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Xu D, Tang L, Zhou J, Wang F, Cao H, Huang Y, Kapranov P. Evidence for widespread existence of functional novel and non-canonical human transcripts. BMC Biol 2023; 21:271. [PMID: 38001496 PMCID: PMC10675921 DOI: 10.1186/s12915-023-01753-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Fraction of functional sequence in the human genome remains a key unresolved question in Biology and the subject of vigorous debate. While a plethora of studies have connected a significant fraction of human DNA to various biochemical processes, the classical definition of function requires evidence of effects on cellular or organismal fitness that such studies do not provide. Although multiple high-throughput reverse genetics screens have been developed to address this issue, they are limited to annotated genomic elements and suffer from non-specific effects, arguing for a strong need to develop additional functional genomics approaches. RESULTS In this work, we established a high-throughput lentivirus-based insertional mutagenesis strategy as a forward genetics screen tool in aneuploid cells. Application of this approach to human cell lines in multiple phenotypic screens suggested the presence of many yet uncharacterized functional elements in the human genome, represented at least in part by novel exons of known and novel genes. The novel transcripts containing these exons can be massively, up to thousands-fold, induced by specific stresses, and at least some can represent bi-cistronic protein-coding mRNAs. CONCLUSIONS Altogether, these results argue that many unannotated and non-canonical human transcripts, including those that appear as aberrant splice products, have biological relevance under specific biological conditions.
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Affiliation(s)
- Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Lu Tang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Junjun Zhou
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fang Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Yu Huang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
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Baldrick P, McIntosh B, Prasad M. Adeno-associated virus (AAV)-based gene therapy products: What are toxicity studies in non-human primates showing us? Regul Toxicol Pharmacol 2023; 138:105332. [PMID: 36592683 DOI: 10.1016/j.yrtph.2022.105332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/01/2023]
Abstract
A number of adeno-associated virus (AAV)-based gene therapy products have entered clinical development, with a few also reaching marketing approval. However, as our knowledge of them grows from nonclinical and clinical testing, it has become apparent that various actual and theoretical safety issues can arise from their use. This review of 19 Good Laboratory Practice (GLP)-compliant toxicity studies in non-human primates (NHPs) with AAV-based gene therapy products via a variety of different dose routes in the period 2017-2021 showed results ranging from no study findings different from controls, or findings considered to be non-adverse, to actual toxicity, with changes highlighting careful monitoring in the clinic. Similar findings were found from a review of a number of published toxicity studies in NHPs. It was confirmed that studies have a role in evaluating for dorsal root ganglion (DRG) and/or peripheral nerve toxicity, hepatotoxicity, adverse immunogenicity and, to a lesser degree, insertional mutagenesis as well as other potential unacceptable findings such as adverse inflammation for ocular therapy candidates. Overall, it was demonstrated that toxicity (and biodistribution) studies in NHPs are a vital part of the safety assessment of AAV-based gene therapy products prior to clinical entry.
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Affiliation(s)
- Paul Baldrick
- Product Development and Market Access Consulting, Clinical Development & Commercialisation Services, Labcorp Drug Development Inc. (formerly Covance), Harrogate, North Yorkshire, HG3 1PY, United Kingdom
| | - Brian McIntosh
- Cell and Gene Therapy, Safety Assessment, Toxicology, Labcorp Drug Development Inc. (formerly Covance), Madison, WI, 53704, USA.
| | - Mayuri Prasad
- Cell and Gene Therapy, Safety Assessment, Toxicology, Labcorp Drug Development Inc. (formerly Covance), Madison, WI, 53704, USA.
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Gahurová D, Krajčiová D, Reichwalderová K, Slaninová M. Insertional mutagenesis in Chlamydomonas reinhardtii: An effective strategy for the identification of new genes involved in the DNA damage response. Eur J Protistol 2021; 82:125855. [PMID: 34954500 DOI: 10.1016/j.ejop.2021.125855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 11/23/2022]
Abstract
The formation of double-strand breaks in DNA represents a serious stress for all types of organisms and requires a precisely regulated and organized DNA damage response (DDR) to maintain genetic information and genome integrity. Chlamydomonas reinhardtii possesses the characteristics of both plants and animals and is therefore suitable for the identification of novel genes connected to a wide spectrum of metabolic pathways, including DDR. One very effective tool for the detection and subsequent characterization of new mutants in C. reinhardtii is insertional mutagenesis. We isolated several insertion mutants sensitive to DNA-damaging agents that had disrupted or completely deleted genes with putative functions in the DDR. In most of the analysed mutants, we identified various changes at both ends and even inside the inserted cassette. Using recent information from databases, we were also able to supplement the characteristics of the previously described mutant with a pleiotropic phenotype. In addition, we confirmed the effectiveness of hairpin-PCR as a strategy for the identification of insertion flanking sites and as a tool for the detection of changes at the site of insertion, thus enabling a better understanding of insertion events.
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Südfeld C, Hubáček M, Figueiredo D, Naduthodi MIS, van der Oost J, Wijffels RH, Barbosa MJ, D'Adamo S. High-throughput insertional mutagenesis reveals novel targets for enhancing lipid accumulation in Nannochloropsis oceanica. Metab Eng 2021; 66:239-58. [PMID: 33971293 DOI: 10.1016/j.ymben.2021.04.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/07/2021] [Accepted: 04/18/2021] [Indexed: 12/17/2022]
Abstract
The microalga Nannochloropsis oceanica is considered a promising platform for the sustainable production of high-value lipids and biofuel feedstocks. However, current lipid yields of N. oceanica are too low for economic feasibility. Gaining fundamental insights into the lipid metabolism of N. oceanica could open up various possibilities for the optimization of this species through genetic engineering. Therefore, the aim of this study was to discover novel genes associated with an elevated neutral lipid content. We constructed an insertional mutagenesis library of N. oceanica, selected high lipid mutants by five rounds of fluorescence-activated cell sorting, and identified disrupted genes using a novel implementation of a rapid genotyping procedure. One particularly promising mutant (HLM23) was disrupted in a putative APETALA2-like transcription factor gene. HLM23 showed a 40%-increased neutral lipid content, increased photosynthetic performance, and no growth impairment. Furthermore, transcriptome analysis revealed an upregulation of genes related to plastidial fatty acid biosynthesis, glycolysis and the Calvin-Benson-Bassham cycle in HLM23. Insights gained in this work can be used in future genetic engineering strategies for increased lipid productivity of Nannochloropsis.
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Goshayeshi L, Yousefi Taemeh S, Dehdilani N, Nasiri M, Ghahramani Seno MM, Dehghani H. CRISPR/dCas9-mediated transposition with specificity and efficiency of site-directed genomic insertions. FASEB J 2021; 35:e21359. [PMID: 33496003 DOI: 10.1096/fj.202001830rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 12/28/2022]
Abstract
The ability and efficiency of targeted nucleases to perform sequence replacements or insertions into the genome are limited. This limited efficiency for sequence replacements or insertions can be explained by the dependency on DNA repair pathways, the possibility of cellular toxicity, and unwanted activation of proto-oncogenes. The piggyBac (PB) transposase uses a very efficient enzymatic mechanism to integrate DNA fragments into the genome in a random manner. In this study, we fused an RNA-guided catalytically inactive Cas9 (dCas9) to the PB transposase and used dual sgRNAs to localize this molecule to specific genomic targets. We designed and used a promoter/reporter complementation assay to register and recover cells harboring-specific integrations, where only by complementation upon correct genomic integration, the reporter can be activated. Using an RNA-guided piggyBac transposase and dual sgRNAs, we were able to achieve site-directed integrations in the human ROSA26 safe harbor region in 0.32% of cells. These findings show that the methodology used in this study can be used for targeting genomic regions. An application for this finding could be in cancer cells to insert sequences into specific target regions that are intended to be destroyed, or to place promoter cargos behind the tumor suppressor genes to activate them.
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Affiliation(s)
- Lena Goshayeshi
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sara Yousefi Taemeh
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Nima Dehdilani
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammadreza Nasiri
- Recombinant Proteins Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad M Ghahramani Seno
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hesam Dehghani
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
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Rasool RS, Padder BA, Wani AA, Shah MD, Masoodi KZ, Khan NA, Banoo A, Khan I. Thyrostroma carpophilum insertional mutagenesis: A step towards understanding its pathogenicity mechanism. J Microbiol Methods 2020; 171:105885. [PMID: 32147575 DOI: 10.1016/j.mimet.2020.105885] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 11/24/2022]
Abstract
Thyrostroma carpophilum, a causal agent of shot hole disease of stone fruits, cause severe loss in economically important fruit crops of Kashmir. Understanding its pathogenesis at molecular level will aid in devising a better management strategy. In this study, we optimized Agrobacterium tumefaciens mediated transformation (ATMT) conditions for T. carpophilum using PBIF2-EGFP construct. Using this protocol, we obtained 328 positive transformants per 104 spores and subsequent sub-culturing of transformants on selective and non-selective media resulted in stable T-DNA integration. Southern blot analysis revealed that most of the transformants embodied single T-DNA integration. Using this method, we obtained a small-scale transformant library (2050 transformants). Among this pool, we tested 1005 transformants for their pathogenicity; out of which 185 showed complete pathogenicity loss, 35 displayed reduced virulence and 785 were pathogenically similar to wild type. Out of this experimental stock, three transformants from each category were randomly selected to dissect the infection assay. The findings deciphered that transformants with complete pathogenicity loss failed to penetrate the host tissue and a few transformants failed to sporulate in laboratory. Transformants from reduced category could not form appressorium and occasionally sporulated. Transformants similar to wild type were morphologically and pathogenically similar to wild type because of un-alteration in their modus operandi. Our work provides a new platform to understand the pathogenicity mechanism of T. carpophilum. The optimized ATMT protocol will help in developing large transformant library that can help to identify the virulence arsenals necessary for the pathogen to cause disease.
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Ryu AJ, Kang NK, Jeon S, Hur DH, Lee EM, Lee DY, Jeong BR, Chang YK, Jeong KJ. Development and characterization of a Nannochloropsis mutant with simultaneously enhanced growth and lipid production. Biotechnol Biofuels 2020; 13:38. [PMID: 32158502 PMCID: PMC7057510 DOI: 10.1186/s13068-020-01681-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/13/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND The necessity to develop high lipid-producing microalgae is emphasized for the commercialization of microalgal biomass, which is environmentally friendly and sustainable. Nannochloropsis are one of the best industrial microalgae and have been widely studied for their lipids, including high-value polyunsaturated fatty acids (PUFAs). Many reports on the genetic and biological engineering of Nannochloropsis to improve their growth and lipid contents have been published. RESULTS We performed insertional mutagenesis in Nannochloropsis salina, and screened mutants with high lipid contents using fluorescence-activated cell sorting (FACS). We isolated a mutant, Mut68, which showed improved growth and a concomitant increase in lipid contents. Mut68 exhibited 53% faster growth rate and 34% higher fatty acid methyl ester (FAME) contents after incubation for 8 days, resulting in a 75% increase in FAME productivity compared to that in the wild type (WT). By sequencing the whole genome, we identified the disrupted gene in Mut68 that encoded trehalose-6-phosphate (T6P) synthase (TPS). TPS is composed of two domains: TPS domain and T6P phosphatase (TPP) domain, which catalyze the initial formation of T6P and dephosphorylation to trehalose, respectively. Mut68 was disrupted at the TPP domain in the C-terminal half, which was confirmed by metabolic analyses revealing a great reduction in the trehalose content in Mut68. Consistent with the unaffected N-terminal TPS domain, Mut68 showed moderate increase in T6P that is known for regulation of sugar metabolism, growth, and lipid biosynthesis. Interestingly, the metabolic analyses also revealed a significant increase in stress-related amino acids, including proline and glutamine, which may further contribute to the Mut68 phenotypes. CONCLUSION We have successfully isolated an insertional mutant showing improved growth and lipid production. Moreover, we identified the disrupted gene encoding TPS. Consistent with the disrupted TPP domain, metabolic analyses revealed a moderate increase in T6P and greatly reduced trehalose. Herein, we provide an excellent proof of concept that the selection of insertional mutations via FACS can be employed for the isolation of mutants with improved growth and lipid production. In addition, trehalose and genes encoding TPS will provide novel targets for chemical and genetic engineering, in other microalgae and organisms as well as Nannochloropsis.
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Affiliation(s)
- Ae Jin Ryu
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Advanced Biomass R&D Center (ABC), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Nam Kyu Kang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Present Address: Carl. R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Seungjib Jeon
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Advanced Biomass R&D Center (ABC), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Dong Hoon Hur
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Eun Mi Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Do Yup Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Byeong-ryool Jeong
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Present Address: School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Korea
- Present Address: Single-Cell Center, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Qingdao, 266101 Shandong China
| | - Yong Keun Chang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Advanced Biomass R&D Center (ABC), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
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Li J, Hong N, Peng B, Wu H, Gu Q. Transformation of Corynespora cassiicola by Agrobacterium tumefaciens. Fungal Biol 2019; 123:669-675. [PMID: 31416586 DOI: 10.1016/j.funbio.2019.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/28/2019] [Accepted: 05/24/2019] [Indexed: 11/16/2022]
Abstract
The fungus causing target spot disease, Corynespora cassiicola (Berk. & M. A. Curtis) C. T. Wei, poses an increasing threat to watermelon (Citrullus lanatus), muskmelon (Cucumis melo), and cucumber (Cucumis sativus); the most economically important cucurbit crops grown in China. An understanding of the molecular mechanisms underlying the pathogenicity of C. cassiicola is essential for the development of new strategies to control this disease-causing fungus. Agrobacterium tumefaciens-mediated transformation (ATMT) might be useful to obtain transformants of C. cassiicola, for the ultimate identification of genes involved in pathogenicity. In the present work, we established and optimized an ATMT protocol using A. tumefaciens strain AGL-1 carrying the vector pATMT1 for C. cassiicola. Efficiency of ATMT was 102-148 transformants per 106 conidia and successive subculturing of transformants on non-selective and selective media demonstrated that the integrated transfer (T)-DNA was stably inherited in C. cassiicola transformants. The integration of the hygromycin B phosphotransferase (hph) gene into C. cassiicola was validated by PCR and Southern blot analyses, which revealed that nearly 90 % of the transformants contained single-copy T-DNA. The transformants with altered phenotypes were characterized. Three of these transformants completely lost pathogenicity and other three showed strongly impaired pathogenicity relative to the Cc-GX strain on muskmelon leaves. These results strongly suggest that ATMT may be used as a molecular tool for identifying genes relevant to pathogenicity in the fungus C. cassiicola, an emerging threat to several agronomically important plants in China.
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Affiliation(s)
- Junxiang Li
- Henan Provincial Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, Henan, China; College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Ni Hong
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Bin Peng
- Henan Provincial Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, Henan, China
| | - Huijie Wu
- Henan Provincial Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, Henan, China
| | - Qinsheng Gu
- Henan Provincial Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, Henan, China.
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Abstract
Transposable element (TE) insertions are responsible for a significant fraction of spontaneous germ line mutations reported in inbred mouse strains. This major contribution of TEs to the mutational landscape in mouse contrasts with the situation in human, where their relative contribution as germ line insertional mutagens is much lower. In this focussed review, we provide comprehensive lists of TE-induced mouse mutations, discuss the different TE types involved in these insertional mutations and elaborate on particularly interesting cases. We also discuss differences and similarities between the mutational role of TEs in mice and humans.
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Affiliation(s)
- Liane Gagnier
- 1Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
| | - Victoria P Belancio
- 2Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| | - Dixie L Mager
- 1Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
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Abstract
Cancer is a complex disease that originates from genetic changes leading to multiple phenotypic manifestations that ultimately result in suffering and death from cancer. Attempts have been made to define the phenotypic and genetic "hallmarks" of cancer, but many of these "hallmarks" remain descriptive, while the underlying mechanisms responsible for these hallmarks remain elusive. For decades, cancer researchers have been methodically identifying the molecular mechanisms that result in tumor initiation, growth, metastases, and resistance to therapy. Great strides forward have been made and we are entering an era of "precision medicine" with the goal of treating each cancer based on its unique etiology. Increasingly, the decision to use targeted therapies and immunotherapies in the clinic is based on the genotype of the cancer being treated. For example, specific tyrosine kinase inhibitors are only prescribed to patients that express the tyrosine kinase protein on their cancer cells. Likewise, a genetically unstable cancer is predictive for successful immunotherapy. Knowledge of the specific genetic changes that result in overproduction of oncogenes and reduced production of tumor suppressors is crucial for advancing therapeutic options for cancer. The first chapter of this book presents a brief history of cancer gene discovery. In the remaining chapters of this book, we present protocols using in silico, in vitro, and in vivo techniques for identifying genetic drivers of cancer, in the hope that these protocols will be used to increase our knowledge of the molecular mechanisms driving cancer.
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Abstract
Transposable elements are DNA sequences with the ability to move from one genomic location to another. The movement of class II transposable elements has been functionally harnessed and separated into two distinct DNA transposon components: the terminal inverted repeat sequences that flank genetic cargo to be mobilized and a transposase enzyme capable of recognizing the terminal inverted repeat sequences and catalyzing the transposition reaction. In particular, the Sleeping Beauty (SB) system was the first successful demonstration of transposon-based gene transfer in vertebrate species. Over the years, several improvements have been made to SB technology and more recent studies have demonstrated the versatility of the system for many applications including insertional mutagenesis, gene transfer, and transgenesis. These genetic engineering advances made available by SB both augment and advance large-scale efforts that have been directed toward identifying how genes and environmental factors influence human health in recent years. In the age of personalized medicine, the versatility of SB provides numerous genetic engineering avenues for answering novel questions in basic and applied research. This chapter discusses the use of SB-based insertional mutagenesis in mice for the efficient identification of candidate cancer genes across numerous types of cancers.
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Affiliation(s)
- Kelsie L Becklin
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- College of Veterinary Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Branden A Smeester
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- College of Veterinary Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
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Abstract
While sequencing and array-based studies are creating catalogues of genetic alterations in cancer, discriminating cancer drivers among the large sets of epigenetically, transcriptionally or posttranslationally dysregulated genes remains a challenge. Transposon-based genetic screening in mice has proven to be a powerful approach to address this challenge. Insertional mutagenesis directly flags biologically relevant genes and, combined with the transposon's unique molecular fingerprint, facilitates the recovery of insertion sites. We have generated transgenic mouse lines harboring different versions of PiggyBac-based oncogenic transposons, which in conjunction with PiggyBac transposase mice can be used for whole-body or tissue-specific insertional mutagenesis screens. We have also developed QiSeq, a method for (semi-)quantitative transposon insertion site sequencing, which overcomes biasing limitations of previous library preparation methods. QiSeq can be used in multiplexed high-throughput formats for candidate cancer gene discovery and gives insights into the clonal distribution of insertions for the study of genetic tumor evolution.
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Liu Y, Koh CMJ, Yap SA, Du M, Hlaing MM, Ji L. Identification of novel genes in the carotenogenic and oleaginous yeast Rhodotorula toruloides through genome-wide insertional mutagenesis. BMC Microbiol 2018; 18:14. [PMID: 29466942 PMCID: PMC5822628 DOI: 10.1186/s12866-018-1151-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 01/30/2018] [Indexed: 01/15/2023] Open
Abstract
Background Rhodotorula toruloides is an outstanding producer of lipids and carotenoids. Currently, information on the key metabolic pathways and their molecular basis of regulation remains scarce, severely limiting efforts to engineer it as an industrial host. Results We have adapted Agrobacterium tumefaciens-mediated transformation (ATMT) as a gene-tagging tool for the identification of novel genes in R. toruloides. Multiple factors affecting transformation efficiency in several species in the Pucciniomycotina subphylum were optimized. The Agrobacterium transfer DNA (T-DNA) showed predominantly single-copy chromosomal integrations in R. toruloides, which were trackable by high efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR). To demonstrate the application of random T-DNA insertions for strain improvement and gene hunting, 3 T-DNA insertional libraries were screened against cerulenin, nile red and tetrazolium violet respectively, resulting in the identification of 22 mutants with obvious phenotypes in fatty acid or lipid metabolism. Similarly, 5 carotenoid biosynthetic mutants were obtained through visual screening of the transformants. To further validate the gene tagging strategy, one of the carotenoid production mutants, RAM5, was analyzed in detail. The mutant had a T-DNA inserted at the putative phytoene desaturase gene CAR1. Deletion of CAR1 by homologous recombination led to a phenotype similar to RAM5 and it could be genetically complemented by re-introduction of the wild-type CAR1 genome sequence. Conclusions T-DNA insertional mutagenesis is an efficient forward genetic tool for gene discovery in R. toruloides and related oleaginous yeast species. It is also valuable for metabolic engineering in these hosts. Further analysis of the 27 mutants identified in this study should augment our knowledge of the lipid and carotenoid biosynthesis, which may be exploited for oil and isoprenoid metabolic engineering. Electronic supplementary material The online version of this article (10.1186/s12866-018-1151-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanbin Liu
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
| | - Chong Mei John Koh
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Sihui Amy Yap
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Minge Du
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Mya Myintzu Hlaing
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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14
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Kong F, Li-Beisson Y. Identification of Insertion Site by RESDA-PCR in Chlamydomonas Mutants Generated by AphVIII Random Insertional Mutagenesis. Bio Protoc 2018; 8:e2718. [PMID: 34179256 DOI: 10.21769/bioprotoc.2718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/16/2018] [Accepted: 01/18/2018] [Indexed: 11/02/2022] Open
Abstract
Chlamydomonas reinhardtii is frequently used as a model organism to study fundamental processes in photosynthesis, metabolism, and flagellar biology. Versatile tool boxes have been developed for this alga ( Fuhrmann et al., 1999 ; Schroda et al., 2000 ; Schroda, 2006). Among them, forward genetic approach has been intensively used, mostly because of the high efficiency in the generation of hundreds of thousands of mutants by random insertional mutagenesis and the haploid nature therefore phenotypic analysis can be done in the first generation ( Cagnon et al., 2013 ; Tunçay et al., 2013 ). A major bottleneck in the application of high throughput methods in a forward genetic approach is the identification of the genetic lesion(s) responsible for the observed phenotype. In this protocol, we describe in detail an improved version of the restriction enzyme site-directed amplification PCR (RESDA-PCR) originally reported in (González- Ballester et al., 2005 ). The improvement includes optimization of primer combination, the choice of DNA polymerase, optimization of PCR cycle parameters, and application of direct sequencing of the PCR products. These modifications make it easier to get specific PCR products as well as speeding up subcloning steps to obtain sequencing data faster.
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Affiliation(s)
- Fantao Kong
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et Biotechnologie, CEA Cadarache, Saint-Paul-lez-Durance, France.,Centre National de la Recherche Scientifique, UMR7265, Saint-Paul-lez-Durance, France.,Aix-Marseille Université, UMR7265, Marseille, France
| | - Yonghua Li-Beisson
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et Biotechnologie, CEA Cadarache, Saint-Paul-lez-Durance, France.,Centre National de la Recherche Scientifique, UMR7265, Saint-Paul-lez-Durance, France.,Aix-Marseille Université, UMR7265, Marseille, France
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15
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Gerhards NM, Rottenberg S. New tools for old drugs: Functional genetic screens to optimize current chemotherapy. Drug Resist Updat 2018; 36:30-46. [PMID: 29499836 DOI: 10.1016/j.drup.2018.01.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/29/2017] [Accepted: 01/06/2018] [Indexed: 12/26/2022]
Abstract
Despite substantial advances in the treatment of various cancers, many patients still receive anti-cancer therapies that hardly eradicate tumor cells but inflict considerable side effects. To provide the best treatment regimen for an individual patient, a major goal in molecular oncology is to identify predictive markers for a personalized therapeutic strategy. Regarding novel targeted anti-cancer therapies, there are usually good markers available. Unfortunately, however, targeted therapies alone often result in rather short remissions and little cytotoxic effect on the cancer cells. Therefore, classical chemotherapy with frequent long remissions, cures, and a clear effect on cancer cell eradication remains a corner stone in current anti-cancer therapy. Reliable biomarkers which predict the response of tumors to classical chemotherapy are rare, in contrast to the situation for targeted therapy. For the bulk of cytotoxic therapeutic agents, including DNA-damaging drugs, drugs targeting microtubules or antimetabolites, there are still no reliable biomarkers used in the clinic to predict tumor response. To make progress in this direction, meticulous studies of classical chemotherapeutic drug action and resistance mechanisms are required. For this purpose, novel functional screening technologies have emerged as successful technologies to study chemotherapeutic drug response in a variety of models. They allow a systematic analysis of genetic contributions to a drug-responsive or −sensitive phenotype and facilitate a better understanding of the mode of action of these drugs. These functional genomic approaches are not only useful for the development of novel targeted anti-cancer drugs but may also guide the use of classical chemotherapeutic drugs by deciphering novel mechanisms influencing a tumor’s drug response. Moreover, due to the advances of 3D organoid cultures from patient tumors and in vivo screens in mice, these genetic screens can be applied using conditions that are more representative of the clinical setting. Patient-derived 3D organoid lines furthermore allow the characterization of the “essentialome”, the specific set of genes required for survival of these cells, of an individual tumor, which could be monitored over the course of treatment and help understanding how drug resistance evolves in clinical tumors. Thus, we expect that these functional screens will enable the discovery of novel cancer-specific vulnerabilities, and through clinical validation, move the field of predictive biomarkers forward. This review focuses on novel advanced techniques to decipher the interplay between genetic alterations and drug response.
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16
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Abstract
Iron acquisition systems are critical for bacterial pathogenesis and thus have been proposed as attractive targets for iron-dependent pathogen control. Of these systems, high-affinity iron acquisition mediated by siderophore, a small iron chelator, is the most efficient iron-scavenging mechanism in gram-negative bacteria. Campylobacter does not produce any siderophores but has the ability to utilize exogenous siderophores. In particular, the enterobactin (Ent)-mediated iron scavenging is tightly linked to Campylobacter pathogenesis. To date, Ent, a triscatecholate with the highest known affinity for ferric iron, is a well-characterized siderophore used by Campylobacter for iron acquisition during in vivo infection. Here, we describe the key methods used to characterize Ent-mediated high affinity iron acquisition system in Campylobacter jejuni.
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Affiliation(s)
- Ximin Zeng
- Department of Animal Science, University of Tennessee, 2506 River Drive, Knoxville, TN, 37996-4574, USA
| | - Jun Lin
- Department of Animal Science, University of Tennessee, 2506 River Drive, Knoxville, TN, 37996-4574, USA.
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17
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Gill US, Serrani-Yarce JC, Lee HK, Mysore KS. Tissue Culture (Somatic Embryogenesis)-Induced Tnt1 Retrotransposon-Based Mutagenesis in Brachypodium distachyon. Methods Mol Biol 2018; 1667:57-63. [PMID: 29039003 DOI: 10.1007/978-1-4939-7278-4_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Brachypodium distachyon is a model grass species for economically important cereal crops. Efforts are in progress to develop useful functional genomic resources in Brachypodium. A tobacco retrotransposon, Tnt1, has been used successfully in recent past to generate insertional mutagenesis in several dicot plant species. Tnt1 retrotransposon replicates, transposes, and inserts at multiple random genomic locations in the plant genome. Transposition occurs only during somatic embryogenesis but not during seed transmission. We developed Brachypodium transgenic plants that can express the Tnt1 element. Here, we describe an efficient tissue culture-based approach to generate Tnt1 insertional mutant population using transgenic Brachypodium line expressing the Tnt1 retrotransposon.
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Affiliation(s)
- Upinder S Gill
- Noble Research Institute, LLC., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Juan C Serrani-Yarce
- Noble Research Institute, LLC., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Hee-Kyung Lee
- Noble Research Institute, LLC., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Kirankumar S Mysore
- Noble Research Institute, LLC., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA.
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18
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Smirnov AV, Kontsevaya GV, Feofanova NA, Anisimova MV, Serova IA, Gerlinskaya LA, Battulin NR, Moshkin MP, Serov OL. Unexpected phenotypic effects of a transgene integration causing a knockout of the endogenous Contactin-5 gene in mice. Transgenic Res 2017; 27:1-13. [PMID: 29264679 DOI: 10.1007/s11248-017-0053-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/01/2017] [Indexed: 01/06/2023]
Abstract
Contactins (Cntn1-6) are a family of neuronal membrane proteins expressed in the brain. They are required for establishing cell-to-cell contacts between neurons and for the growth and maturation of the axons. In humans, structural genomic variations in the Contactin genes are implicated in neurodevelopmental disorders. In addition, population genetic studies associate Contactins loci with obesity and hypertension. Cntn5 knockout mice were first described in 2003, but showed no gross physiological or behavioral abnormalities (just minor auditory defects). We report a novel Cntn5 knockout mouse line generated by a random transgene integration as an outcome of pronuclear microinjection. Investigation of the transgene integration site revealed that the 6Kbp transgene construct coding for the human granulocyte-macrophage colony-stimulating factor (hGMCSF) replaced 170 Kbp of the Cntn5 gene, including four exons. Reverse transcription PCR analysis of the Cntn5 transcripts in the wild-type and transgenic mouse lines showed that splicing of the transgene leads to a set of chimeric hGMCSF-Cntn5 transcript variants, none of which encode functional Cntn5 protein due to introduction of stop codons. Although Cntn5 knockout animals displayed no abnormalities in behavior, we noted that they were leaner, with less body mass and fat percentage than wild-type animals. Their cardiovascular parameters (heart rate, blood pressure and blood flow speed) were elevated compared to controls. These findings link Cntn5 deficiency to obesity and hypertension.
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Affiliation(s)
- Alexander V Smirnov
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia.
| | - Galina V Kontsevaya
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia A Feofanova
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Margarita V Anisimova
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Irina A Serova
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lyudmila A Gerlinskaya
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nariman R Battulin
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Mikhail P Moshkin
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Oleg L Serov
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia. .,Novosibirsk State University, Novosibirsk, Russia.
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19
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Vu TX, Ngo TT, Mai LTD, Bui TT, Le DH, Bui HTV, Nguyen HQ, Ngo BX, Tran VT. A highly efficient Agrobacterium tumefaciens-mediated transformation system for the postharvest pathogen Penicillium digitatum using DsRed and GFP to visualize citrus host colonization. J Microbiol Methods 2018; 144:134-44. [PMID: 29175534 DOI: 10.1016/j.mimet.2017.11.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/21/2017] [Accepted: 11/21/2017] [Indexed: 11/21/2022]
Abstract
Penicillium digitatum is a major postharvest pathogen of citrus crops. This fungus broadly spreads worldwide and causes green mold disease, which results in severe losses for citrus production. Understanding of the citrus infection by P. digitatum may help develop effective strategies for controlling this pathogen. In this study, we have characterized a virulent strain of P. digitatum isolated in Vietnam and established a highly efficient Agrobacterium tumefaciens-mediated transformation (ATMT) system for this fungal strain with two newly constructed binary vectors. These binary vectors harbor dominant selectable markers for hygromycin or nourseothricin resistance, and expression cassettes for the red fluorescent protein (DsRed) or the green fluorescent protein (GFP), respectively. Using the established ATMT system, the transformation efficiency of the Vietnamese strain could reach a very high yield of 1240±165 transformants per 106 spores. Interestingly, we found that GFP is much better than DsRed for in situ visualization of citrus fruit colonization by the fungus. Additionally, we showed that the transformation system can also be used to generate T-DNA insertion mutants for screening non-pathogenic or less virulent strains. Our work provides a new platform including a virulent tropical strain of P. digitatum, an optimized ATMT method and two newly constructed binary vectors for investigation of the postharvest pathogen. This platform will help develop strategies to dissect molecular mechanisms of host-pathogen interactions in more detail as well as to identify potential genes of pathogenicity by either insertional mutagenesis or gene disruption in this important pathogenic fungus.
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20
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Xu X, Tailor CS, Grunebaum E. Gene therapy for primary immune deficiencies: a Canadian perspective. Allergy Asthma Clin Immunol 2017; 13:14. [PMID: 28261277 PMCID: PMC5327566 DOI: 10.1186/s13223-017-0184-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/11/2017] [Indexed: 12/11/2022]
Abstract
The use of gene therapy (GT) for the treatment of primary immune deficiencies (PID) including severe combined immune deficiency (SCID) has progressed significantly in the recent years. In particular, long-term studies have shown that adenosine deaminase (ADA) gene delivery into ADA-deficient hematopoietic stem cells that are then transplanted into the patients corrects the abnormal function of the ADA enzyme, which leads to immune reconstitution. In contrast, the outcome was disappointing for patients with X-linked SCID, Wiskott-Aldrich syndrome and chronic granulomatous disease who received GT followed by autologous gene corrected transplantations, as many developed hematological malignancies. The malignancies were attributed to the predilection of the viruses used for gene delivery to integrated at oncogenic areas. The availability of safer and more efficient self-inactivating lentiviruses for gene delivery has reignited the interest in GT for many PID that are now in various stages of pre-clinical studies and clinical trials. Moreover, advances in early diagnosis of PID and gene editing technology coupled with enhanced abilities to generate and manipulate stem cells ex vivo are expected to further contribute to the benefit of GT for PID. Here we review the past, the present and the future of GT for PID, with particular emphasis on the Canadian perspective.
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Affiliation(s)
- Xiaobai Xu
- Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON Canada
| | | | - Eyal Grunebaum
- Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON Canada
- Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, ON Canada
- University of Toronto, Toronto, ON Canada
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21
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Abstract
Chronic hepatitis B virus (HBV) infection is a major cause of liver cirrhosis and hepatocellular carcinoma (HCC), leading to ~600,000 deaths per year worldwide. Many of the steps that occur during progression from the normal liver to cirrhosis and/or HCC are unknown. Integration of HBV DNA into random sites in the host cell genome occurs as a by-product of the HBV replication cycle and forms a unique junction between virus and cellular DNA. Analyses of integrated HBV DNA have revealed that HCCs are clonal and imply that they develop from the transformation of hepatocytes, the only liver cell known to be infected by HBV. Integrated HBV DNA has also been shown, at least in some tumors, to cause insertional mutagenesis in cancer driver genes, which may facilitate the development of HCC. Studies of HBV DNA integration in the histologically normal liver have provided additional insight into HBV-associated liver disease, suggesting that hepatocytes with a survival or growth advantage undergo high levels of clonal expansion even in the absence of oncogenic transformation. Here we describe inverse nested PCR (invPCR), a highly sensitive method that allows detection, sequencing, and enumeration of virus-cell DNA junctions formed by the integration of HBV DNA. The invPCR protocol is composed of two major steps: inversion of the virus-cell DNA junction and single-molecule nested PCR. The invPCR method is highly specific and inexpensive and can be tailored to DNA extracted from large or small amounts of liver. This procedure also allows detection of genome-wide random integration of any known DNA sequence and is therefore a useful technique for molecular biology, virology, and genetic research.
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Affiliation(s)
- Thomas Tu
- Liver Cell Biology Laboratory, Centenary Institute, Sydney, NSW, 2050, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, 2050, Australia
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Allison R Jilbert
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.
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22
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Abstract
Dissecting the contribution of genes to virulence in fulfillment of Molecular Koch's postulates is essential for developing prevention and treatment strategies for bacterial pathogens. This chapter will discuss the application of a targeted, intron-based insertional mutagenesis method for creating mutants in the obligate, intracellular bacterial pathogen Chlamydia trachomatis. The methods employed for intron targeting, mutant selection, and mutant verification will be outlined including available selection markers, gene targeting strategies, and potential pitfalls.
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Affiliation(s)
- Charlotte E Key
- Department of Microbiology, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA
| | - Derek J Fisher
- Department of Microbiology, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA.
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23
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Abstract
Cancer has been recognized for thousands of years. Egyptians believed that cancer occurred at the will of the gods. Hippocrates believed human disease resulted from an imbalance of the four humors: blood, phlegm, yellow bile, and black bile with cancer being caused by excess black bile. The lymph theory of cancer replaced the humoral theory and the blastema theory replaced the lymph theory. Rudolph Virchow was the first to recognize that cancer cells like all cells came from other cells and believed chronic irritation caused cancer. At the same time there was a belief that trauma caused cancer, though it never evolved after many experiments inducing trauma. The birth of virology occurred in 1892 when Dimitri Ivanofsky demonstrated that diseased tobacco plants remained infective after filtering their sap through a filter that trapped bacteria. Martinus Beijerinck would call the tiny infective agent a virus and both Dimitri Ivanofsky and Marinus Beijerinck would become the fathers of virology. Not to long thereafter, Payton Rous founded the field of tumor virology in 1911 with his discovery of a transmittable sarcoma of chickens by what would come to be called Rous sarcoma virus or RSV for short. The first identified human tumor virus was the Epstein-Barr virus (EBV), named after Tony Epstein and Yvonne Barr who visualized the virus particles in Burkitt's lymphoma cells by electron microscopy in 1965. Since that time, many viruses have been associated with carcinogenesis including the most studied, human papilloma virus associated with cervical carcinoma, many other anogenital carcinomas, and oropharyngeal carcinoma. The World Health Organization currently estimates that approximately 22% of worldwide cancers are attributable to infectious etiologies, of which viral etiologies is estimated at 15-20%. The field of tumor virology/viral carcinogenesis has not only identified viruses as etiologic agents of human cancers, but has also given molecular insights to all human cancers including the oncogene activation and tumor suppressor gene inactivation.
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Affiliation(s)
- A J Smith
- Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - L A Smith
- Texas Tech University Health Sciences Center, Lubbock, TX, United States.
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24
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Stephan BI, Alvarez Crespo MC, Kemppainen MJ, Pardo AG. Agrobacterium-mediated insertional mutagenesis in the mycorrhizal fungus Laccaria bicolor. Curr Genet 2016; 63:215-227. [PMID: 27387518 DOI: 10.1007/s00294-016-0627-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/22/2016] [Accepted: 06/24/2016] [Indexed: 11/24/2022]
Abstract
Agrobacterium-mediated gene transfer (AMT) is extensively employed as a tool in fungal functional genomics and accordingly, in previous studies we used AMT on a dikaryotic strain of the ectomycorrhizal basidiomycete Laccaria bicolor. The interest in this fungus derives from its capacity to establish a symbiosis with tree roots, thereby playing a major role in nutrient cycling of forest ecosystems. The ectomycorrhizal symbiosis is a highly complex interaction involving many genes from both partners. To advance in the functional characterization of fungal genes, AMT was used on a monokaryotic L. bicolor. A collection of over 1200 transgenic strains was produced, of which 200 randomly selected strains were analyzed for their genomic T-DNA insertion patterns. By means of insertional mutagenesis, a number of transgenic strains were obtained displaying differential growth features. Moreover, mating with a compatible strain resulted in dikaryons that retained altered phenotypic features of the transgenic monokaryon. The analysis of the T-DNA integration pattern revealed mostly similar results to those reported in earlier studies, confirming the usefulness of AMT on different genetic backgrounds of L. bicolor. Taken together, our studies display the great versatility and potentiality of AMT as a tool for the genetic characterization of L. bicolor.
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Affiliation(s)
- B I Stephan
- Laboratorio de Micología Molecular, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Consejo Nacional de Investigaciones Científicas y Técnicas, Roque Saenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - M C Alvarez Crespo
- Laboratorio de Micología Molecular, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Consejo Nacional de Investigaciones Científicas y Técnicas, Roque Saenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - M J Kemppainen
- Laboratorio de Micología Molecular, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Consejo Nacional de Investigaciones Científicas y Técnicas, Roque Saenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - A G Pardo
- Laboratorio de Micología Molecular, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Consejo Nacional de Investigaciones Científicas y Técnicas, Roque Saenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina.
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25
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Fronza R, Vasciaveo A, Benso A, Schmidt M. A Graph Based Framework to Model Virus Integration Sites. Comput Struct Biotechnol J 2016; 14:69-77. [PMID: 27257470 PMCID: PMC4874582 DOI: 10.1016/j.csbj.2015.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 10/20/2015] [Accepted: 10/23/2015] [Indexed: 12/03/2022] Open
Abstract
With next generation sequencing thousands of virus and viral vector integration genome targets are now under investigation to uncover specific integration preferences and to define clusters of integration, termed common integration sites (CIS), that may allow to assess gene therapy safety or to detect disease related genomic features such as oncogenes. Here, we addressed the challenge to: 1) define the notion of CIS on graph models, 2) demonstrate that the structure of CIS enters in the category of scale-free networks and 3) show that our network approach analyzes CIS dynamically in an integrated systems biology framework using the Retroviral Transposon Tagged Cancer Gene Database (RTCGD) as a testing dataset.
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Affiliation(s)
- Raffaele Fronza
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
| | - Alessandro Vasciaveo
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Alfredo Benso
- Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Manfred Schmidt
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
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26
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Abstract
Biological systems are highly complex, and for this reason there is a considerable degree of uncertainty as to the consequences of making significant interventions into their workings. Since a number of new technologies are already impinging on living systems, including our bodies, many of us have become participants in large-scale "social experiments". I will discuss biological complexity and its relevance to the technologies that brought us BSE/vCJD and the controversy over GM foods. Then I will consider some of the complexities of our social dynamics, and argue for making a shift from using the precautionary principle to employing the approach of evaluating the introduction of new technologies by conceiving of them as social experiments.
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Affiliation(s)
- Ronnie Hawkins
- Department of Philosophy, University of Central Florida, Orlando, FL, 32816-1352, USA.
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27
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El Khatib MM, Ohmine S, Jacobus EJ, Tonne JM, Morsy SG, Holditch SJ, Schreiber CA, Uetsuka K, Fusaki N, Wigle DA, Terzic A, Kudva YC, Ikeda Y. Tumor-Free Transplantation of Patient-Derived Induced Pluripotent Stem Cell Progeny for Customized Islet Regeneration. Stem Cells Transl Med 2016; 5:694-702. [PMID: 26987352 PMCID: PMC4835241 DOI: 10.5966/sctm.2015-0017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 09/23/2015] [Indexed: 01/27/2023] Open
Abstract
UNLABELLED Human induced pluripotent stem cells (iPSCs) and derived progeny provide invaluable regenerative platforms, yet their clinical translation has been compromised by their biosafety concern. Here, we assessed the safety of transplanting patient-derived iPSC-generated pancreatic endoderm/progenitor cells. Transplantation of progenitors from iPSCs reprogrammed by lentiviral vectors (LV-iPSCs) led to the formation of invasive teratocarcinoma-like tumors in more than 90% of immunodeficient mice. Moreover, removal of primary tumors from LV-iPSC progeny-transplanted hosts generated secondary and metastatic tumors. Combined transgene-free (TGF) reprogramming and elimination of residual pluripotent cells by enzymatic dissociation ensured tumor-free transplantation, ultimately enabling regeneration of type 1 diabetes-specific human islet structures in vivo. The incidence of tumor formation in TGF-iPSCs was titratable, depending on the oncogenic load, with reintegration of the cMYC expressing vector abolishing tumor-free transplantation. Thus, transgene-free cMYC-independent reprogramming and elimination of residual pluripotent cells are mandatory steps in achieving transplantation of iPSC progeny for customized and safe islet regeneration in vivo. SIGNIFICANCE Pluripotent stem cell therapy for diabetes relies on the safety as well as the quality of derived insulin-producing cells. Data from this study highlight prominent tumorigenic risks of induced pluripotent stem cell (iPSC) products, especially when reprogrammed with integrating vectors. Two major underlying mechanisms in iPSC tumorigenicity are residual pluripotent cells and cMYC overload by vector integration. This study also demonstrated that combined transgene-free reprogramming and enzymatic dissociation allows teratoma-free transplantation of iPSC progeny in the mouse model in testing the tumorigenicity of iPSC products. Further safety assessment and improvement in iPSC specification into a mature β cell phenotype would lead to safe islet replacement therapy for diabetes.
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Affiliation(s)
| | - Seiga Ohmine
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Egon J Jacobus
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jason M Tonne
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Salma G Morsy
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Sara J Holditch
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Claire A Schreiber
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Koji Uetsuka
- Laboratory of Animal Health and Hygiene, Department of Biological Production Science, College of Agriculture, Ibaraki University, Ibaraki, Japan
| | - Noemi Fusaki
- PRESTO, Japan Science and Technology Agency, Saitama, Japan Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Dennis A Wigle
- Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Andre Terzic
- Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota, USA Division of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota, USA Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota, USA
| | - Yogish C Kudva
- Division of Endocrinology, Mayo Clinic, Rochester, Minnesota, USA
| | - Yasuhiro Ikeda
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota, USA
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Abstract
Colorectal cancer (CRC) constitutes a major public health problem as the third most commonly diagnosed and third most lethal malignancy worldwide. The prevalence and the physical accessibility to colorectal tumors have made CRC an ideal model for the study of tumor genetics. Early research efforts using patient derived CRC samples led to the discovery of several highly penetrant mutations (e.g., APC, KRAS, MMR genes) in both hereditary and sporadic CRC tumors. This knowledge has enabled researchers to develop genetically engineered and chemically induced tumor models of CRC, both of which have had a substantial impact on our understanding of the molecular basis of CRC. Despite these advances, the morbidity and mortality of CRC remains a cause for concern and highlight the need to uncover novel genetic drivers of CRC. This review focuses on mouse models of CRC with particular emphasis on a newly developed cancer gene discovery tool, the Sleeping Beauty transposon-based mutagenesis model of CRC.
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MESH Headings
- Adenomatous Polyposis Coli/genetics
- Adenomatous Polyposis Coli/metabolism
- Adenomatous Polyposis Coli/pathology
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Colorectal Neoplasms, Hereditary Nonpolyposis/genetics
- Colorectal Neoplasms, Hereditary Nonpolyposis/metabolism
- Colorectal Neoplasms, Hereditary Nonpolyposis/pathology
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Humans
- Mice
- Mutation
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/metabolism
- Neoplasms, Experimental/pathology
- Phenotype
- Transposases/genetics
- Transposases/metabolism
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29
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Liu N, Chen GQ, Ning GA, Shi HB, Zhang CL, Lu JP, Mao LJ, Feng XX, Liu XH, Su ZZ, Lin FC. Agrobacterium tumefaciens-mediated transformation: An efficient tool for insertional mutagenesis and targeted gene disruption in Harpophora oryzae. Microbiol Res 2015; 182:40-8. [PMID: 26686612 DOI: 10.1016/j.micres.2015.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 09/22/2015] [Accepted: 09/28/2015] [Indexed: 12/01/2022]
Abstract
The endophytic filamentous fungus Harpophora oryzae is a beneficial endosymbiont isolated from the wild rice. H. oryzae could not only effectively improve growth rate and biomass yield of rice crops, but also induce systemic resistance against the rice blast fungus, Magnaporthe oryzae. In this study, Agrobacterium tumefaciens-mediated transformation (ATMT) was employed and optimized to modify the H. oryzae genes by either random DNA fragment integration or targeted gene replacement. Our results showed that co-cultivation of H. oryzae conidia with A. tumefaciens in the presence of acetosyringone for 48 h at 22 °C could lead to a relatively highest frequency of transformation, and 200 μM acetosyringone (AS) pre-cultivation of A. tumefaciens is also suggested. ATMT-mediated knockout mutagenesis was accomplished with the gene-deletion cassettes using a yeast homologous recombination method with a yeast-Escherichia-Agrobacterium shuttle vector pKOHo. Using the ATMT-mediated knockout mutagenesis, we successfully deleted three genes of H. oryzae (HoATG5, HoATG7, and HoATG8), and then got the null mutants ΔHoatg5, ΔHoatg7, and ΔHoatg8. These results suggest that ATMT is an efficient tool for gene modification including randomly insertional mutagenesis and gene deletion mutagenesis in H. oryzae.
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Affiliation(s)
- Ning Liu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Guo-Qing Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guo-Ao Ning
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Huan-Bin Shi
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chu-Long Zhang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jian-Ping Lu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Li-Juan Mao
- Analysis Center of Agrobiology and Environmental Science, Zhejiang University, Hangzhou, China
| | - Xiao-Xiao Feng
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiao-Hong Liu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhen-Zhu Su
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
| | - Fu-Cheng Lin
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China; China Tobacco Gene Research Center, Zhengzhou Tobacco Institute of CNTC, Zhengzhou, China.
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30
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Lin F, Liu Q, Yuan Y, Hong Y. Development of retroviral vectors for insertional mutagenesis in medaka haploid cells. Gene 2015; 573:296-302. [PMID: 26192464 DOI: 10.1016/j.gene.2015.07.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/02/2015] [Accepted: 07/16/2015] [Indexed: 01/14/2023]
Abstract
Insertional mutagenesis (IM) by retrovirus (RV) is a high-throughput approach for interrogating gene functions in model species. Haploid cell provides a unique system for genetic screening by IM and prosperous progress has been achieved in mammal cells. However, little was known in lower vertebrate cells. Here, we report development of retroviral vectors (rvSAchCVgfp, rvSAchCVpf and rvSAchSTpf) and establishment of IM library in medaka haploid cells. Each vector contains a modified gene trapping (GT) cassette, which could extend the mutated cell population including GT insertions not in-frame or in weakly expressed genes. Virus titration determined by flow cytometry showed that rvSAchSTpf possessed the highest supernatant virus titer (1.5×10(5)TU/ml) in medaka haploid cell, while rvSAchCVpf produced the lowest titer (2.8×10(4)TU/ml). However, quantification of proviral DNAs in transduced cells by droplet digital PCR (ddPCR) demonstrated that the "real titer" may be similar among the three vectors. Furthermore, an IM library was established by FACS of haploid cells transduced with rvSAchCVgfp at a MOI of 0.1. A single copy RV integration in the majority of cells was confirmed by ddPCR in the library. Notably, there was a significant decrease of haploid cell percentage after FACS, suggesting potential trapping for survival/growth essential genes. Our results demonstrated successful development of retroviral vectors for IM in medaka haploid cells, serving for haploid genetic screening of host factors for virus infection and genes underlying certain cellular processes in fish model.
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Affiliation(s)
- Fan Lin
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Qizhi Liu
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Yongming Yuan
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Yunhan Hong
- Department of Biological Sciences, National University of Singapore, Singapore.
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31
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Esher SK, Granek JA, Alspaugh JA. Rapid mapping of insertional mutations to probe cell wall regulation in Cryptococcus neoformans. Fungal Genet Biol 2015; 82:9-21. [PMID: 26112692 DOI: 10.1016/j.fgb.2015.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 06/13/2015] [Accepted: 06/16/2015] [Indexed: 11/16/2022]
Abstract
Random insertional mutagenesis screens are important tools in microbial genetics studies. Investigators in fungal systems have used the plant pathogen Agrobacterium tumefaciens to create tagged, random mutations for genetic screens in their fungal species of interest through a unique process of trans-kingdom cellular transconjugation. However, identifying the locations of insertion has traditionally required tedious PCR-based methods, limiting the effective throughput of this system. We have developed an efficient genomic sequencing and analysis method (AIM-Seq) to facilitate identification of randomly generated genomic insertions in microorganisms. AIM-Seq combines batch sampling, whole genome sequencing, and a novel bioinformatics pipeline, AIM-HII, to rapidly identify sites of genomic insertion. We have specifically applied this technique to Agrobacterium-mediated transconjugation in the human fungal pathogen Cryptococcus neoformans. With this approach, we have screened a library of C. neoformans cell wall mutants, selecting twenty-seven mutants of interest for analysis by AIM-Seq. We identified thirty-five putative genomic insertions in known and previously unknown regulators of cell wall processes in this pathogenic fungus. We confirmed the relevance of a subset of these by creating independent mutant strains and analyzing resulting cell wall phenotypes. Through our sequence-based analysis of these mutations, we observed "typical" insertions of the Agrobacterium transfer DNA as well as atypical insertion events, including large deletions and chromosomal rearrangements. Initially applied to C. neoformans, this mutant analysis tool can be applied to a wide range of experimental systems and methods of mutagenesis, facilitating future microbial genetic screens.
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Affiliation(s)
- Shannon K Esher
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Joshua A Granek
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Bioinformatics and Biostatistics, Duke University School of Medicine, Durham, NC 27710, USA; Duke Center for the Genomics of Microbial Systems, Duke University School of Medicine, Durham, NC 27710, USA.
| | - J Andrew Alspaugh
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
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32
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Perin G, Bellan A, Segalla A, Meneghesso A, Alboresi A, Morosinotto T. Generation of random mutants to improve light-use efficiency of Nannochloropsis gaditana cultures for biofuel production. Biotechnol Biofuels 2015; 8:161. [PMID: 26413160 PMCID: PMC4583171 DOI: 10.1186/s13068-015-0337-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/09/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND The productivity of an algal culture depends on how efficiently it converts sunlight into biomass and lipids. Wild-type algae in their natural environment evolved to compete for light energy and maximize individual cell growth; however, in a photobioreactor, global productivity should be maximized. Improving light use efficiency is one of the primary aims of algae biotechnological research, and genetic engineering can play a major role in attaining this goal. RESULTS In this work, we generated a collection of Nannochloropsis gaditana mutant strains and screened them for alterations in the photosynthetic apparatus. The selected mutant strains exhibited diverse phenotypes, some of which are potentially beneficial under the specific artificial conditions of a photobioreactor. Particular attention was given to strains showing reduced cellular pigment contents, and further characterization revealed that some of the selected strains exhibited improved photosynthetic activity; in at least one case, this trait corresponded to improved biomass productivity in lab-scale cultures. CONCLUSIONS This work demonstrates that genetic modification of N. gaditana has the potential to generate strains with improved biomass productivity when cultivated under the artificial conditions of a photobioreactor.
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Affiliation(s)
- Giorgio Perin
- />Dipartimento di Biologia, Università di Padova, Via U. Bassi 58/B, 35121 Padua, Italy
| | - Alessandra Bellan
- />Dipartimento di Biologia, Università di Padova, Via U. Bassi 58/B, 35121 Padua, Italy
- />Centro studi di economia e tecnica dell’energia Giorgio Levi Cases, Università di Padova, Padua, Italy
| | - Anna Segalla
- />Dipartimento di Biologia, Università di Padova, Via U. Bassi 58/B, 35121 Padua, Italy
| | - Andrea Meneghesso
- />Dipartimento di Biologia, Università di Padova, Via U. Bassi 58/B, 35121 Padua, Italy
| | - Alessandro Alboresi
- />Dipartimento di Biologia, Università di Padova, Via U. Bassi 58/B, 35121 Padua, Italy
| | - Tomas Morosinotto
- />Dipartimento di Biologia, Università di Padova, Via U. Bassi 58/B, 35121 Padua, Italy
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33
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Tschida BR, Largaespada DA, Keng VW. Mouse models of cancer: Sleeping Beauty transposons for insertional mutagenesis screens and reverse genetic studies. Semin Cell Dev Biol 2014; 27:86-95. [PMID: 24468652 DOI: 10.1016/j.semcdb.2014.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 11/01/2013] [Accepted: 01/07/2014] [Indexed: 01/04/2023]
Abstract
The genetic complexity and heterogeneity of cancer has posed a problem in designing rationally targeted therapies effective in a large proportion of human cancer. Genomic characterization of many cancer types has provided a staggering amount of data that needs to be interpreted to further our understanding of this disease. Forward genetic screening in mice using Sleeping Beauty (SB) based insertional mutagenesis is an effective method for candidate cancer gene discovery that can aid in distinguishing driver from passenger mutations in human cancer. This system has been adapted for unbiased screens to identify drivers of multiple cancer types. These screens have already identified hundreds of candidate cancer-promoting mutations. These can be used to develop new mouse models for further study, which may prove useful for therapeutic testing. SB technology may also hold the key for rapid generation of reverse genetic mouse models of cancer, and has already been used to model glioblastoma and liver cancer.
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Dabrowska MJ, Ejegod D, Lassen LB, Johnsen HE, Wabl M, Pedersen FS, Dybkær K. Gene expression profiling of murine T-cell lymphoblastic lymphoma identifies deregulation of S-phase initiating genes. Leuk Res 2013; 37:1383-90. [PMID: 23896059 DOI: 10.1016/j.leukres.2013.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 03/24/2013] [Accepted: 04/08/2013] [Indexed: 12/11/2022]
Abstract
In a search for genes and pathways implicated in T-cell lymphoblastic lymphoma (T-LBL) development, we used a murine lymphoma model, where mice of the NMRI-inbred strain were inoculated with murine leukemia virus mutants. The resulting tumors were analyzed by integration analysis and global gene expression profiling to determine the effect of the retroviral integrations on the nearby genes, and the deregulated pathways in the tumors. Gene expression profiling identified increased expression of genes involved in the minichromosome maintenance and origin of recognition pathway as well as downregulation in negative regulators of G1/S transition, indicating increased S-phase initiation in murine T-LBLs.
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35
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Revalska M, Vassileva V, Goormachtig S, Van Hautegem T, Ratet P, Iantcheva A. Recent Progress in Development of Tnt1 Functional Genomics Platform for Medicago truncatula and Lotus japonicus in Bulgaria. Curr Genomics 2011; 12:147-52. [PMID: 21966253 PMCID: PMC3129049 DOI: 10.2174/138920211795564313] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Revised: 01/18/2011] [Accepted: 02/01/2011] [Indexed: 01/17/2023] Open
Abstract
Legumes, as protein-rich crops, are widely used for human food, animal feed and vegetable oil production. Over the past decade, two legume species, Medicago truncatula and Lotus japonicus, have been adopted as model legumes for genomics and physiological studies. The tobacco transposable element, Tnt1, is a powerful tool for insertional mutagenesis and gene inactivation in plants. A large collection of Tnt1-tagged lines of M. truncatula cv. Jemalong was generated during the course of the project 'GLIP': Grain Legumes Integrated Project, funded by the European Union (www.eugrainlegumes.org). In the project 'IFCOSMO': Integrated Functional and COmparative genomics Studies on the MOdel Legumes Medicago truncatula and Lotus japonicus, supported by a grant from the Ministry of Education, Youth and Science, Bulgaria, these lines are used for development of functional genomics platform of legumes in Bulgaria. This review presents recent advances in the evaluation of the M. truncatula Tnt1 mutant collection and outlines the steps that are taken in using the Tnt1-tagging for generation of a mutant collection of the second model legume L. japonicus. Both collections will provide a number of legume-specific mutants and serve as a resource for functional and comparative genomics research on legumes. Genomics technologies are expected to advance genetics and breeding of important legume crops (pea, faba bean, alfalfa and clover) in Bulgaria and worldwide.
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36
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Abstract
Hematopoietic stem cell (HSC) therapy using replication-incompetent retroviral vectors is a promising approach to provide life-long correction for genetic defects. HSC gene therapy clinical studies have resulted in functional cures for several diseases, but in some studies clonal expansion or leukemia has occurred. This is due to the dyregulation of endogenous host gene expression from vector provirus insertional mutagenesis. Insertional mutagenesis screens using replicating retroviruses have been used extensively to identify genes that influence oncogenesis. However, retroviral mutagenesis screens can also be used to determine the role of genes in biological processes such as stem cell engraftment. The aim of this review is to describe the potential for vector insertion site data from gene therapy studies to provide novel insights into mechanisms of HSC engraftment. In HSC gene therapy studies dysregulation of host genes by replication-incompetent vector proviruses may lead to enrichment of repopulating clones with vector integrants near genes that influence engraftment. Thus, data from HSC gene therapy studies can be used to identify novel candidate engraftment genes. As HSC gene therapy use continues to expand, the vector insertion site data collected will be of great interest to help identify novel engraftment genes and may ultimately lead to new therapies to improve engraftment.
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Affiliation(s)
- John M Powers
- Department of Pharmaceutical Sciences, Washington State University, Pullman, Washington, USA
| | - Grant D Trobridge
- Department of Pharmaceutical Sciences, Washington State University, Pullman, Washington, USA ; School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
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