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Francis JC, Capper A, Rust AG, Ferro K, Ning J, Yuan W, de Bono J, Pettitt SJ, Swain A. Identification of genes that promote PI3K pathway activation and prostate tumour formation. Oncogene 2024; 43:1824-1835. [PMID: 38654106 PMCID: PMC11164682 DOI: 10.1038/s41388-024-03028-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024]
Abstract
We have performed a functional in vivo mutagenesis screen to identify genes that, when altered, cooperate with a heterozygous Pten mutation to promote prostate tumour formation. Two genes, Bzw2 and Eif5a2, which have been implicated in the process of protein translation, were selected for further validation. Using prostate organoid models, we show that either Bzw2 downregulation or EIF5A2 overexpression leads to increased organoid size and in vivo prostate growth. We show that both genes impact the PI3K pathway and drive a sustained increase in phospho-AKT expression, with PTEN protein levels reduced in both models. Mechanistic studies reveal that EIF5A2 is directly implicated in PTEN protein translation. Analysis of patient datasets identified EIF5A2 amplifications in many types of human cancer, including the prostate. Human prostate cancer samples in two independent cohorts showed a correlation between increased levels of EIF5A2 and upregulation of a PI3K pathway gene signature. Consistent with this, organoids with high levels of EIF5A2 were sensitive to AKT inhibitors. Our study identified novel genes that promote prostate cancer formation through upregulation of the PI3K pathway, predicting a strategy to treat patients with genetic aberrations in these genes particularly relevant for EIF5A2 amplified tumours.
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Affiliation(s)
- Jeffrey C Francis
- Division of Cancer Biology, Institute of Cancer Research, London, SW3 6JB, UK
| | - Amy Capper
- Division of Cancer Biology, Institute of Cancer Research, London, SW3 6JB, UK
| | - Alistair G Rust
- Genomics Facility, Institute of Cancer Research, London, UK
- Genomic Data Sciences, GlaxoSmithKline, Stevenage, UK
| | - Klea Ferro
- Division of Cancer Biology, Institute of Cancer Research, London, SW3 6JB, UK
| | - Jian Ning
- Tumour Modelling Facility, Institute of Cancer Research, London, SW3 6JB, UK
| | - Wei Yuan
- Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Johann de Bono
- Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Stephen J Pettitt
- The CRUK Gene Function Laboratory, Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, SW3 6JB, UK
| | - Amanda Swain
- Division of Cancer Biology, Institute of Cancer Research, London, SW3 6JB, UK.
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2
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Schillo JL, Feddersen CR, Peplinski RM, Powell LS, Varzavand A, Stipp CS, Riordan JD, Dupuy AJ. Single-cell genomics analysis reveals complex genetic interactions in an in vivo model of acquired BRAF inhibitor resistance. NAR Cancer 2024; 6:zcad061. [PMID: 38213996 PMCID: PMC10782916 DOI: 10.1093/narcan/zcad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/20/2023] [Accepted: 12/21/2023] [Indexed: 01/13/2024] Open
Abstract
The evolution of therapeutic resistance is a major obstacle to the success of targeted oncology drugs. While both inter- and intratumoral heterogeneity limit our ability to detect resistant subpopulations that pre-exist or emerge during treatment, our ability to analyze tumors with single-cell resolution is limited. Here, we utilized a cell-based transposon mutagenesis method to identify mechanisms of BRAF inhibitor resistance in a model of cutaneous melanoma. This screen identified overexpression of NEDD4L and VGLL3 as significant drivers of BRAF inhibitor resistance in vivo. In addition, we describe a novel single-cell genomics profiling method to genotype thousands of individual cells within tumors driven by transposon mutagenesis. This approach revealed a surprising genetic diversity among xenograft tumors and identified recurrent co-occurring mutations that emerge within distinct tumor subclones. Taken together, these observations reveal an unappreciated genetic complexity that drives BRAF inhibitor resistance.
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Affiliation(s)
- Jacob L Schillo
- Department of Anatomy & Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA
| | - Charlotte R Feddersen
- Department of Anatomy & Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Medical Scientist Training Program, The University of Iowa, Iowa City, IA 52242, USA
| | - Rebekah M Peplinski
- Department of Anatomy & Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA
| | - Lexy S Powell
- Department of Anatomy & Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Afshin Varzavand
- Holden Comprehensive Cancer Center, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Christopher S Stipp
- Holden Comprehensive Cancer Center, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Jesse D Riordan
- Department of Anatomy & Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Adam J Dupuy
- Department of Anatomy & Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA
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3
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Zhu EY, Schillo JL, Murray SD, Riordan JD, Dupuy AJ. Understanding cancer drug resistance with Sleeping Beauty functional genomic screens: Application to MAPK inhibition in cutaneous melanoma. iScience 2023; 26:107805. [PMID: 37860756 PMCID: PMC10582486 DOI: 10.1016/j.isci.2023.107805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/10/2023] [Accepted: 08/29/2023] [Indexed: 10/21/2023] Open
Abstract
Combined BRAF and MEK inhibition is an effective treatment for BRAF-mutant cutaneous melanoma. However, most patients progress on this treatment due to drug resistance. Here, we applied the Sleeping Beauty transposon system to understand how melanoma evades MAPK inhibition. We found that the specific drug resistance mechanisms differed across melanomas in our genetic screens of five cutaneous melanoma cell lines. While drivers that reactivated MAPK were highly conserved, many others were cell-line specific. One such driver, VAV1, activated a de-differentiated transcriptional program like that of hyperactive RAC1, RAC1P29S. To target this mechanism, we showed that an inhibitor of SRC, saracatinib, blunts the VAV1-induced transcriptional reprogramming. Overall, we highlighted the importance of accounting for melanoma heterogeneity in treating cutaneous melanoma with MAPK inhibitors. Moreover, we demonstrated the utility of the Sleeping Beauty transposon system in understanding cancer drug resistance.
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Affiliation(s)
- Eliot Y. Zhu
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Jacob L. Schillo
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Sarina D. Murray
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Jesse D. Riordan
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Adam J. Dupuy
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
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4
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Bredthauer C, Fischer A, Ahari AJ, Cao X, Weber J, Rad L, Rad R, Wachutka L, Gagneur J. Transmicron: accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens. Nucleic Acids Res 2023; 51:e21. [PMID: 36617985 PMCID: PMC9976929 DOI: 10.1093/nar/gkac1215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/06/2022] [Accepted: 12/17/2022] [Indexed: 01/10/2023] Open
Abstract
Transposon screens are powerful in vivo assays used to identify loci driving carcinogenesis. These loci are identified as Common Insertion Sites (CISs), i.e. regions with more transposon insertions than expected by chance. However, the identification of CISs is affected by biases in the insertion behaviour of transposon systems. Here, we introduce Transmicron, a novel method that differs from previous methods by (i) modelling neutral insertion rates based on chromatin accessibility, transcriptional activity and sequence context and (ii) estimating oncogenic selection for each genomic region using Poisson regression to model insertion counts while controlling for neutral insertion rates. To assess the benefits of our approach, we generated a dataset applying two different transposon systems under comparable conditions. Benchmarking for enrichment of known cancer genes showed improved performance of Transmicron against state-of-the-art methods. Modelling neutral insertion rates allowed for better control of false positives and stronger agreement of the results between transposon systems. Moreover, using Poisson regression to consider intra-sample and inter-sample information proved beneficial in small and moderately-sized datasets. Transmicron is open-source and freely available. Overall, this study contributes to the understanding of transposon biology and introduces a novel approach to use this knowledge for discovering cancer driver genes.
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Affiliation(s)
- Carl Bredthauer
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Computational Health Center, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Anja Fischer
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Ata Jadid Ahari
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany
| | - Xueqi Cao
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Julia Weber
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Lena Rad
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Institute for Experimental Cancer Therapy, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Medicine II, Klinikum rechts der Isar, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Leonhard Wachutka
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany
| | - Julien Gagneur
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Computational Health Center, Helmholtz Zentrum Munich, Neuherberg, Germany.,Institute of Human Genetics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
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5
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Rogers LM, Wang Z, Mott SL, Dupuy AJ, Weiner GJ. A Genetic Screen to Identify Gain- and Loss-of-Function Modifications that Enhance T-cell Infiltration into Tumors. Cancer Immunol Res 2020; 8:1206-1214. [PMID: 32611665 PMCID: PMC7483799 DOI: 10.1158/2326-6066.cir-20-0056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/14/2020] [Accepted: 06/26/2020] [Indexed: 11/16/2022]
Abstract
T-cell-mediated cancer immunotherapies, including anti-PD-1 and T cells expressing chimeric antigen receptors (CAR-T cells), are becoming standard treatments for many cancer types. CAR-T therapy, in particular, has been successful in treating circulating, but not solid, tumors. One challenge limiting immunotherapy success is that tumors lacking T-cell infiltration do not respond to treatment. Therefore, one potential strategy to overcome resistance is to enhance the ability of T cells to traffic into tumors. Here, we describe an unbiased in vivo genetic screen approach utilizing the Sleeping Beauty mutagenesis system to identify candidate genes in T cells that might be modified to drive intratumoral T-cell accumulation. This screen identified over 400 candidate genes in three tumor models. These results indicated substantial variation in gene candidate selection, depending on the tumor model and whether or not mice were treated with anti-PD-1, yet some candidate genes were identified in all tumor models and with anti-PD-1 therapy. Inhibition of the most frequently mutated gene, Aak1, affected chemokine receptor expression and enhanced T-cell trafficking in vitro and in vivo Screen candidates should be further validated as therapeutic targets, with particular relevance to enhancing infiltration of adoptively transferred T cells into solid tumors.
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Affiliation(s)
- Laura M Rogers
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa.
| | - Zhaoming Wang
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
| | - Sarah L Mott
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
| | - Adam J Dupuy
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa
| | - George J Weiner
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa
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6
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Noorani I, Bradley A, de la Rosa J. CRISPR and transposon in vivo screens for cancer drivers and therapeutic targets. Genome Biol 2020; 21:204. [PMID: 32811551 PMCID: PMC7437018 DOI: 10.1186/s13059-020-02118-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/23/2020] [Indexed: 02/07/2023] Open
Abstract
Human cancers harbor substantial genetic, epigenetic, and transcriptional changes, only some of which drive oncogenesis at certain times during cancer evolution. Identifying the cancer-driver alterations amongst the vast swathes of "passenger" changes still remains a major challenge. Transposon and CRISPR screens in vivo provide complementary methods for achieving this, and each platform has its own advantages. Here, we review recent major technological breakthroughs made with these two approaches and highlight future directions. We discuss how each genetic screening platform can provide unique insight into cancer evolution, including intra-tumoral heterogeneity, metastasis, and immune evasion, presenting transformative opportunities for targeted therapeutic intervention.
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Affiliation(s)
- Imran Noorani
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
- Department of Neurosurgery, University of Cambridge, Cambridge, CB2 0QQ, UK.
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Allan Bradley
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Jorge de la Rosa
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
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7
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Feddersen CR, Schillo JL, Varzavand A, Vaughn HR, Wadsworth LS, Voigt AP, Zhu EY, Jennings BM, Mullen SA, Bobera J, Riordan JD, Stipp CS, Dupuy AJ. Src-Dependent DBL Family Members Drive Resistance to Vemurafenib in Human Melanoma. Cancer Res 2019; 79:5074-5087. [PMID: 31416844 PMCID: PMC6774858 DOI: 10.1158/0008-5472.can-19-0244] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/05/2019] [Accepted: 08/06/2019] [Indexed: 12/25/2022]
Abstract
The use of selective BRAF inhibitors (BRAFi) has produced remarkable outcomes for patients with advanced cutaneous melanoma harboring a BRAFV600E mutation. Unfortunately, the majority of patients eventually develop drug-resistant disease. We employed a genetic screening approach to identify gain-of-function mechanisms of BRAFi resistance in two independent melanoma cell lines. Our screens identified both known and unappreciated drivers of BRAFi resistance, including multiple members of the DBL family. Mechanistic studies identified a DBL/RAC1/PAK signaling axis capable of driving resistance to both current and next-generation BRAFis. However, we show that the SRC inhibitor, saracatinib, can block the DBL-driven resistance. Our work highlights the utility of our straightforward genetic screening method in identifying new drug combinations to combat acquired BRAFi resistance. SIGNIFICANCE: A simple, rapid, and flexible genetic screening approach identifies genes that drive resistance to MAPK inhibitors when overexpressed in human melanoma cells.
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Affiliation(s)
- Charlotte R Feddersen
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Jacob L Schillo
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Afshin Varzavand
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa
| | - Hayley R Vaughn
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Lexy S Wadsworth
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Andrew P Voigt
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Eliot Y Zhu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Brooke M Jennings
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa
| | - Sarah A Mullen
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa
| | - Jeremy Bobera
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa
| | - Jesse D Riordan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Christopher S Stipp
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa.
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa.
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
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8
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Ramakrishnan M, Zhou M, Pan C, Hänninen H, Yrjälä K, Vinod KK, Tang D. Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of Bamboo Ppmar2 Mariner-Like Element. Int J Mol Sci 2019; 20:ijms20153692. [PMID: 31357686 PMCID: PMC6696609 DOI: 10.3390/ijms20153692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 11/16/2022] Open
Abstract
Mariner-like elements (MLE) are a super-family of DNA transposons widespread in animal and plant genomes. Based on their transposition characteristics, such as random insertions and high-frequency heterogeneous transpositions, several MLEs have been developed to be used as tools in gene tagging and gene therapy. Two active MLEs, Ppmar1 and Ppmar2, have previously been identified in moso bamboo (Phyllostachys edulis). Both of these have a preferential insertion affinity to AT-rich region and their insertion sites are close to random in the host genome. In Ppmar2 element, we studied the affinities of terminal inverted repeats (TIRs) to DNA binding domain (DBD) and their influence on the transposition activity. We could identify two putative boxes in the TIRs which play a significant role in defining the TIR's affinities to the DBD. Seven mutated TIRs were constructed, differing in affinities based on similarities with those of other plant MLEs. Gel mobility shift assays showed that the TIR mutants with mutation sites G669A-C671A had significantly higher affinities than the mutants with mutation sites C657T-A660T. The high-affinity TIRs indicated that their transposition frequency was 1.5-2.0 times higher than that of the wild type TIRs in yeast transposition assays. The MLE mutants with low-affinity TIRs had relatively lower transposition frequency from that of wild types. We conclude that TIR affinity to DBD significantly affects the transposition activity of Ppmar2. The mutant MLEs highly active TIRs constructed in this study can be used as a tool for bamboo genetic studies.
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Affiliation(s)
- Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
| | - Chunfang Pan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Heikki Hänninen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Kunnummal Kurungara Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Rice Breeding and Genetics Research Centre, Aduthurai, Tamil Nadu 612101, India
| | - Dingqin Tang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
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9
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Feddersen CR, Wadsworth LS, Zhu EY, Vaughn HR, Voigt AP, Riordan JD, Dupuy AJ. A simplified transposon mutagenesis method to perform phenotypic forward genetic screens in cultured cells. BMC Genomics 2019; 20:497. [PMID: 31208320 PMCID: PMC6580595 DOI: 10.1186/s12864-019-5888-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/06/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The introduction of genome-wide shRNA and CRISPR libraries has facilitated cell-based screens to identify loss-of-function mutations associated with a phenotype of interest. Approaches to perform analogous gain-of-function screens are less common, although some reports have utilized arrayed viral expression libraries or the CRISPR activation system. However, a variety of technical and logistical challenges make these approaches difficult for many labs to execute. In addition, genome-wide shRNA or CRISPR libraries typically contain of hundreds of thousands of individual engineered elements, and the associated complexity creates issues with replication and reproducibility for these methods. RESULTS Here we describe a simple, reproducible approach using the SB transposon system to perform phenotypic cell-based genetic screens. This approach employs only three plasmids to perform unbiased, whole-genome transposon mutagenesis. We also describe a ligation-mediated PCR method that can be used in conjunction with the included software tools to map raw sequence data, identify candidate genes associated with phenotypes of interest, and predict the impact of recurrent transposon insertions on candidate gene function. Finally, we demonstrate the high reproducibility of our approach by having three individuals perform independent replicates of a mutagenesis screen to identify drivers of vemurafenib resistance in cultured melanoma cells. CONCLUSIONS Collectively, our work establishes a facile, adaptable method that can be performed by labs of any size to perform robust, genome-wide screens to identify genes that influence phenotypes of interest.
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Affiliation(s)
- Charlotte R. Feddersen
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Lexy S. Wadsworth
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Eliot Y. Zhu
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Hayley R. Vaughn
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Andrew P. Voigt
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Jesse D. Riordan
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Adam J. Dupuy
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52246 USA
- Department of Anatomy & Cell Biology, Cancer Biology Graduate Program, University of Iowa, MERF, 375 Newton Road, Iowa City, IA 3202 USA
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10
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Ziyad S, Riordan JD, Cavanaugh AM, Su T, Hernandez GE, Hilfenhaus G, Morselli M, Huynh K, Wang K, Chen JN, Dupuy AJ, Iruela-Arispe ML. A Forward Genetic Screen Targeting the Endothelium Reveals a Regulatory Role for the Lipid Kinase Pi4ka in Myelo- and Erythropoiesis. Cell Rep 2019; 22:1211-1224. [PMID: 29386109 PMCID: PMC5828030 DOI: 10.1016/j.celrep.2018.01.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/05/2017] [Accepted: 01/05/2018] [Indexed: 11/19/2022] Open
Abstract
Given its role as the source of definitive hematopoietic cells, we sought to determine whether mutations initiated in the hemogenic endothelium would yield hematopoietic abnormalities or malignancies. Here, we find that endothelium-specific transposon mutagenesis in mice promotes hematopoietic pathologies that are both myeloid and lymphoid in nature. Frequently mutated genes included previously recognized cancer drivers and additional candidates, such as Pi4ka, a lipid kinase whose mutation was found to promote myeloid and erythroid dysfunction. Subsequent validation experiments showed that targeted inactivation of the Pi4ka catalytic domain or reduction in mRNA expression inhibited myeloid and erythroid cell differentiation in vitro and promoted anemia in vivo through a mechanism involving deregulation of AKT, MAPK, SRC, and JAK-STAT signaling. Finally, we provide evidence linking PI4KAP2, previously considered a pseudogene, to human myeloid and erythroid leukemia.
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Affiliation(s)
- Safiyyah Ziyad
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jesse D Riordan
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Ann M Cavanaugh
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Trent Su
- Institute for Quantitative and Computational Biology and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gloria E Hernandez
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Georg Hilfenhaus
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marco Morselli
- Institute for Quantitative and Computational Biology and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kristine Huynh
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin Wang
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jau-Nian Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - M Luisa Iruela-Arispe
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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11
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Kieckhaefer JE, Maina F, Wells R, Wangensteen KJ. Liver Cancer Gene Discovery Using Gene Targeting, Sleeping Beauty, and CRISPR/Cas9. Semin Liver Dis 2019; 39:261-274. [PMID: 30912094 PMCID: PMC7485130 DOI: 10.1055/s-0039-1678725] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is a devastating and prevalent cancer with limited treatment options. Technological advances have enabled genetic screens to be employed in HCC model systems to characterize genes regulating tumor initiation and growth. Relative to traditional methods for studying cancer biology, such as candidate gene approaches or expression analysis, genetic screens have several advantages: they are unbiased, with no a priori selection; can directly annotate gene function; and can uncover gene-gene interactions. In HCC, three main types of screens have been conducted and are reviewed here: (1) transposon-based mutagenesis screens, (2) knockdown screens using RNA interference (RNAi) or the CRISPR/Cas9 system, and (3) overexpression screens using CRISPR activation (CRISPRa) or cDNAs. These methods will be valuable in future genetic screens to delineate the mechanisms underlying drug resistance and to identify new treatments for HCC.
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Affiliation(s)
- Julia E. Kieckhaefer
- Department of Medicine, Division of Gastroenterology, University of Pennsylvania, Philadelphia, PA, USA
| | - Flavio Maina
- Aix Marseille University, CNRS, Developmental Biology Institute of Marseille (IBDM), Parc Scientifique de Luminy, Marseille, France
| | - Rebecca Wells
- Department of Medicine, Division of Gastroenterology, University of Pennsylvania, Philadelphia, PA, USA
- Pathology and Laboratory Medicine and Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Kirk J. Wangensteen
- Department of Medicine, Division of Gastroenterology, University of Pennsylvania, Philadelphia, PA, USA
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12
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Prahallad A, Jensen MR, Chapeau EA. Deciphering mechanisms of response and resistance in large-scale mouse cancer screens. Curr Opin Genet Dev 2019; 54:48-54. [PMID: 30954760 DOI: 10.1016/j.gde.2019.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/08/2019] [Accepted: 02/16/2019] [Indexed: 11/27/2022]
Abstract
Acquired resistance is a major limitation for the successful treatment of cancer patients. Although numerous efficacious cancer therapeutics have been developed in the past decades, resistance arises due to a variety of reasons including tumoral genetic alterations, or modulation of factors in the tumor environment. Understanding the mechanistic reasons for tumor relapse supports the identification of novel combination therapies that could lead to more durable responses. Here, we will review large-scale in vivo screens in pre-clinical cancer models that employed genetic and pharmacological agents toward elucidating acquired drug resistance and informing on beneficial combinations to be tested in clinical trials.
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Affiliation(s)
- Anirudh Prahallad
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Emilie Anne Chapeau
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland.
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13
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Guimaraes-Young A, Feddersen CR, Dupuy AJ. Sleeping Beauty Mouse Models of Cancer: Microenvironmental Influences on Cancer Genetics. Front Oncol 2019; 9:611. [PMID: 31338332 PMCID: PMC6629774 DOI: 10.3389/fonc.2019.00611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/21/2019] [Indexed: 12/13/2022] Open
Abstract
The Sleeping Beauty (SB) transposon insertional mutagenesis system offers a streamlined approach to identify genetic drivers of cancer. With a relatively random insertion profile, SB is uniquely positioned for conducting unbiased forward genetic screens. Indeed, SB mouse models of cancer have revealed insights into the genetics of tumorigenesis. In this review, we highlight experiments that have exploited the SB system to interrogate the genetics of cancer in distinct biological contexts. We also propose experimental designs that could further our understanding of the relationship between tumor microenvironment and tumor progression.
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Affiliation(s)
- Amy Guimaraes-Young
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Charlotte R Feddersen
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
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14
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O'Donnell KA. Advances in functional genetic screening with transposons and CRISPR/Cas9 to illuminate cancer biology. Curr Opin Genet Dev 2018; 49:85-94. [PMID: 29587177 PMCID: PMC6312197 DOI: 10.1016/j.gde.2018.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/27/2018] [Accepted: 03/08/2018] [Indexed: 12/18/2022]
Abstract
Large-scale genome sequencing studies have identified a wealth of mutations in human tumors and have dramatically advanced the field of cancer genetics. However, the functional consequences of an altered gene in tumor progression cannot always be inferred from mutation status alone. This underscores the critical need for complementary methods to assign functional significance to mutated genes in cancer. Transposons are mobile genetic elements that serve as powerful tools for insertional mutagenesis. Over the last decade, investigators have employed mouse models with ondemand transposon-mediated mutagenesis to perform unbiased genetic screens to identify clinically relevant genes that participate in the pathogenesis of human cancer. Two distinct DNA transposon mutagenesis systems, Sleeping Beauty (SB) and PiggyBac (PB), have been applied extensively in vivo and more recently, in ex vivo settings. These studies have informed our understanding of the genes and pathways that drive cancer initiation, progression, and metastasis. This review highlights the latest progress on cancer gene identification for specific cancer subtypes, as well as new technological advances and incorporation of the CRISPR/Cas9 toolbox into transposon-mediated functional genetic studies.
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Affiliation(s)
- Kathryn A O'Donnell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States; Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States.
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15
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Narayanavari SA, Chilkunda SS, Ivics Z, Izsvák Z. Sleeping Beauty transposition: from biology to applications. Crit Rev Biochem Mol Biol 2016; 52:18-44. [PMID: 27696897 DOI: 10.1080/10409238.2016.1237935] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Sleeping Beauty (SB) is the first synthetic DNA transposon that was shown to be active in a wide variety of species. Here, we review studies from the last two decades addressing both basic biology and applications of this transposon. We discuss how host-transposon interaction modulates transposition at different steps of the transposition reaction. We also discuss how the transposon was translated for gene delivery and gene discovery purposes. We critically review the system in clinical, pre-clinical and non-clinical settings as a non-viral gene delivery tool in comparison with viral technologies. We also discuss emerging SB-based hybrid vectors aimed at combining the attractive safety features of the transposon with effective viral delivery. The success of the SB-based technology can be fundamentally attributed to being able to insert fairly randomly into genomic regions that allow stable long-term expression of the delivered transgene cassette. SB has emerged as an efficient and economical toolkit for safe and efficient gene delivery for medical applications.
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Affiliation(s)
- Suneel A Narayanavari
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
| | - Shreevathsa S Chilkunda
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
| | - Zoltán Ivics
- b Division of Medical Biotechnology , Paul Ehrlich Institute , Langen , Germany
| | - Zsuzsanna Izsvák
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
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16
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Smith RP, Riordan JD, Feddersen CR, Dupuy AJ. A Hybrid Adenoviral Vector System Achieves Efficient Long-Term Gene Expression in the Liver via piggyBac Transposition. Hum Gene Ther 2016; 26:377-85. [PMID: 25808258 DOI: 10.1089/hum.2014.123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Much research has gone into the development of hybrid gene delivery systems that combine the broad tropism and efficient transduction of adenoviral vectors with the ability to achieve stable expression of cargo genes. In addition to gene therapy applications, such a system has considerable advantages for studies of gene function in vivo, permitting fine-tuned genetic manipulation with higher throughput than can be achieved using standard transgenic and DNA targeting techniques. Existing strategies are limited, however, by low integration efficiencies, small cargo capacity, and/or a dependence on target cell division. The utility of this approach could be enhanced by a system that provides all of the following: (1) efficient delivery, (2) stable expression in a high percentage of target cells (whether mitotic or not), (3) large cargo capacity, (4) flexibility to use with a wide range of additional experimental conditions, and (5) simple experimental technique. Here we report the initial characterization of a hybrid system that meets these criteria by utilizing piggyBac (PB) transposition to achieve genomic integration from adenoviral vectors. We demonstrate stable expression of an adenovirus (Ad)-PB-delivered reporter gene in ∼20-40% of hepatocytes following standard tail vein injection. Its high efficiency and flexibility relative to existing hybrid adenoviral gene delivery approaches indicate a considerable potential utility of the Ad-PB system for therapeutic gene delivery and in vivo studies of gene function.
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Affiliation(s)
- Ryan P Smith
- Department of Anatomy and Cell Biology, Roy J. & Lucille A. Carver College of Medicine, University of Iowa , Iowa City, IA 52242
| | - Jesse D Riordan
- Department of Anatomy and Cell Biology, Roy J. & Lucille A. Carver College of Medicine, University of Iowa , Iowa City, IA 52242
| | - Charlotte R Feddersen
- Department of Anatomy and Cell Biology, Roy J. & Lucille A. Carver College of Medicine, University of Iowa , Iowa City, IA 52242
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, Roy J. & Lucille A. Carver College of Medicine, University of Iowa , Iowa City, IA 52242
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17
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Temiz NA, Moriarity BS, Wolf NK, Riordan JD, Dupuy AJ, Largaespada DA, Sarver AL. RNA sequencing of Sleeping Beauty transposon-induced tumors detects transposon-RNA fusions in forward genetic cancer screens. Genome Res 2015; 26:119-29. [PMID: 26553456 PMCID: PMC4691744 DOI: 10.1101/gr.188649.114] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 11/04/2015] [Indexed: 11/24/2022]
Abstract
Forward genetic screens using Sleeping Beauty (SB)-mobilized T2/Onc transposons have been used to identify common insertion sites (CISs) associated with tumor formation. Recurrent sites of transposon insertion are commonly identified using ligation-mediated PCR (LM-PCR). Here, we use RNA sequencing (RNA-seq) data to directly identify transcriptional events mediated by T2/Onc. Surprisingly, the majority (∼80%) of LM-PCR identified junction fragments do not lead to observable changes in RNA transcripts. However, in CIS regions, direct transcriptional effects of transposon insertions are observed. We developed an automated method to systematically identify T2/Onc-genome RNA fusion sequences in RNA-seq data. RNA fusion-based CISs were identified corresponding to both DNA-based CISs (Cdkn2a, Mycl1, Nf2, Pten, Sema6d, and Rere) and additional regions strongly associated with cancer that were not observed by LM-PCR (Myc, Akt1, Pth, Csf1r, Fgfr2, Wisp1, Map3k5, and Map4k3). In addition to calculating recurrent CISs, we also present complementary methods to identify potential driver events via determination of strongly supported fusions and fusions with large transcript level changes in the absence of multitumor recurrence. These methods independently identify CIS regions and also point to cancer-associated genes like Braf. We anticipate RNA-seq analyses of tumors from forward genetic screens will become an efficient tool to identify causal events.
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Affiliation(s)
- Nuri A Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Branden S Moriarity
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA; Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA; Brain Tumor Program, University of Minnesota, Minneapolis, Minnesota 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Natalie K Wolf
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA; Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Jesse D Riordan
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa 52242, USA
| | - David A Largaespada
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA; Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA; Brain Tumor Program, University of Minnesota, Minneapolis, Minnesota 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Aaron L Sarver
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
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18
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Dhivya S, Premkumar K. Nomadic genetic elements contribute to oncogenic translocations: Implications in carcinogenesis. Crit Rev Oncol Hematol 2015; 98:81-93. [PMID: 26548742 DOI: 10.1016/j.critrevonc.2015.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 10/05/2015] [Accepted: 10/27/2015] [Indexed: 12/22/2022] Open
Abstract
Chromosomal translocations as molecular signatures have been reported in various malignancies but, the mechanism behind which is largely unknown. Swapping of chromosomal fragments occurs by induction of double strand breaks (DSBs), most of which were initially assumed de novo. However, decoding of human genome proved that transposable elements (TE) might have profound influence on genome integrity. TEs are highly conserved mobile genetic elements that generate DSBs, subsequently resulting in large chromosomal rearrangements. Previously TE insertions were thought to be harmless, but recently gains attention due to the origin of spectrum of post-insertional genomic alterations and subsequent transcriptional alterations leading to development of deleterious effects mainly carcinogenesis. Though the existing knowledge on the cancer-associated TE dynamics is very primitive, exploration of underlying mechanism promises better therapeutic strategies for cancer. Thus, this review focuses on the prevalence of TE in the genome, associated genomic instability upon transposition activation and impact on tumorigenesis.
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Affiliation(s)
- Sridaran Dhivya
- Cancer Genetics and Nanomedicine Laboratory, Department of Biomedical Science, School of Basic Medical Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - Kumpati Premkumar
- Cancer Genetics and Nanomedicine Laboratory, Department of Biomedical Science, School of Basic Medical Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India.
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19
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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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20
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Moriarity BS, Largaespada DA. Sleeping Beauty transposon insertional mutagenesis based mouse models for cancer gene discovery. Curr Opin Genet Dev 2015; 30:66-72. [PMID: 26051241 DOI: 10.1016/j.gde.2015.04.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 04/23/2015] [Indexed: 01/04/2023]
Abstract
Large-scale genomic efforts to study human cancer, such as the cancer gene atlas (TCGA), have identified numerous cancer drivers in a wide variety of tumor types. However, there are limitations to this approach, the mutations and expression or copy number changes that are identified are not always clearly functionally relevant, and only annotated genes and genetic elements are thoroughly queried. The use of complimentary, nonbiased, functional approaches to identify drivers of cancer development and progression is ideal to maximize the rate at which cancer discoveries are achieved. One such approach that has been successful is the use of the Sleeping Beauty (SB) transposon-based mutagenesis system in mice. This system uses a conditionally expressed transposase and mutagenic transposon allele to target mutagenesis to somatic cells of a given tissue in mice to cause random mutations leading to tumor development. Analysis of tumors for transposon common insertion sites (CIS) identifies candidate cancer genes specific to that tumor type. While similar screens have been performed in mice with the PiggyBac (PB) transposon and viral approaches, we limit extensive discussion to SB. Here we discuss the basic structure of these screens, screens that have been performed, methods used to identify CIS.
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Affiliation(s)
- Branden S Moriarity
- Department of Pediatrics, University of Minnesota Minneapolis, MN 55455, United States; Center for Genome Engineering, University of Minnesota Minneapolis, MN 55455, United States; Masonic Cancer Center, University of Minnesota Minneapolis, MN 55455, United States
| | - David A Largaespada
- Department of Pediatrics, University of Minnesota Minneapolis, MN 55455, United States; Center for Genome Engineering, University of Minnesota Minneapolis, MN 55455, United States; Masonic Cancer Center, University of Minnesota Minneapolis, MN 55455, United States; Department of Genetics, Cell Biology, and Development, University of Minnesota Minneapolis, MN 55455, United States.
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