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Direct Readout of Neural Stem Cell Transgenesis with an Integration-Coupled Gene Expression Switch. Neuron 2020; 107:617-630.e6. [PMID: 32559415 PMCID: PMC7447981 DOI: 10.1016/j.neuron.2020.05.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 04/22/2020] [Accepted: 05/26/2020] [Indexed: 12/29/2022]
Abstract
Stable genomic integration of exogenous transgenes is essential in neurodevelopmental and stem cell studies. Despite tools driving increasingly efficient genomic insertion with DNA vectors, transgenesis remains fundamentally hindered by the impossibility of distinguishing integrated from episomal transgenes. Here, we introduce an integration-coupled On genetic switch, iOn, which triggers gene expression upon incorporation into the host genome through transposition, thus enabling rapid and accurate identification of integration events following transfection with naked plasmids. In vitro, iOn permits rapid drug-free stable transgenesis of mouse and human pluripotent stem cells with multiple vectors. In vivo, we demonstrate faithful cell lineage tracing, assessment of regulatory elements, and mosaic analysis of gene function in somatic transgenesis experiments that reveal neural progenitor potentialities and interaction. These results establish iOn as a universally applicable strategy to accelerate and simplify genetic engineering in cultured systems and model organisms by conditioning transgene activation to genomic integration. A gene expression switch powered by genomic integration Accelerated readout of additive transgenesis with one or multiple vectors Faithful lineage tracing and mosaic analysis by somatic transfection Near-universal applicability in cultured cells and animal models
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Friedrich MJ, Rad L, Bronner IF, Strong A, Wang W, Weber J, Mayho M, Ponstingl H, Engleitner T, Grove C, Pfaus A, Saur D, Cadiñanos J, Quail MA, Vassiliou GS, Liu P, Bradley A, Rad R. Genome-wide transposon screening and quantitative insertion site sequencing for cancer gene discovery in mice. Nat Protoc 2017; 12:289-309. [PMID: 28079877 DOI: 10.1038/nprot.2016.164] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transposon-mediated forward genetics screening in mice has emerged as a powerful tool for cancer gene discovery. It pinpoints cancer drivers that are difficult to find with other approaches, thus complementing the sequencing-based census of human cancer genes. We describe here a large series of mouse lines for insertional mutagenesis that are compatible with two transposon systems, PiggyBac and Sleeping Beauty, and give guidance on the use of different engineered transposon variants for constitutive or tissue-specific cancer gene discovery screening. We also describe a method for semiquantitative transposon insertion site sequencing (QiSeq). The QiSeq library preparation protocol exploits acoustic DNA fragmentation to reduce bias inherent to widely used restriction-digestion-based approaches for ligation-mediated insertion site amplification. Extensive multiplexing in combination with next-generation sequencing allows affordable ultra-deep transposon insertion site recovery in high-throughput formats within 1 week. Finally, we describe principles of data analysis and interpretation for obtaining insights into cancer gene function and genetic tumor evolution.
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Affiliation(s)
| | - Lena Rad
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Iraad F Bronner
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Alexander Strong
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Wei Wang
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Julia Weber
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Matthew Mayho
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Hannes Ponstingl
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Thomas Engleitner
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Carolyn Grove
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Anja Pfaus
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Dieter Saur
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Juan Cadiñanos
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK.,Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo, Spain
| | - Michael A Quail
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - George S Vassiliou
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Pentao Liu
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Roland Rad
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
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Bii VM, Trobridge GD. Identifying Cancer Driver Genes Using Replication-Incompetent Retroviral Vectors. Cancers (Basel) 2016; 8:cancers8110099. [PMID: 27792127 PMCID: PMC5126759 DOI: 10.3390/cancers8110099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 10/12/2016] [Accepted: 10/17/2016] [Indexed: 12/16/2022] Open
Abstract
Identifying novel genes that drive tumor metastasis and drug resistance has significant potential to improve patient outcomes. High-throughput sequencing approaches have identified cancer genes, but distinguishing driver genes from passengers remains challenging. Insertional mutagenesis screens using replication-incompetent retroviral vectors have emerged as a powerful tool to identify cancer genes. Unlike replicating retroviruses and transposons, replication-incompetent retroviral vectors lack additional mutagenesis events that can complicate the identification of driver mutations from passenger mutations. They can also be used for almost any human cancer due to the broad tropism of the vectors. Replication-incompetent retroviral vectors have the ability to dysregulate nearby cancer genes via several mechanisms including enhancer-mediated activation of gene promoters. The integrated provirus acts as a unique molecular tag for nearby candidate driver genes which can be rapidly identified using well established methods that utilize next generation sequencing and bioinformatics programs. Recently, retroviral vector screens have been used to efficiently identify candidate driver genes in prostate, breast, liver and pancreatic cancers. Validated driver genes can be potential therapeutic targets and biomarkers. In this review, we describe the emergence of retroviral insertional mutagenesis screens using replication-incompetent retroviral vectors as a novel tool to identify cancer driver genes in different cancer types.
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Affiliation(s)
- Victor M Bii
- College of Pharmacy, Washington State University, WSU Spokane PBS 323, P.O. Box 1495, Spokane, WA 99210, USA.
| | - Grant D Trobridge
- College of Pharmacy, Washington State University, WSU Spokane PBS 323, P.O. Box 1495, Spokane, WA 99210, USA.
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA.
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Bii VM, Rae DT, Trobridge GD. A novel gammaretroviral shuttle vector insertional mutagenesis screen identifies SHARPIN as a breast cancer metastasis gene and prognostic biomarker. Oncotarget 2015; 6:39507-20. [PMID: 26506596 PMCID: PMC4741842 DOI: 10.18632/oncotarget.6232] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 10/14/2015] [Indexed: 12/21/2022] Open
Abstract
Breast cancer (BC) is the second leading cause of malignancy among U.S. women. Metastasis results in a poor prognosis and increased mortality, but the molecular mechanisms by which metastatic tumors occur are not well understood. Identifying the genes that drive the metastatic process could provide targets for improved therapy and biomarkers to improve BC patient outcomes. Using a forward mutagenesis screen, BC cells mutagenized with a replication-incompetent gammaretroviral vector (γRV) were xenotransplanted into the mammary fat pad of immunodeficient mice. In this approach the vector provirus dysregulates nearby genes, providing a selective advantage to transduced cells to form metastases. Metastatic tumors were analyzed for proviral integration sites to identify nearby candidate metastasis genes. The γRV has a transgene cassette that allows for rescue in bacteria and rapid identification of vector integration sites. Using this approach, we identified the previously described metastasis gene WWTR1 (TAZ), and three other novel candidate metastasis genes including SHARPIN. SHARPIN was independently validated in vivo as a BC metastasis gene. Analysis of patient data showed that SHARPIN expression predicts metastasis-free survival after adjuvant therapy. Our approach has broad potential to identify genes involved in oncogenic processes for BC and other cancers. We show here it can identify both known (WWTR1) and novel (SHARPIN) BC metastasis genes.
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Affiliation(s)
- Victor M. Bii
- Washington State University College of Pharmacy, WSU Spokane, Spokane, WA, USA
| | - Dustin T. Rae
- Washington State University College of Pharmacy, WSU Spokane, Spokane, WA, USA
| | - Grant D. Trobridge
- Washington State University College of Pharmacy, WSU Spokane, Spokane, WA, USA
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
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DeNicola GM, Karreth FA, Adams DJ, Wong CC. The utility of transposon mutagenesis for cancer studies in the era of genome editing. Genome Biol 2015; 16:229. [PMID: 26481584 PMCID: PMC4612416 DOI: 10.1186/s13059-015-0794-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The use of transposons as insertional mutagens to identify cancer genes in mice has generated a wealth of information over the past decade. Here, we discuss recent major advances in transposon-mediated insertional mutagenesis screens and compare this technology with other screening strategies.
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Affiliation(s)
- Gina M DeNicola
- Meyer Cancer Center, Weill Cornell Medical College, New York, NY, 10021, USA
| | - Florian A Karreth
- Meyer Cancer Center, Weill Cornell Medical College, New York, NY, 10021, USA.
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1HH, UK
| | - Chi C Wong
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1HH, UK. .,Department of Haematology, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK.
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Schinke EN, Bii V, Nalla A, Rae DT, Tedrick L, Meadows GG, Trobridge GD. A novel approach to identify driver genes involved in androgen-independent prostate cancer. Mol Cancer 2014; 13:120. [PMID: 24885513 PMCID: PMC4098713 DOI: 10.1186/1476-4598-13-120] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/13/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Insertional mutagenesis screens have been used with great success to identify oncogenes and tumor suppressor genes. Typically, these screens use gammaretroviruses (γRV) or transposons as insertional mutagens. However, insertional mutations from replication-competent γRVs or transposons that occur later during oncogenesis can produce passenger mutations that do not drive cancer progression. Here, we utilized a replication-incompetent lentiviral vector (LV) to perform an insertional mutagenesis screen to identify genes in the progression to androgen-independent prostate cancer (AIPC). METHODS Prostate cancer cells were mutagenized with a LV to enrich for clones with a selective advantage in an androgen-deficient environment provided by a dysregulated gene(s) near the vector integration site. We performed our screen using an in vitro AIPC model and also an in vivo xenotransplant model for AIPC. Our approach identified proviral integration sites utilizing a shuttle vector that allows for rapid rescue of plasmids in E. coli that contain LV long terminal repeat (LTR)-chromosome junctions. This shuttle vector approach does not require PCR amplification and has several advantages over PCR-based techniques. RESULTS Proviral integrations were enriched near prostate cancer susceptibility loci in cells grown in androgen-deficient medium (p < 0.001), and five candidate genes that influence AIPC were identified; ATPAF1, GCOM1, MEX3D, PTRF, and TRPM4. Additionally, we showed that RNAi knockdown of ATPAF1 significantly reduces growth (p < 0.05) in androgen-deficient conditions. CONCLUSIONS Our approach has proven effective for use in PCa, identifying a known prostate cancer gene, PTRF, and also several genes not previously associated with prostate cancer. The replication-incompetent shuttle vector approach has broad potential applications for cancer gene discovery, and for interrogating diverse biological and disease processes.
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Affiliation(s)
| | | | | | | | | | | | - Grant D Trobridge
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99210-1495, USA.
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