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Dopeso H, Rodrigues P, Cartón-García F, Macaya I, Bilic J, Anguita E, Jing L, Brotons B, Vivancos N, Beà L, Sánchez-Martín M, Landolfi S, Hernandez-Losa J, Ramon y Cajal S, Nieto R, Vicario M, Farre R, Schwartz S, van Ijzendoorn SC, Kobayashi K, Martinez-Barriocanal Á, Arango D. RhoA downregulation in the murine intestinal epithelium results in chronic Wnt activation and increased tumorigenesis. iScience 2024; 27:109400. [PMID: 38523777 PMCID: PMC10959657 DOI: 10.1016/j.isci.2024.109400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 12/23/2023] [Accepted: 02/28/2024] [Indexed: 03/26/2024] Open
Abstract
Rho GTPases are molecular switches regulating multiple cellular processes. To investigate the role of RhoA in normal intestinal physiology, we used a conditional mouse model overexpressing a dominant negative RhoA mutant (RhoAT19N) in the intestinal epithelium. Although RhoA inhibition did not cause an overt phenotype, increased levels of nuclear β-catenin were observed in the small intestinal epithelium of RhoAT19N mice, and the overexpression of multiple Wnt target genes revealed a chronic activation of Wnt signaling. Elevated Wnt signaling in RhoAT19N mice and intestinal organoids did not affect the proliferation of intestinal epithelial cells but significantly interfered with their differentiation. Importantly, 17-month-old RhoAT19N mice showed a significant increase in the number of spontaneous intestinal tumors. Altogether, our results indicate that RhoA regulates the differentiation of intestinal epithelial cells and inhibits tumor initiation, likely through the control of Wnt signaling, a key regulator of proliferation and differentiation in the intestine.
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Affiliation(s)
- Higinio Dopeso
- Group of Biomedical Research in Digestive Tract Tumors, Vall d’Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Paulo Rodrigues
- Group of Biomedical Research in Digestive Tract Tumors, Vall d’Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Fernando Cartón-García
- Group of Biomedical Research in Digestive Tract Tumors, Vall d’Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Irati Macaya
- Group of Biomedical Research in Digestive Tract Tumors, Vall d’Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Josipa Bilic
- Group of Biomedical Research in Digestive Tract Tumors, Vall d’Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Estefanía Anguita
- Group of Biomedical Research in Digestive Tract Tumors, Vall d’Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
- Group of Molecular Oncology, Biomedical Research Institute of Lleida (IRBLleida), 25198 Lleida, Spain
| | - Li Jing
- Group of Biomedical Research in Digestive Tract Tumors, Vall d’Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
- Group of Molecular Oncology, Biomedical Research Institute of Lleida (IRBLleida), 25198 Lleida, Spain
| | - Bruno Brotons
- Group of Molecular Oncology, Biomedical Research Institute of Lleida (IRBLleida), 25198 Lleida, Spain
| | - Núria Vivancos
- Group of Molecular Oncology, Biomedical Research Institute of Lleida (IRBLleida), 25198 Lleida, Spain
| | - Laia Beà
- Group of Molecular Oncology, Biomedical Research Institute of Lleida (IRBLleida), 25198 Lleida, Spain
| | - Manuel Sánchez-Martín
- Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
- Servicio de Transgénesis, Nucleus, Universidad de Salamanca, 37007 Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Stefania Landolfi
- Translational Molecular Pathology, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Javier Hernandez-Losa
- Translational Molecular Pathology, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Santiago Ramon y Cajal
- Translational Molecular Pathology, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Rocío Nieto
- Group of Biomedical Research in Digestive Tract Tumors, Vall d’Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - María Vicario
- Digestive System Research Unit, Vall d’Hebron University Hospital Research Institute (VHIR), 08035 Barcelona, Spain
| | - Ricard Farre
- Department of Chronic Diseases and Metabolism (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), Leuven 3000, Belgium
| | - Simo Schwartz
- Group of Drug Delivery and Targeting, Vall d'Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
- Clinical Biochemistry Department, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
| | - Sven C.D. van Ijzendoorn
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Cell Biology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Kazuto Kobayashi
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Águeda Martinez-Barriocanal
- Group of Biomedical Research in Digestive Tract Tumors, Vall d’Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
- Group of Molecular Oncology, Biomedical Research Institute of Lleida (IRBLleida), 25198 Lleida, Spain
| | - Diego Arango
- Group of Biomedical Research in Digestive Tract Tumors, Vall d’Hebron University Hospital Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
- Group of Molecular Oncology, Biomedical Research Institute of Lleida (IRBLleida), 25198 Lleida, Spain
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2
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Applications of piggyBac Transposons for Genome Manipulation in Stem Cells. Stem Cells Int 2021; 2021:3829286. [PMID: 34567130 PMCID: PMC8460389 DOI: 10.1155/2021/3829286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/16/2021] [Indexed: 12/20/2022] Open
Abstract
Transposons are mobile genetic elements in the genome. The piggyBac (PB) transposon system is increasingly being used for stem cell research due to its high transposition efficiency and seamless excision capacity. Over the past few decades, forward genetic screens based on PB transposons have been successfully established to identify genes associated with drug resistance and stem cell-related characteristics. Moreover, PB transposon is regarded as a promising gene therapy vector and has been used in some clinically relevant stem cells. Here, we review the recent progress on the basic biology of PB, highlight its applications in current stem cell research, and discuss its advantages and challenges.
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Brandt AC, Koehn OJ, Williams CL. SmgGDS: An Emerging Master Regulator of Prenylation and Trafficking by Small GTPases in the Ras and Rho Families. Front Mol Biosci 2021; 8:685135. [PMID: 34222337 PMCID: PMC8242357 DOI: 10.3389/fmolb.2021.685135] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/27/2021] [Indexed: 11/17/2022] Open
Abstract
Newly synthesized small GTPases in the Ras and Rho families are prenylated by cytosolic prenyltransferases and then escorted by chaperones to membranes, the nucleus, and other sites where the GTPases participate in a variety of signaling cascades. Understanding how prenylation and trafficking are regulated will help define new therapeutic strategies for cancer and other disorders involving abnormal signaling by these small GTPases. A growing body of evidence indicates that splice variants of SmgGDS (gene name RAP1GDS1) are major regulators of the prenylation, post-prenylation processing, and trafficking of Ras and Rho family members. SmgGDS-607 binds pre-prenylated small GTPases, while SmgGDS-558 binds prenylated small GTPases. This review discusses the history of SmgGDS research and explains our current understanding of how SmgGDS splice variants regulate the prenylation and trafficking of small GTPases. We discuss recent evidence that mutant forms of RabL3 and Rab22a control the release of small GTPases from SmgGDS, and review the inhibitory actions of DiRas1, which competitively blocks the binding of other small GTPases to SmgGDS. We conclude with a discussion of current strategies for therapeutic targeting of SmgGDS in cancer involving splice-switching oligonucleotides and peptide inhibitors.
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Affiliation(s)
- Anthony C Brandt
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Olivia J Koehn
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Carol L Williams
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
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Ahmed HMM, Heese F, Wimmer EA. Improvement on the genetic engineering of an invasive agricultural pest insect, the cherry vinegar fly, Drosophila suzukii. BMC Genet 2020; 21:139. [PMID: 33339511 PMCID: PMC7747376 DOI: 10.1186/s12863-020-00940-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background The invasive fly Drosophila suzukii has become an established fruit pest in Europe, the USA, and South America with no effective and safe pest management. Genetic engineering enables the development of transgene-based novel genetic control strategies against insect pests and disease vectors. This, however, requires the establishment of reliable germline transformation techniques. Previous studies have shown that D. suzukii is amenable to transgenesis using the transposon-based vectors piggyBac and Minos, site-specific recombination (lox/Cre), and CRISPR/Cas9 genome editing. Results We experienced differences in the usability of piggyBac-based germline transformation in different strains of D. suzukii: we obtained no transgenic lines in a US strain, a single rare transgenic line in an Italian strain, but observed a reliable transformation rate of 2.5 to 11% in a strain from the French Alps. This difference in efficiency was confirmed by comparative examination of these three strains. In addition, we used an attP landing site line to successfully established φC31-integrase-mediated plasmid integration at a rate of 10% and generated landing site lines with two attP sequences to effectively perform φC31-Recombinase Mediated Cassette Exchange (φC31-RMCE) with 11% efficiency. Moreover, we isolated and used the endogenous regulatory regions of Ds nanos to express φC31 integrase maternally to generate self-docking lines for φC31-RMCE. Besides, we isolated the promoter/enhancer of Ds serendipity α to drive the heterologous tetracycline-controlled transactivator (tTA) during early embryonic development and generated a testes-specific tTA driver line using the endogenous beta-2-tubulin (β2t) promoter/enhancer. Conclusion Our results provide evidence that the D. suzukii strain AM derived from the French Alps is more suitable for piggyBac germline transformation than other strains. We demonstrated the feasibility of using φC31-RMCE in the cherry vinegar fly and generated a set of lines that can be used for highly efficient integration of larger constructs. The φC31-based integration will facilitate modification and stabilization of previously generated transgenic lines that carry at least one attP site in the transgene construction. An early embryo-specific and a spermatogenesis-specific driver line were generated for future use of the binary expression system tet-off to engineer tissue- and stage-specific effector gene expression for genetic pest control strategies. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-020-00940-5.
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Affiliation(s)
- Hassan M M Ahmed
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, 37077, Göttingen, Germany.,Department of Crop Protection, Faculty of Agriculture-University of Khartoum, P.O. Box 32, 13314, Khartoum North, Khartoum, Sudan
| | - Fabienne Heese
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Ernst A Wimmer
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, 37077, Göttingen, Germany.
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Belair C, Sim S, Kim KY, Tanaka Y, Park IH, Wolin SL. The RNA exosome nuclease complex regulates human embryonic stem cell differentiation. J Cell Biol 2019; 218:2564-2582. [PMID: 31308215 PMCID: PMC6683745 DOI: 10.1083/jcb.201811148] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 05/21/2019] [Accepted: 06/12/2019] [Indexed: 01/09/2023] Open
Abstract
This work shows that the exosome modulates the levels of LINE-1 retrotransposons and specific miRNAs, lncRNAs, and mRNAs that encode developmental regulators or affect their expression. The exosome restrains stem cell differentiation in part by degrading transcripts encoding FOXH1, a transcription factor crucial for mesendoderm formation. A defining feature of embryonic stem cells (ESCs) is the ability to differentiate into all three germ layers. Pluripotency is maintained in part by a unique transcription network that maintains expression of pluripotency-specific transcription factors and represses developmental genes. While the mechanisms that establish this transcription network are well studied, little is known of the posttranscriptional surveillance pathways that degrade differentiation-related RNAs. We report that the surveillance pathway mediated by the RNA exosome nuclease complex represses ESC differentiation. Depletion of the exosome expedites differentiation of human ESCs into all three germ layers. LINE-1 retrotransposons and specific miRNAs, lncRNAs, and mRNAs that encode developmental regulators or affect their expression are all bound by the exosome and increase in level upon exosome depletion. The exosome restrains differentiation in part by degrading transcripts encoding FOXH1, a transcription factor crucial for mesendoderm formation. Our studies establish the exosome as a regulator of human ESC differentiation and reveal the importance of RNA decay in maintaining pluripotency.
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Affiliation(s)
- Cedric Belair
- Department of Cell Biology, Yale School of Medicine, New Haven, CT.,RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD
| | - Soyeong Sim
- Department of Cell Biology, Yale School of Medicine, New Haven, CT.,RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD
| | - Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT
| | - Yoshiaki Tanaka
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT
| | | | - Sandra L Wolin
- Department of Cell Biology, Yale School of Medicine, New Haven, CT .,RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD
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6
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Genome-Scale CRISPRa Screen Identifies Novel Factors for Cellular Reprogramming. Stem Cell Reports 2019; 12:757-771. [PMID: 30905739 PMCID: PMC6450436 DOI: 10.1016/j.stemcr.2019.02.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/17/2019] [Accepted: 02/20/2019] [Indexed: 01/03/2023] Open
Abstract
Primed epiblast stem cells (EpiSCs) can be reverted to a pluripotent embryonic stem cell (ESC)-like state by expression of single reprogramming factor. We used CRISPR activation to perform a genome-scale, reprogramming screen in EpiSCs and identified 142 candidate genes. Our screen validated a total of 50 genes, previously not known to contribute to reprogramming, of which we chose Sall1 for further investigation. We show that Sall1 augments reprogramming of mouse EpiSCs and embryonic fibroblasts and that these induced pluripotent stem cells are indeed fully pluripotent including formation of chimeric mice. We also demonstrate that Sall1 synergizes with Nanog in reprogramming and that overexpression in ESCs delays their conversion back to EpiSCs. Lastly, using RNA sequencing, we identify and validate Klf5 and Fam189a2 as new downstream targets of Sall1 and Nanog. In summary, our work demonstrates the power of using CRISPR technology in understanding molecular mechanisms that mediate complex cellular processes such as reprogramming. Genome-scale CRISPRa screen in mouse EpiSCs identifies novel reprogramming factors 50 novel genes, including Sall1 and Fam189a2, identified to mediate reprogramming Sall1 synergizes with Nanog to increase reprogramming efficiency in EpiSCs and MEFs RNA-seq provides insight into downstream pathways of Sall1 and Nanog-mediated reprogramming
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7
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Schumann GG, Fuchs NV, Tristán-Ramos P, Sebe A, Ivics Z, Heras SR. The impact of transposable element activity on therapeutically relevant human stem cells. Mob DNA 2019; 10:9. [PMID: 30899334 PMCID: PMC6408843 DOI: 10.1186/s13100-019-0151-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/27/2019] [Indexed: 12/11/2022] Open
Abstract
Human stem cells harbor significant potential for basic and clinical translational research as well as regenerative medicine. Currently ~ 3000 adult and ~ 30 pluripotent stem cell-based, interventional clinical trials are ongoing worldwide, and numbers are increasing continuously. Although stem cells are promising cell sources to treat a wide range of human diseases, there are also concerns regarding potential risks associated with their clinical use, including genomic instability and tumorigenesis concerns. Thus, a deeper understanding of the factors and molecular mechanisms contributing to stem cell genome stability are a prerequisite to harnessing their therapeutic potential for degenerative diseases. Chemical and physical factors are known to influence the stability of stem cell genomes, together with random mutations and Copy Number Variants (CNVs) that accumulated in cultured human stem cells. Here we review the activity of endogenous transposable elements (TEs) in human multipotent and pluripotent stem cells, and the consequences of their mobility for genomic integrity and host gene expression. We describe transcriptional and post-transcriptional mechanisms antagonizing the spread of TEs in the human genome, and highlight those that are more prevalent in multipotent and pluripotent stem cells. Notably, TEs do not only represent a source of mutations/CNVs in genomes, but are also often harnessed as tools to engineer the stem cell genome; thus, we also describe and discuss the most widely applied transposon-based tools and highlight the most relevant areas of their biomedical applications in stem cells. Taken together, this review will contribute to the assessment of the risk that endogenous TE activity and the application of genetically engineered TEs constitute for the biosafety of stem cells to be used for substitutive and regenerative cell therapies.
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Affiliation(s)
- Gerald G Schumann
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Nina V Fuchs
- 2Host-Pathogen Interactions, Paul-Ehrlich-Institut, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany
| | - Pablo Tristán-Ramos
- 3GENYO. Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada-Avenida de la Ilustración, 114, 18016 Granada, Spain.,4Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
| | - Attila Sebe
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Zoltán Ivics
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Sara R Heras
- 3GENYO. Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada-Avenida de la Ilustración, 114, 18016 Granada, Spain.,4Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
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Trubitsyna M, Michlewski G, Finnegan DJ, Elfick A, Rosser SJ, Richardson JM, French CE. Use of mariner transposases for one-step delivery and integration of DNA in prokaryotes and eukaryotes by transfection. Nucleic Acids Res 2017; 45:e89. [PMID: 28204586 PMCID: PMC5449632 DOI: 10.1093/nar/gkx113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 02/06/2017] [Indexed: 11/20/2022] Open
Abstract
Delivery of DNA to cells and its subsequent integration into the host genome is a fundamental task in molecular biology, biotechnology and gene therapy. Here we describe an IP-free one-step method that enables stable genome integration into either prokaryotic or eukaryotic cells. A synthetic mariner transposon is generated by flanking a DNA sequence with short inverted repeats. When purified recombinant Mos1 or Mboumar-9 transposase is co-transfected with transposon-containing plasmid DNA, it penetrates prokaryotic or eukaryotic cells and integrates the target DNA into the genome. In vivo integrations by purified transposase can be achieved by electroporation, chemical transfection or Lipofection of the transposase:DNA mixture, in contrast to other published transposon-based protocols which require electroporation or microinjection. As in other transposome systems, no helper plasmids are required since transposases are not expressed inside the host cells, thus leading to generation of stable cell lines. Since it does not require electroporation or microinjection, this tool has the potential to be applied for automated high-throughput creation of libraries of random integrants for purposes including gene knock-out libraries, screening for optimal integration positions or safe genome locations in different organisms, selection of the highest production of valuable compounds for biotechnology, and sequencing.
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Affiliation(s)
- Maryia Trubitsyna
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Gracjan Michlewski
- Institute of Cell Biology, School of Biological Sciences, Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - David J Finnegan
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Alistair Elfick
- Institute of BioEngineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3JL, UK
| | - Susan J Rosser
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, UK Centre for Mammalian Synthetic Biology, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Julia M Richardson
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Christopher E French
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
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Identification of apilimod as a first-in-class PIKfyve kinase inhibitor for treatment of B-cell non-Hodgkin lymphoma. Blood 2017; 129:1768-1778. [PMID: 28104689 DOI: 10.1182/blood-2016-09-736892] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/12/2017] [Indexed: 12/15/2022] Open
Abstract
We identified apilimod as an antiproliferative compound by high-throughput screening of clinical-stage drugs. Apilimod exhibits exquisite specificity for phosphatidylinositol-3-phosphate 5-kinase (PIKfyve) lipid kinase and has selective cytotoxic activity in B-cell non-Hodgkin lymphoma (B-NHL) compared with normal cells. Apilimod displays nanomolar activity in vitro, and in vivo studies demonstrate single-agent efficacy as well as synergy with approved B-NHL drugs. Using biochemical and knockdown approaches, and discovery of a kinase domain mutation conferring resistance, we demonstrate that apilimod-mediated cytotoxicity is driven by PIKfyve inhibition. Furthermore, a critical role for lysosome dysfunction as a major factor contributing to apilimod's cytotoxicity is supported by a genome-wide CRISPR screen. In the screen, TFEB (master transcriptional regulator of lysosomal biogenesis) and endosomal/lysosomal genes CLCN7, OSTM1, and SNX10 were identified as important determinants of apilimod sensitivity. These findings thus suggest that disruption of lysosomal homeostasis with apilimod represents a novel approach to treat B-NHL.
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10
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Yang D, Liao R, Zheng Y, Sun L, Xu T. Analysis of PBase Binding Profile Indicates an Insertion Target Selection Mechanism Dependent on TTAA, But Not Transcriptional Activity. Int J Biol Sci 2016; 12:1074-82. [PMID: 27570481 PMCID: PMC4997051 DOI: 10.7150/ijbs.15589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 05/15/2016] [Indexed: 12/20/2022] Open
Abstract
Transposons and retroviruses are important pathogenic agents and tools for mutagenesis and transgenesis. Insertion target selection is a key feature for a given transposon or retrovirus. The piggyBac (PB) transposon is highly active in mice and human cells, which has a much better genome-wide distribution compared to the retrovirus and P-element. However, the underlying reason is not clear. Utilizing a tagged functional PB transposase (PBase), we were able to conduct genome-wide profiling for PBase binding sites in the mouse genome. We have shown that PBase binding mainly depends on the distribution of the tetranucleotide TTAA, which is not affected by the presence of PB DNA. Furthermore, PBase binding is negatively influenced by the methylation of CG sites in the genome. Analysis of a large collection of PB insertions in mice has revealed an insertion profile similar to the PBase binding profile. Interestingly, this profile is not correlated with transcriptional active genes in the genome or transcriptionally active regions within a transcriptional unit. This differs from what has been previously shown for P-element and retroviruses insertions. Our study provides an explanation for PB's genome-wide insertion distribution and also suggests that PB target selection relies on a new mechanism independent of active transcription and open chromatin structure.
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Affiliation(s)
- Dong Yang
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Fudan-Yale Center for Biomedical Research, Innovation Center for International Cooperation of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200433; 2. Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, New Haven, CT 06536
| | - Ruiqi Liao
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Fudan-Yale Center for Biomedical Research, Innovation Center for International Cooperation of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200433
| | - Yun Zheng
- 3. Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Ling Sun
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Fudan-Yale Center for Biomedical Research, Innovation Center for International Cooperation of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200433
| | - Tian Xu
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Fudan-Yale Center for Biomedical Research, Innovation Center for International Cooperation of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200433; 2. Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, New Haven, CT 06536
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11
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Gonzales KAU, Ng HH. Biological Networks Governing the Acquisition, Maintenance, and Dissolution of Pluripotency: Insights from Functional Genomics Approaches. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2015; 80:189-98. [PMID: 26582790 DOI: 10.1101/sqb.2015.80.027326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The repertoire of transcripts encoded by the genome contributes to the diversity of cellular states. Functional genomics aims to comprehensively uncover the roles of these transcripts to reconstruct biological networks and transform this information into useful knowledge. High-throughput functional screening has served as a powerful genetic discovery tool by enabling massively parallel implementation of biological assays. In recent years, high-throughput screening has unearthed crucial players in the regulation of different aspects of pluripotency, which is a unique property that enables a cell to differentiate into multiple cell types of the three major lineages. Pluripotency thus represents an interesting biological paradigm for studying the acquisition, maintenance, and dissolution of cellular states. In this review, we highlight the major findings of high-throughput studies to dissect these three aspects of pluripotency for the mouse and human systems. Collectively, they provide new insights into cell fate maintenance and transition. In addition, we also discuss the opportunities and challenges awaiting high-throughput screening in the future.
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Affiliation(s)
| | - Huck-Hui Ng
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore 138672, Singapore Department of Biochemistry, National University of Singapore, Singapore 117597, Singapore Department of Biological Sciences, National University of Singapore, Singapore 117597, Singapore School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
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