10.1089/crispr.2022.0099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/12/2023] [Indexed: 04/19/2023] Open
Abstract
Microinjected transgenes, both large and small, are known to insert randomly into the mouse genome. Traditional methods of mapping a transgene are challenging, thus complicating breeding strategies and accurate interpretation of phenotypes, particularly when a transgene disrupts critical coding or noncoding sequences. As the vast majority of transgenic mouse lines remain unmapped, we developed CRISPR-Cas9 Long-Read Sequencing (CRISPR-LRS) to ascertain transgene integration loci. This novel approach mapped a wide size range of transgenes and uncovered more complex transgene-induced host genome re-arrangements than previously appreciated. CRISPR-LRS offers a facile, informative approach to establish robust breeding practices and will enable researchers to study a gene without confounding genetic issues. Finally, CRISPR-LRS will find utility in rapidly and accurately interrogating gene/genome editing fidelity in experimental and clinical settings.
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Affiliation(s)
- W. Bart Bryant
- Department of Medicine and Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Allison Yang
- Department of Medicine and Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Susan H. Griffin
- Department of Medicine and Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Wei Zhang
- Department of Medicine and Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Ashiq M. Rafiq
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Weiping Han
- Department of Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Ferenc Deak
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Mary Katherine Mills
- Department of Department of Biology and Geology, University of South Carolina Aiken, Aiken, South Carolina, USA
| | - Xiaochun Long
- Department of Medicine and Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Joseph M. Miano
- Department of Medicine and Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
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Proviral ALV-LTR Sequence Is Essential for Continued Proliferation of the ALV-Transformed B Cell Line. Int J Mol Sci 2022; 23:ijms231911263. [PMID: 36232572 PMCID: PMC9569804 DOI: 10.3390/ijms231911263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/30/2022] [Accepted: 09/14/2022] [Indexed: 11/25/2022] Open
Abstract
Avian leukosis virus (ALV) induces B-cell lymphomas and other malignancies in chickens through insertional activation of oncogenes, and c-myc activation has been commonly identified in ALV-induced tumors. Using ALV-transformed B-lymphoma-derived HP45 cell line, we applied in situ CRISPR-Cas9 editing of integrated proviral long terminal repeat (LTR) to examine the effects on gene expression and cell proliferation. Targeted deletion of LTR resulted in significant reduction in expression of a number of LTR-regulated genes including c-myc. LTR deletion also induced apoptosis of HP45 cells, affecting their proliferation, demonstrating the significance of LTR-mediated regulation of critical genes. Compared to the global effects on expression and functions of multiple genes in LTR-deleted cells, deletion of c-myc had a major effect on the HP45 cells proliferation with the phenotype similar to the LTR deletion, demonstrating the significance of c-myc expression in ALV-induced lymphomagenesis. Overall, our studies have not only shown the potential of targeted editing of the LTR for the global inhibition of retrovirus-induced transformation, but also have provided insights into the roles of LTR-regulated genes in ALV-induced neoplastic transformation.
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Fan Y, Chen W, Wei R, Qiang W, Pearson JD, Yu T, Bremner R, Chen D. Mapping transgene insertion sites reveals the α-Cre transgene expression in both developing retina and olfactory neurons. Commun Biol 2022; 5:411. [PMID: 35505181 PMCID: PMC9065156 DOI: 10.1038/s42003-022-03379-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 04/18/2022] [Indexed: 02/05/2023] Open
Abstract
The Tg(Pax6-cre,GFP)2Pgr (α-Cre) mouse is a commonly used Cre line thought to be retinal-specific. Using targeted locus amplification (TLA), we mapped the insertion site of the transgene, and defined primers useful to deduce zygosity. Further analyses revealed four tandem copies of the transgene. The insertion site mapped to clusters of vomeronasal and olfactory receptor genes. Using R26R and Ai14 Cre reporter mice, we confirmed retinal Cre activity, but also detected expression in Gα0+ olfactory neurons. Most α-Cre+ olfactory neurons do not express Pax6, implicating the influence of neighboring regulatory elements. RT-PCR and buried food pellet test did not detect any effects of the transgene on flanking genes in the nasal mucosa and retina. Together, these data precisely map α-Cre, show that it does not affect surrounding loci, but reveal previously unanticipated transgene expression in olfactory neurons. The α-Cre mouse can be a valuable tool in both retinal and olfactory research. The Pax6-α-Cre mouse line used in retinal studies actually contains four transgene insertion within gene clusters of olfactory and vomeronasal receptors, leading to expression in not just retinal, but also olfactory and vomeronasal sensory neurons.
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Affiliation(s)
- Yimeng Fan
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Wenyue Chen
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Ran Wei
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Qiang
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Joel D Pearson
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Departments of Ophthalmology and Visual Science, and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Tao Yu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Departments of Ophthalmology and Visual Science, and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Rod Bremner
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Departments of Ophthalmology and Visual Science, and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
| | - Danian Chen
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China. .,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China. .,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Departments of Ophthalmology and Visual Science, and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
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Ryu J, Chan W, Wettengel JM, Hanna CB, Burwitz BJ, Hennebold JD, Bimber BN. Rapid, accurate mapping of transgene integration in viable rhesus macaque embryos using enhanced-specificity tagmentation-assisted PCR. Mol Ther Methods Clin Dev 2022; 24:241-254. [PMID: 35211637 PMCID: PMC8829455 DOI: 10.1016/j.omtm.2022.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 01/16/2022] [Indexed: 11/19/2022]
Abstract
Genome engineering is a powerful tool for in vitro research and the creation of novel model organisms and has growing clinical applications. Randomly integrating vectors, such as lentivirus- or transposase-based methods, are simple and easy to use but carry risks arising from insertional mutagenesis. Here we present enhanced-specificity tagmentation-assisted PCR (esTag-PCR), a rapid and accurate method for mapping transgene integration and copy number. Using stably transfected HepG2 cells, we demonstrate that esTag-PCR has higher integration site detection accuracy and efficiency than alternative tagmentation-based methods. Next, we performed esTag-PCR on rhesus macaque embryos derived from zygotes injected with piggyBac transposase and transposon/transgene plasmid. Using low-input trophectoderm biopsies, we demonstrate that esTag-PCR accurately maps integration events while preserving blastocyst viability. We used these high-resolution data to evaluate the performance of piggyBac-mediated editing of rhesus macaque embryos, demonstrating that increased concentration of transposon/transgene plasmid can increase the fraction of embryos with stable integration; however, the number of integrations per embryo also increases, which may be problematic for some applications. Collectively, esTag-PCR represents an important improvement to the detection of transgene integration, provides a method to validate and screen edited embryos before implantation, and represents an important advance in the creation of transgenic animal models.
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Affiliation(s)
- Junghyun Ryu
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - William Chan
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jochen M. Wettengel
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, München, 81675 Germany
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Carol B. Hanna
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Benjamin J. Burwitz
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
- Division of Pathobiology, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jon D. Hennebold
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
- Department of Obstetrics & Gynecology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Benjamin N. Bimber
- Division of Pathobiology, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
- Corresponding author Benjamin N. Bimber, PhD, Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA.
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Grassi L, Harris C, Zhu J, Hardman C, Hatton D. DetectIS: a pipeline to rapidly detect exogenous DNA integration sites using DNA or RNA paired-end sequencing data. Bioinformatics 2021; 37:4230-4232. [PMID: 33978747 PMCID: PMC9502153 DOI: 10.1093/bioinformatics/btab366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 11/13/2022] Open
Abstract
Motivation Recombinant DNA technology is widely used for different applications in biology, medicine and bio-technology. Viral transduction and plasmid transfection are among the most frequently used techniques to generate recombinant cell lines. Many of these methods result in the random integration of the plasmid into the host genome. Rapid identification of the integration sites is highly desirable in order to characterize these engineered cell lines. Results We developed detectIS: a pipeline specifically designed to identify genomic integration sites of exogenous DNA, either a plasmid containing one or more transgenes or a virus. The pipeline is based on a Nextflow workflow combined with a Singularity image containing all the necessary software, ensuring high reproducibility and scalability of the analysis. We tested it on simulated datasets and RNA-seq data from a human sample infected with Hepatitis B virus. Comparisons with other state of the art tools show that our method can identify the integration site in different recombinant cell lines, with accurate results, lower computational demand and shorter execution times. Availability and implementation The Nextflow workflow, the Singularity image and a test dataset are available at https://github.com/AstraZeneca/detectIS. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Luigi Grassi
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZenec, Cambridge, UK a
| | - Claire Harris
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZenec, Cambridge, UK a
| | - Jie Zhu
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, USA
| | - Colin Hardman
- Data Science & Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Diane Hatton
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZenec, Cambridge, UK a
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Generation of H11-albumin-rtTA Transgenic Mice: A Tool for Inducible Gene Expression in the Liver. G3-GENES GENOMES GENETICS 2019; 9:591-599. [PMID: 30591434 PMCID: PMC6385985 DOI: 10.1534/g3.118.200963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The modification of the mouse genome by site-specific gene insertion of transgenes and other genetic elements allows the study of gene function in different developmental stages and in the pathogenesis of diseases. Here, we generated a “genomic safe harbor” Hipp11 (H11) locus-specific knock-in transgenic mouse line in which the albumin promoter is used to drive the expression of the reverse tetracycline transactivator (rtTA) in the liver. The newly generated H11-albumin-rtTA transgenic mice were bred with tetracycline-operator-Histone-2B-green fluorescent protein (TetO-H2BGFP) mice to assess inducibility and tissue-specificity. Expression of the H2BGFP fusion protein was observed exclusively upon doxycycline (Dox) induction in the liver of H11-albumin-rtTA/TetO-H2BGFP double transgenic mice. To further analyze the ability of the Dox-inducible H11-albumin-rtTA mice to implement conditional DNA recombination, H11-albumin-rtTA transgenic mice were crossed with TetO-Cre and Ai14 mice to generate H11-albumin-rtTA/TetO-Cre/Ai14 triple transgenic mice. We successfully confirmed that the Cre-mediated recombination efficiency was as strong in Dox-induced H11-albumin-rtTA /TetO-Cre/Ai14 mice as in the control albumin-Cre/A14 mice. Finally, to characterize the expression-inducing effects of Dox in H11-albumin-rtTA/TetO-H2BGFP mice in detail, we examined GFP expression in embryos at different developmental stages and found that newly conceived H11-albumin-rtTA/TetO-H2BGFP embryos of Dox-treated pregnant female mice were expressing reporter GFP by E16.5. Our study demonstrates that these new H11-albumin-rtTA transgenic mice are a powerful and efficient tool for the temporally and spatially conditional manipulation of gene expression in the liver, and illustrates how genetic crosses with these new mice enable the generation of complex multi-locus transgenic animals for mechanistic studies.
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Cain-Hom C, Splinter E, van Min M, Simonis M, van de Heijning M, Martinez M, Asghari V, Cox JC, Warming S. Efficient mapping of transgene integration sites and local structural changes in Cre transgenic mice using targeted locus amplification. Nucleic Acids Res 2017; 45:e62. [PMID: 28053125 PMCID: PMC5416772 DOI: 10.1093/nar/gkw1329] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/20/2016] [Indexed: 12/23/2022] Open
Abstract
Cre/LoxP technology is widely used in the field of mouse genetics for spatial and/or temporal regulation of gene function. For Cre lines generated via pronuclear microinjection of a Cre transgene construct, the integration site is random and in most cases not known. Integration of a transgene can disrupt an endogenous gene, potentially interfering with interpretation of the phenotype. In addition, knowledge of where the transgene is integrated is important for planning of crosses between animals carrying a conditional allele and a given Cre allele in case the alleles are on the same chromosome. We have used targeted locus amplification (TLA) to efficiently map the transgene location in seven previously published Cre and CreERT2 transgenic lines. In all lines, transgene insertion was associated with structural changes of variable complexity, illustrating the importance of testing for rearrangements around the integration site. In all seven lines the exact integration site and breakpoint sequences were identified. Our methods, data and genotyping assays can be used as a resource for the mouse community and our results illustrate the power of the TLA method to not only efficiently map the integration site of any transgene, but also provide additional information regarding the transgene integration events.
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Affiliation(s)
- Carol Cain-Hom
- Department of Transgenic Technology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Erik Splinter
- Cergentis BV, Yalelaan 62, 3584 CM Utrecht, the Netherlands
| | - Max van Min
- Cergentis BV, Yalelaan 62, 3584 CM Utrecht, the Netherlands
| | | | | | - Maria Martinez
- Department of Transgenic Technology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Vida Asghari
- Department of Transgenic Technology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - J Colin Cox
- Department of Transgenic Technology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Søren Warming
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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