1
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Karagiannis D, Wu W, Li A, Hayashi M, Chen X, Yip M, Mangipudy V, Xu X, Sánchez-Rivera FJ, Soto-Feliciano YM, Ye J, Papagiannakopoulos T, Lu C. Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors. Cell Rep 2024; 43:113629. [PMID: 38165806 PMCID: PMC10853943 DOI: 10.1016/j.celrep.2023.113629] [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: 12/06/2022] [Revised: 10/27/2023] [Accepted: 12/12/2023] [Indexed: 01/04/2024] Open
Abstract
The interplay between metabolism and chromatin signaling is implicated in cancer progression. However, whether and how metabolic reprogramming in tumors generates chromatin vulnerabilities remain unclear. Lung adenocarcinoma (LUAD) tumors frequently harbor aberrant activation of the NRF2 antioxidant pathway, which drives aggressive and chemo-resistant disease. Using a chromatin-focused CRISPR screen, we report that NRF2 activation sensitizes LUAD cells to genetic and chemical inhibition of class I histone deacetylases (HDACs). This association is observed across cultured cells, mouse models, and patient-derived xenografts. Integrative epigenomic, transcriptomic, and metabolomic analysis demonstrates that HDAC inhibition causes widespread redistribution of H4ac and its reader protein, which transcriptionally downregulates metabolic enzymes. This results in reduced flux into amino acid metabolism and de novo nucleotide synthesis pathways that are preferentially required for the survival of NRF2-active cancer cells. Together, our findings suggest NRF2 activation as a potential biomarker for effective repurposing of HDAC inhibitors to treat solid tumors.
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Affiliation(s)
- Dimitris Karagiannis
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Warren Wu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Albert Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Makiko Hayashi
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michaela Yip
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vaibhav Mangipudy
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xinjing Xu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Francisco J Sánchez-Rivera
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Yadira M Soto-Feliciano
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jiangbin Ye
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thales Papagiannakopoulos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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2
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Karagiannis D, Wu W, Li A, Hayashi M, Chen X, Yip M, Mangipudy V, Xu X, Sánchez-Rivera FJ, Soto-Feliciano YM, Ye J, Papagiannakopoulos T, Lu C. Metabolic Reprogramming by Histone Deacetylase Inhibition Selectively Targets NRF2-activated tumors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538118. [PMID: 37162970 PMCID: PMC10168258 DOI: 10.1101/2023.04.24.538118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Interplay between metabolism and chromatin signaling have been implicated in cancer initiation and progression. However, whether and how metabolic reprogramming in tumors generates specific epigenetic vulnerabilities remain unclear. Lung adenocarcinoma (LUAD) tumors frequently harbor mutations that cause aberrant activation of the NRF2 antioxidant pathway and drive aggressive and chemo-resistant disease. We performed a chromatin-focused CRISPR screen and report that NRF2 activation sensitized LUAD cells to genetic and chemical inhibition of class I histone deacetylases (HDAC). This association was consistently observed across cultured cells, syngeneic mouse models and patient-derived xenografts. HDAC inhibition causes widespread increases in histone H4 acetylation (H4ac) at intergenic regions, but also drives re-targeting of H4ac reader protein BRD4 away from promoters with high H4ac levels and transcriptional downregulation of corresponding genes. Integrative epigenomic, transcriptomic and metabolomic analysis demonstrates that these chromatin changes are associated with reduced flux into amino acid metabolism and de novo nucleotide synthesis pathways that are preferentially required for the survival of NRF2-active cancer cells. Together, our findings suggest that metabolic alterations such as NRF2 activation could serve as biomarkers for effective repurposing of HDAC inhibitors to treat solid tumors.
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3
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Soto-Feliciano YM, Sánchez-Rivera FJ, Perner F, Barrows DW, Kastenhuber ER, Ho YJ, Carroll T, Xiong Y, Anand D, Soshnev AA, Gates L, Beytagh MC, Cheon D, Gu S, Liu XS, Krivtsov AV, Meneses M, de Stanchina E, Stone RM, Armstrong SA, Lowe SW, Allis CD. A Molecular Switch between Mammalian MLL Complexes Dictates Response to Menin-MLL Inhibition. Cancer Discov 2023; 13:146-169. [PMID: 36264143 PMCID: PMC9827117 DOI: 10.1158/2159-8290.cd-22-0416] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/18/2022] [Accepted: 10/17/2022] [Indexed: 01/16/2023]
Abstract
Menin interacts with oncogenic MLL1-fusion proteins, and small molecules that disrupt these associations are in clinical trials for leukemia treatment. By integrating chromatin-focused and genome-wide CRISPR screens with genetic, pharmacologic, and biochemical approaches, we discovered a conserved molecular switch between the MLL1-Menin and MLL3/4-UTX chromatin-modifying complexes that dictates response to Menin-MLL inhibitors. MLL1-Menin safeguards leukemia survival by impeding the binding of the MLL3/4-UTX complex at a subset of target gene promoters. Disrupting the Menin-MLL1 interaction triggers UTX-dependent transcriptional activation of a tumor-suppressive program that dictates therapeutic responses in murine and human leukemia. Therapeutic reactivation of this program using CDK4/6 inhibitors mitigates treatment resistance in leukemia cells that are insensitive to Menin inhibitors. These findings shed light on novel functions of evolutionarily conserved epigenetic mediators like MLL1-Menin and MLL3/4-UTX and are relevant to understand and target molecular pathways determining therapeutic responses in ongoing clinical trials. SIGNIFICANCE Menin-MLL inhibitors silence a canonical HOX- and MEIS1-dependent oncogenic gene expression program in leukemia. We discovered a parallel, noncanonical transcriptional program involving tumor suppressor genes that are repressed in Menin-MLL inhibitor-resistant leukemia cells but that can be reactivated upon combinatorial treatment with CDK4/6 inhibitors to augment therapy responses. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
| | | | - Florian Perner
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts.,Internal Medicine C, Greifswald University Medical Center, Greifswald, Germany
| | - Douglas W. Barrows
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York.,Bioinformatics Resource Center, The Rockefeller University, New York, New York
| | - Edward R. Kastenhuber
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yu-Jui Ho
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, New York
| | - Yijun Xiong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Disha Anand
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Internal Medicine C, Greifswald University Medical Center, Greifswald, Germany
| | - Alexey A. Soshnev
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York
| | - Leah Gates
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York
| | - Mary Clare Beytagh
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York
| | - David Cheon
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York
| | - Shengqing Gu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - X. Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrei V. Krivtsov
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Maximiliano Meneses
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard M. Stone
- Leukemia Division, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Scott A. Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts.,Corresponding Authors: C. David Allis, The Rockefeller University, Allis Lab, Box #78, 1230 York Avenue, New York, NY 10065. Phone: 212-327-7839; E-mail: ; Scott W. Lowe, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, Cancer Biology and Genetics Program, New York, NY, 10065. Phone: 646-888-3342; E-mail: ; and Scott A. Armstrong, Harvard Medical School, Dana-Farber Cancer Institute, Department of Pediatric Oncology, Boston, MA, 02115. Phone: 617-632-2991; E-mail:
| | - Scott W. Lowe
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Corresponding Authors: C. David Allis, The Rockefeller University, Allis Lab, Box #78, 1230 York Avenue, New York, NY 10065. Phone: 212-327-7839; E-mail: ; Scott W. Lowe, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, Cancer Biology and Genetics Program, New York, NY, 10065. Phone: 646-888-3342; E-mail: ; and Scott A. Armstrong, Harvard Medical School, Dana-Farber Cancer Institute, Department of Pediatric Oncology, Boston, MA, 02115. Phone: 617-632-2991; E-mail:
| | - C. David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York.,Corresponding Authors: C. David Allis, The Rockefeller University, Allis Lab, Box #78, 1230 York Avenue, New York, NY 10065. Phone: 212-327-7839; E-mail: ; Scott W. Lowe, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, Cancer Biology and Genetics Program, New York, NY, 10065. Phone: 646-888-3342; E-mail: ; and Scott A. Armstrong, Harvard Medical School, Dana-Farber Cancer Institute, Department of Pediatric Oncology, Boston, MA, 02115. Phone: 617-632-2991; E-mail:
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4
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Dahn ML, Marcato P. In Vivo Genome-Wide Pooled RNAi Screens in Cancer Cells to Identify Determinants of Chemotherapy/Drug Response. Methods Mol Biol 2021; 2381:189-200. [PMID: 34590277 DOI: 10.1007/978-1-0716-1740-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Large-scale RNAi screens (i.e., genome-wide arrays and pools) can reveal the essential biological functions of previously uncharacterized genes. Due to the nature of the selection process involved in screens, RNAi screens are also very useful for identifying genes involved in drug responses. The information gained from these screens could be used to predict a cancer patient's response to a specific drug (i.e., precision medicine) or identify anti-cancer drug resistance genes, which could be targeted to improve treatment outcomes. In this capacity, screens have been most often performed in vitro. However, there is limitation to performing these screens in vitro: genes which are required in only an in vivo setting (e.g., rely on the tumor microenvironment for function) will not be identified. As such, it can be desirable to perform RNAi screens in vivo. Here we outline the additional technical details that should be considered for performing genome-wide RNAi drug screens of cancer cells under in vivo conditions (i.e., tumor xenografts).
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Affiliation(s)
- Margaret L Dahn
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Paola Marcato
- Department of Pathology, Dalhousie University, Halifax, NS, Canada. .,Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.
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5
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Cipponi A, Goode DL, Bedo J, McCabe MJ, Pajic M, Croucher DR, Rajal AG, Junankar SR, Saunders DN, Lobachevsky P, Papenfuss AT, Nessem D, Nobis M, Warren SC, Timpson P, Cowley M, Vargas AC, Qiu MR, Generali DG, Keerthikumar S, Nguyen U, Corcoran NM, Long GV, Blay JY, Thomas DM. MTOR signaling orchestrates stress-induced mutagenesis, facilitating adaptive evolution in cancer. Science 2020; 368:1127-1131. [PMID: 32499442 DOI: 10.1126/science.aau8768] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/09/2019] [Accepted: 04/10/2020] [Indexed: 12/12/2022]
Abstract
In microorganisms, evolutionarily conserved mechanisms facilitate adaptation to harsh conditions through stress-induced mutagenesis (SIM). Analogous processes may underpin progression and therapeutic failure in human cancer. We describe SIM in multiple in vitro and in vivo models of human cancers under nongenotoxic drug selection, paradoxically enhancing adaptation at a competing intrinsic fitness cost. A genome-wide approach identified the mechanistic target of rapamycin (MTOR) as a stress-sensing rheostat mediating SIM across multiple cancer types and conditions. These observations are consistent with a two-phase model for drug resistance, in which an initially rapid expansion of genetic diversity is counterbalanced by an intrinsic fitness penalty, subsequently normalizing to complete adaptation under the new conditions. This model suggests synthetic lethal strategies to minimize resistance to anticancer therapy.
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Affiliation(s)
- Arcadi Cipponi
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia. .,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - David L Goode
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Justin Bedo
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Computing and Information Systems, the University of Melbourne, Parkville, VIC, Australia.,Peter MacCallum Cancer Centre, Parkville, VIC, Australia
| | - Mark J McCabe
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Marina Pajic
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - David R Croucher
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Alvaro Gonzalez Rajal
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Simon R Junankar
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Darren N Saunders
- School of Medical Sciences, University of New South Wales, NSW, Australia
| | | | - Anthony T Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Computing and Information Systems, the University of Melbourne, Parkville, VIC, Australia.,Peter MacCallum Cancer Centre, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Danielle Nessem
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Max Nobis
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Sean C Warren
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Paul Timpson
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Mark Cowley
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ana C Vargas
- Douglass Hanly Moir Pathology, Turramurra, NSW, Australia
| | - Min R Qiu
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.,Anatomical and Molecular Oncology Pathology, SYDPATH, St. Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Daniele G Generali
- Department of Medical, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Breast Cancer Unit and Translational Research Unit, ASST Cremona, Cremona, Italy
| | - Shivakumar Keerthikumar
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Uyen Nguyen
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Niall M Corcoran
- Division of Urology, Royal Melbourne Hospital, Parkville, VIC, Australia.,Department of Urology, Peninsula Health, Frankston, VIC, Australia.,Department of Surgery, University of Melbourne, VIC, Australia
| | - Georgina V Long
- Melanoma Institute Australia, Wollstonecraft, NSW, Australia.,The University of Sydney, Sydney, NSW, Australia.,Royal North Shore Hospital and Mater Hospital, Sydney, NSW, Australia.,Crown Princess Mary Cancer Centre Westmead Hospital, Sydney, NSW, Australia
| | - Jean-Yves Blay
- Centre Leon Berard and Université Claude Bernard Lyon, Lyon, France.,UNICANCER, Paris, France
| | - David M Thomas
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia. .,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
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6
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Abstract
The discovery of CRISPR-Cas9 systems has fueled a rapid expansion of gene editing
adoption and has impacted pharmaceutical and biotechnology research
substantially. Here, gene editing is used at an industrial scale to identify and
validate new biological targets for precision medicines, with functional genomic
screening having an increasingly important role. Functional genomic strategies
provide a crucial link between observed biological phenomena and the genes that
influence and drive those phenomena. Although such studies are not new, the use
of CRISPR-Cas9 systems in this arena is providing more robust datasets for
target identification and validation. CRISPR-based screening approaches are also
useful later in the drug development pipeline for understanding drug resistance
and sensitivity ahead of entering clinical trials. This review examines the
developing landscape for CRISPR screening technologies within the pharmaceutical
industry and explores the next steps for this constantly evolving screening
platform.
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7
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Synthetic modeling reveals HOXB genes are critical for the initiation and maintenance of human leukemia. Nat Commun 2019; 10:2913. [PMID: 31266935 PMCID: PMC6606637 DOI: 10.1038/s41467-019-10510-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 05/15/2019] [Indexed: 12/23/2022] Open
Abstract
Mechanistic studies in human cancer have relied heavily on cell lines and mouse models, but are limited by in vitro adaptation and species context issues, respectively. More recent efforts have utilized patient-derived xenografts; however, these are hampered by variable genetic background, inability to study early events, and practical issues with availability/reproducibility. We report here an efficient, reproducible model of T-cell leukemia in which lentiviral transduction of normal human cord blood yields aggressive leukemia that appears indistinguishable from natural disease. We utilize this synthetic model to uncover a role for oncogene-induced HOXB activation which is operative in leukemia cells-of-origin and persists in established tumors where it defines a novel subset of patients distinct from other known genetic subtypes and with poor clinical outcome. We show further that anterior HOXB genes are specifically activated in human T-ALL by an epigenetic mechanism and confer growth advantage in both pre-leukemia cells and established clones.
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8
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Gohl DM, Magli A, Garbe J, Becker A, Johnson DM, Anderson S, Auch B, Billstein B, Froehling E, McDevitt SL, Beckman KB. Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification. Genome Biol 2019; 20:85. [PMID: 31036053 PMCID: PMC6489363 DOI: 10.1186/s13059-019-1691-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/09/2019] [Indexed: 01/15/2023] Open
Abstract
Quantification of DNA sequence tags from engineered constructs such as plasmids, transposons, or other transgenes underlies many functional genomics measurements. Typically, such measurements rely on PCR followed by next-generation sequencing. However, PCR amplification can introduce significant quantitative error. We describe REcount, a novel PCR-free direct counting method. Comparing measurements of defined plasmid pools to droplet digital PCR data demonstrates that REcount is highly accurate and reproducible. We use REcount to provide new insights into clustering biases due to molecule length across different Illumina sequencers and illustrate the impacts on interpretation of next-generation sequencing data and the economics of data generation.
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Affiliation(s)
- Daryl M. Gohl
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 USA
| | - Alessandro Magli
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455 USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455 USA
| | - John Garbe
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | - Aaron Becker
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | | | - Shea Anderson
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | - Benjamin Auch
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | - Bradley Billstein
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
- Present Address: Illumina, Inc, San Diego, CA 92122 USA
| | - Elyse Froehling
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | - Shana L. McDevitt
- Vincent J. Coates Genomics Sequencing Laboratory, University of California, Berkeley, CA 94720 USA
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9
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Zhang D, Li Y, Zhang X, Cheng Y, Li Z. Enhancement of the polymerase chain reaction by tungsten disulfide. RSC Adv 2019; 9:9373-9378. [PMID: 35520733 PMCID: PMC9062020 DOI: 10.1039/c8ra09689a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/14/2019] [Indexed: 12/15/2022] Open
Abstract
In this paper, we demonstrated that the polymerase chain reaction (PCR) could be dramatically enhanced by tungsten disulfide (WS2). The results showed that the PCR efficiency could be increased with the addition of WS2 and at a lower annealing temperature, which simplified the design and operation of PCR. Moreover, PCR with WS2 showed better specificity and efficiency as compared with graphene oxide (GO) for a human genome DNA sample. The mechanism of enhancement of PCR by WS2 was discussed according to the typical structure and the characteristics of selective adsorption of single-stranded DNA by WS2. The results suggested that WS2 as a PCR enhancer can promote the PCR performance and extend the PCR application in biomedical research, clinical diagnostic, and bioanalysis. WS2 as a PCR enhancer can promote the PCR performance and extend PCR bioapplication.![]()
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Yingcun Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Xuange Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Yongqiang Cheng
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Zhengping Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
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10
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Schuster A, Erasimus H, Fritah S, Nazarov PV, van Dyck E, Niclou SP, Golebiewska A. RNAi/CRISPR Screens: from a Pool to a Valid Hit. Trends Biotechnol 2018; 37:38-55. [PMID: 30177380 DOI: 10.1016/j.tibtech.2018.08.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 02/07/2023]
Abstract
High-throughput genetic screens interfering with gene expression are invaluable tools to identify gene function and phenotype-to-genotype interactions. Implementing such screens in the laboratory is challenging, and the choice between currently available technologies based on RNAi and CRISPR/Cas9 (CRISPR-associated protein 9) is not trivial. Identifying reliable candidate hits requires a streamlined experimental setup adjusted to the specific biological question. Here, we provide a critical assessment of the various RNAi/CRISPR approaches to pooled screens and discuss their advantages and pitfalls. We specify a set of best practices for key parameters enabling a reproducible screen and provide a detailed overview of analysis methods and repositories for identifying the best candidate gene hits.
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Affiliation(s)
- Anne Schuster
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Hélène Erasimus
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Sabrina Fritah
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Petr V Nazarov
- Genomics and Proteomics Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Eric van Dyck
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Simone P Niclou
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg; KG Jebsen Brain Tumour Research Center, Department of Biomedicine, University of Bergen, Bergen, Norway; Co-senior authors.
| | - Anna Golebiewska
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg; Co-senior authors.
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11
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Oyaro M, Wylie J, Chen CY, Ondondo RO, Kramvis A. Human immunodeficiency virus infection predictors and genetic diversity of hepatitis B virus and hepatitis C virus co-infections among drug users in three major Kenyan cities. South Afr J HIV Med 2018; 19:737. [PMID: 29707384 PMCID: PMC5913779 DOI: 10.4102/sajhivmed.v19i1.737] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 10/02/2017] [Indexed: 12/28/2022] Open
Abstract
Background Drug users act as reservoirs and transmission channels for hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus (HIV) infections to the general population worldwide. Periodic epidemiological studies to monitor the prevalence and genetic diversity of these infections to inform on interventions are limited. Objective of the study The objective of this study was to determine the predictors of HIV infection and genetic diversity of HBV and HCV among drug users in Kenya. Materials and methods A cross-sectional study on previous drug use history among drug users was conducted in three Kenyan cities using a respondent-driven sampling method between January 2011 and September 2012. Blood samples were collected and analysed for the presence of HBV, HCV and HIV serological markers and to determine the genotypes of HBV and HCV. Results The overall prevalence of HBV, HCV and HIV among drug users was 4.3%, 6.5% and 11.1%, respectively, with evidence of HBV/HIV, HCV/HIV and HBV/HCV/HIV co-infections. The HBV circulating genotypes were A1 (69%) and D6 (19%), whereas HCV genotypes were 1a (72%) and 4a (22%). Injection drug use was a significant predictor of HIV/HCV infections. Younger age (30 years; aOR (adjusted odds ratio) = 0.50, 95% CI (confidence interval): 0.33–0.76; p < 0.001) and early sexual debut (aOR = 0.54, 95% CI: 0.40–0.82; p < 0.05) were negatively associated with detection of any of the three infections. Injecting drug use was positively associated with HCV infection (aOR = 5.37, 95% CI: 2.61–11.06; p < 0.001). Conclusion This high level of genetic diversity exhibited by HBV and HCV isolates requires urgent implementation of harm reduction strategies and continuous monitoring for effective management of the patients.
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Affiliation(s)
- Micah Oyaro
- Immunology Unit, Department of Human Pathology, University of Nairobi, Kenya
| | - John Wylie
- Department of Medical Microbiology, University of Manitoba, Canada
| | - Chien-Yu Chen
- Hepatitis Virus Diversity Research Unit (HVDRU), Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, South Africa
| | - Raphael O Ondondo
- Department of Medical Laboratory Sciences, Masinde Muliro University of Science and Technology, Kenya.,Kenya Medical Research Institute, Centre for Microbiology Research, Nairobi, Kenya
| | - Anna Kramvis
- Hepatitis Virus Diversity Research Unit (HVDRU), Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, South Africa
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12
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Leko V, Sripathy S, Adrianse RL, Loe T, Park A, Lao U, Foss EJ, Bartolomei MS, Bedalov A. Pooled shRNA Screen for Reactivation of MeCP2 on the Inactive X Chromosome. J Vis Exp 2018. [PMID: 29553562 DOI: 10.3791/56398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Forward genetic screens using reporter genes inserted into the heterochromatin have been extensively used to investigate mechanisms of epigenetic control in model organisms. Technologies including short hairpin RNAs (shRNAs) and clustered regularly interspaced short palindromic repeats (CRISPR) have enabled such screens in diploid mammalian cells. Here we describe a large-scale shRNA screen for regulators of X-chromosome inactivation (XCI), using a murine cell line with firefly luciferase and hygromycin resistance genes knocked in at the C-terminus of the methyl CpG binding protein 2 (MeCP2) gene on the inactive X-chromosome (Xi). Reactivation of the construct in the reporter cell line conferred survival advantage under hygromycin B selection, enabling us to screen a large shRNA library and identify hairpins that reactivated the reporter by measuring their post-selection enrichment using next-generation sequencing. The enriched hairpins were then individually validated by testing their ability to activate the luciferase reporter on Xi.
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Affiliation(s)
- Vid Leko
- Clinical Research Division, Fred Hutchinson Cancer Research Center; Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health
| | - Smitha Sripathy
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Robin L Adrianse
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Taylor Loe
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Angela Park
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Uyen Lao
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Eric J Foss
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Marisa S Bartolomei
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine
| | - Antonio Bedalov
- Clinical Research Division, Fred Hutchinson Cancer Research Center; Departments of Medicine and Biochemistry, University of Washington;
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13
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Schaefer C, Mallela N, Seggewiß J, Lechtape B, Omran H, Dirksen U, Korsching E, Potratz J. Target discovery screens using pooled shRNA libraries and next-generation sequencing: A model workflow and analytical algorithm. PLoS One 2018; 13:e0191570. [PMID: 29385199 PMCID: PMC5792015 DOI: 10.1371/journal.pone.0191570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 01/08/2018] [Indexed: 11/28/2022] Open
Abstract
In the search for novel therapeutic targets, RNA interference screening has become a valuable tool. High-throughput technologies are now broadly accessible but their assay development from baseline remains resource-intensive and challenging. Focusing on this assay development process, we here describe a target discovery screen using pooled shRNA libraries and next-generation sequencing (NGS) deconvolution in a cell line model of Ewing sarcoma. In a strategy designed for comparative and synthetic lethal studies, we screened for targets specific to the A673 Ewing sarcoma cell line. Methods, results and pitfalls are described for the entire multi-step screening procedure, from lentiviral shRNA delivery to bioinformatics analysis, illustrating a complete model workflow. We demonstrate that successful studies are feasible from the first assay performance and independent of specialized screening units. Furthermore, we show that a resource-saving screen depth of 100-fold average shRNA representation can suffice to generate reproducible target hits despite heterogeneity in the derived datasets. Because statistical analysis methods are debatable for such datasets, we created ProFED, an analysis package designed to facilitate descriptive data analysis and hit calling using an aim-oriented profile filtering approach. In its versatile design, this open-source online tool provides fast and easy analysis of shRNA and other count-based datasets to complement other analytical algorithms.
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Affiliation(s)
- Christiane Schaefer
- Pediatric Hematology and Oncology, University Hospital Münster, Münster, Germany
| | - Nikhil Mallela
- Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jochen Seggewiß
- Institute of Human Genetics, University Hospital Münster, Münster, Germany
| | - Birgit Lechtape
- Pediatric Hematology and Oncology, University Hospital Münster, Münster, Germany
| | - Heymut Omran
- General Pediatrics, University Hospital Münster, Münster, Germany
| | - Uta Dirksen
- Department of Hematology and Oncology, Pediatrics III, West German Cancer Center, German Cancer Consortium (DKTK) Center Essen, University Hospital Essen, Essen, Germany
| | - Eberhard Korsching
- Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jenny Potratz
- Pediatric Hematology and Oncology, University Hospital Münster, Münster, Germany
- General Pediatrics, University Hospital Münster, Münster, Germany
- * E-mail:
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14
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Cluse LA, Nikolic I, Knight D, Madhamshettiwar PB, Luu J, Cowley KJ, Semple T, Arnau GM, Shortt J, Johnstone RW, Simpson KJ. A Comprehensive Protocol Resource for Performing Pooled shRNA and CRISPR Screens. Methods Mol Biol 2018; 1725:201-227. [PMID: 29322420 DOI: 10.1007/978-1-4939-7568-6_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This chapter details a compendium of protocols that collectively enable the reader to perform a pooled shRNA and/or CRISPR screen-with methods to identify and validate positive controls and subsequent hits; establish a viral titer in the cell line of choice; create and screen libraries, sequence strategies, and bioinformatics resources to analyze outcomes. Collectively, this provides an overarching resource from the start to finish of a screening project, making this technology possible in all laboratories.
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Affiliation(s)
- Leonie A Cluse
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Iva Nikolic
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Deborah Knight
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Piyush B Madhamshettiwar
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Jennii Luu
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Karla J Cowley
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Timothy Semple
- Molecular Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Gisela Mir Arnau
- Molecular Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Jake Shortt
- School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Ricky W Johnstone
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia.
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15
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Wang S, Pike AM, Lee SS, Strong MA, Connelly CJ, Greider CW. BRD4 inhibitors block telomere elongation. Nucleic Acids Res 2017; 45:8403-8410. [PMID: 28854735 PMCID: PMC5737673 DOI: 10.1093/nar/gkx561] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/22/2017] [Indexed: 12/25/2022] Open
Abstract
Cancer cells maintain telomere length equilibrium to avoid senescence and apoptosis induced by short telomeres, which trigger the DNA damage response. Limiting the potential for telomere maintenance in cancer cells has been long been proposed as a therapeutic target. Using an unbiased shRNA screen targeting known kinases, we identified bromodomain-containing protein 4 (BRD4) as a telomere length regulator. Four independent BRD4 inhibitors blocked telomere elongation, in a dose-dependent manner, in mouse cells overexpressing telomerase. Long-term treatment with BRD4 inhibitors caused telomere shortening in both mouse and human cells, suggesting BRD4 plays a role in telomere maintenance in vivo. Telomerase enzymatic activity was not directly affected by BRD4 inhibition. BRD4 is in clinical trials for a number of cancers, but its effects on telomere maintenance have not been previously investigated.
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Affiliation(s)
- Steven Wang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alexandra M Pike
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stella S Lee
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Margaret A Strong
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Carla J Connelly
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Carol W Greider
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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16
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Nagy T, Kampmann M. CRISPulator: a discrete simulation tool for pooled genetic screens. BMC Bioinformatics 2017; 18:347. [PMID: 28732459 PMCID: PMC5521134 DOI: 10.1186/s12859-017-1759-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/13/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The rapid adoption of CRISPR technology has enabled biomedical researchers to conduct CRISPR-based genetic screens in a pooled format. The quality of results from such screens is heavily dependent on the selection of optimal screen design parameters, which also affects cost and scalability. However, the cost and effort of implementing pooled screens prohibits experimental testing of a large number of parameters. RESULTS We present CRISPulator, a Monte Carlo method-based computational tool that simulates the impact of screen parameters on the robustness of screen results, thereby enabling users to build intuition and insights that will inform their experimental strategy. CRISPulator enables the simulation of screens relying on either CRISPR interference (CRISPRi) or CRISPR nuclease (CRISPRn). Pooled screens based on cell growth/survival, as well as fluorescence-activated cell sorting according to fluorescent reporter phenotypes are supported. CRISPulator is freely available online ( http://crispulator.ucsf.edu ). CONCLUSIONS CRISPulator facilitates the design of pooled genetic screens by enabling the exploration of a large space of experimental parameters in silico, rather than through costly experimental trial and error. We illustrate its power by deriving non-obvious rules for optimal screen design.
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Affiliation(s)
- Tamas Nagy
- Graduate program in Bioinformatics, University of California, San Francisco, CA 94158 USA
| | - Martin Kampmann
- Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases and California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158 USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158 USA
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17
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Islam MF, Watanabe A, Wong L, Lazarou C, Vizeacoumar FS, Abuhussein O, Hill W, Uppalapati M, Geyer CR, Vizeacoumar FJ. Enhancing the throughput and multiplexing capabilities of next generation sequencing for efficient implementation of pooled shRNA and CRISPR screens. Sci Rep 2017; 7:1040. [PMID: 28432350 PMCID: PMC5430825 DOI: 10.1038/s41598-017-01170-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/20/2017] [Indexed: 11/11/2022] Open
Abstract
Next generation sequencing is becoming the method of choice for functional genomic studies that use pooled shRNA or CRISPR libraries. A key challenge in sequencing these mixed-oligo libraries is that they are highly susceptible to hairpin and/or heteroduplex formation. This results in polyclonal, low quality, and incomplete reads and reduces sequencing throughput. Unfortunately, this challenge is significantly magnified in low-to-medium throughput bench-top sequencers as failed reads significantly perturb the maximization of sequence coverage and multiplexing capabilities. Here, we report a methodology that can be adapted to maximize the coverage on a bench-top, Ion PGM System for smaller shRNA libraries with high efficiency. This ligation-based, half-shRNA sequencing strategy minimizes failed sequences and is also equally amenable to high-throughput sequencers for increased multiplexing. Towards this, we also demonstrate that our strategy to reduce heteroduplex formation improves multiplexing capabilities of pooled CRISPR screens using Illumina NextSeq 500. Overall, our method will facilitate sequencing of pooled shRNA or CRISPR libraries from genomic DNA and maximize sequence coverage.
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Affiliation(s)
- Md Fahmid Islam
- Department of Biochemistry, University of Saskatchewan, Saskatoon, S7N 5E5, Canada
| | - Atsushi Watanabe
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada.,Department of Hematology, Nephrology and Rheumatology, Graduate School of Medicine, Akita University, Akita, Japan
| | - Lai Wong
- Department of Biochemistry, University of Saskatchewan, Saskatoon, S7N 5E5, Canada
| | - Conor Lazarou
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada
| | | | - Omar Abuhussein
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, S7N 5C9, Canada
| | - Wayne Hill
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada
| | - Maruti Uppalapati
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada
| | - C Ronald Geyer
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada.
| | - Franco J Vizeacoumar
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada. .,College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, S7N 5C9, Canada. .,Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, S7N 5E5, Canada.
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18
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Abstract
Genetic screens are invaluable tools for dissection of biological phenomena. Optimization of such screens to enhance discovery of candidate genes and minimize false positives is thus a critical aim. Here, we report several sources of error common to pooled genetic screening techniques used in mammalian cell culture systems, and demonstrate methods to eliminate these errors. We find that reverse transcriptase-mediated recombination during retroviral replication can lead to uncoupling of molecular tags, such as DNA barcodes (BCs), from their associated library elements, leading to chimeric proviral genomes in which BCs are paired to incorrect ORFs, shRNAs, etc This effect depends on the length of homologous sequence between unique elements, and can be minimized with careful vector design. Furthermore, we report that residual plasmid DNA from viral packaging procedures can contaminate transduced cells. These plasmids serve as additional copies of the PCR template during library amplification, resulting in substantial inaccuracies in measurement of initial reference populations for screen normalization. The overabundance of template in some samples causes an imbalance between PCR cycles of contaminated and uncontaminated samples, which results in a systematic artifactual depletion of GC-rich library elements. Elimination of contaminating plasmid DNA using the bacterial endonuclease Benzonase can restore faithful measurements of template abundance and minimize GC bias.
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19
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Ceroni A, Higgins GS, Ebner DV. In Vitro-Pooled shRNA Screening to Identify Determinants of Radiosensitivity. Methods Mol Biol 2016; 1470:103-19. [PMID: 27581288 DOI: 10.1007/978-1-4939-6337-9_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Short hairpin RNA (shRNA)-pooled screening is a valuable and cost-effective tool for assaying the contribution of individual genes to cell viability and proliferation on a genomic scale. Here we describe the key considerations for the design and execution of a pooled shRNA screen to identify determinants of radiosensitivity.
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Affiliation(s)
| | - Geoff S Higgins
- Department of Oncology, University of Oxford-Old Road Campus, Oxford, UK
| | - Daniel V Ebner
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford-Old Road Campus, Oxford, UK
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20
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Wong ASL, Choi GCG, Cheng AA, Purcell O, Lu TK. Massively parallel high-order combinatorial genetics in human cells. Nat Biotechnol 2015; 33:952-61. [PMID: 26280411 DOI: 10.1038/nbt.3326] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/16/2015] [Indexed: 12/19/2022]
Abstract
The systematic functional analysis of combinatorial genetics has been limited by the throughput that can be achieved and the order of complexity that can be studied. To enable massively parallel characterization of genetic combinations in human cells, we developed a technology for rapid, scalable assembly of high-order barcoded combinatorial genetic libraries that can be quantified with high-throughput sequencing. We applied this technology, combinatorial genetics en masse (CombiGEM), to create high-coverage libraries of 1,521 two-wise and 51,770 three-wise barcoded combinations of 39 human microRNA (miRNA) precursors. We identified miRNA combinations that synergistically sensitize drug-resistant cancer cells to chemotherapy and/or inhibit cancer cell proliferation, providing insights into complex miRNA networks. More broadly, our method will enable high-throughput profiling of multifactorial genetic combinations that regulate phenotypes of relevance to biomedicine, biotechnology and basic science.
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Affiliation(s)
- Alan S L Wong
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biological Engineering and Electrical Engineering &Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gigi C G Choi
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biological Engineering and Electrical Engineering &Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Allen A Cheng
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biological Engineering and Electrical Engineering &Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Oliver Purcell
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biological Engineering and Electrical Engineering &Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biological Engineering and Electrical Engineering &Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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21
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Egan ES, Jiang RHY, Moechtar MA, Barteneva NS, Weekes MP, Nobre LV, Gygi SP, Paulo JA, Frantzreb C, Tani Y, Takahashi J, Watanabe S, Goldberg J, Paul AS, Brugnara C, Root DE, Wiegand RC, Doench JG, Duraisingh MT. Malaria. A forward genetic screen identifies erythrocyte CD55 as essential for Plasmodium falciparum invasion. Science 2015; 348:711-4. [PMID: 25954012 DOI: 10.1126/science.aaa3526] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Efforts to identify host determinants for malaria have been hindered by the absence of a nucleus in erythrocytes, which precludes genetic manipulation in the cell in which the parasite replicates. We used cultured red blood cells derived from hematopoietic stem cells to carry out a forward genetic screen for Plasmodium falciparum host determinants. We found that CD55 is an essential host factor for P. falciparum invasion. CD55-null erythrocytes were refractory to invasion by all isolates of P. falciparum because parasites failed to attach properly to the erythrocyte surface. Thus, CD55 is an attractive target for the development of malaria therapeutics. Hematopoietic stem cell-based forward genetic screens may be valuable for the identification of additional host determinants of malaria pathogenesis.
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Affiliation(s)
- Elizabeth S Egan
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA. Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Rays H Y Jiang
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA. Department of Global Health and Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL, USA
| | - Mischka A Moechtar
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Natasha S Barteneva
- Department of Pediatrics, Harvard Medical School and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Luis V Nobre
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Charles Frantzreb
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Yoshihiko Tani
- Japanese Red Cross Kinki Block Blood Center, Osaka, Japan
| | | | - Seishi Watanabe
- Japanese Red Cross Kyushu Block Blood Center, Fukuoka, Japan
| | - Jonathan Goldberg
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Aditya S Paul
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - David E Root
- The Broad Institute of Harvard and Massachussetts Insititute of Technology, Cambridge, MA, USAA
| | - Roger C Wiegand
- The Broad Institute of Harvard and Massachussetts Insititute of Technology, Cambridge, MA, USAA
| | - John G Doench
- The Broad Institute of Harvard and Massachussetts Insititute of Technology, Cambridge, MA, USAA
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA. The Broad Institute of Harvard and Massachussetts Insititute of Technology, Cambridge, MA, USAA.
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22
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Stombaugh J, Licon A, Strezoska Ž, Stahl J, Anderson SB, Banos M, van Brabant Smith A, Birmingham A, Vermeulen A. The Power Decoder Simulator for the Evaluation of Pooled shRNA Screen Performance. ACTA ACUST UNITED AC 2015; 20:965-75. [PMID: 25777298 PMCID: PMC4543901 DOI: 10.1177/1087057115576715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/17/2015] [Indexed: 12/30/2022]
Abstract
RNA interference screening using pooled, short hairpin RNA (shRNA) is a powerful, high-throughput tool for determining the biological relevance of genes for a phenotype. Assessing an shRNA pooled screen’s performance is difficult in practice; one can estimate the performance only by using reproducibility as a proxy for power or by employing a large number of validated positive and negative controls. Here, we develop an open-source software tool, the Power Decoder simulator, for generating shRNA pooled screening experiments in silico that can be used to estimate a screen’s statistical power. Using the negative binomial distribution, it models both the relative abundance of multiple shRNAs within a single screening replicate and the biological noise between replicates for each individual shRNA. We demonstrate that this simulator can successfully model the data from an actual laboratory experiment. We then use it to evaluate the effects of biological replicates and sequencing counts on the performance of a pooled screen, without the necessity of gathering additional data. The Power Decoder simulator is written in R and Python and is available for download under the GNU General Public License v3.0.
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Affiliation(s)
| | - Abel Licon
- Dharmacon, part of GE Healthcare, Lafayette, CO, USA
| | | | - Joshua Stahl
- Dharmacon, part of GE Healthcare, Lafayette, CO, USA
| | | | - Michael Banos
- Dharmacon, part of GE Healthcare, Lafayette, CO, USA
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23
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Hartenian E, Doench JG. Genetic screens and functional genomics using CRISPR/Cas9 technology. FEBS J 2015; 282:1383-93. [DOI: 10.1111/febs.13248] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/01/2015] [Accepted: 02/23/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Ella Hartenian
- Department of Molecular and Cellular Biology; University of California Berkeley; Berkeley, CA USA
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24
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Chou YC, Lai MM, Wu YC, Hsu NC, Jeng KS, Su WC. Variations in genome-wide RNAi screens: lessons from influenza research. J Clin Bioinforma 2015; 5:2. [PMID: 25745555 PMCID: PMC4350949 DOI: 10.1186/s13336-015-0017-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/19/2015] [Indexed: 11/10/2022] Open
Abstract
Genome-wide RNA interference (RNAi) screening is an emerging and powerful technique for genetic screens, which can be divided into arrayed RNAi screen and pooled RNAi screen/selection based on different screening strategies. To date, several genome-wide RNAi screens have been successfully performed to identify host factors essential for influenza virus replication. However, the host factors identified by different research groups are not always consistent. Taking influenza virus screens as an example, we found that a number of screening parameters may directly or indirectly influence the primary hits identified by the screens. This review highlights the differences among the published genome-wide screening approaches and offers recommendations for performing a good pooled shRNA screen/selection.
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Affiliation(s)
- Yu-Chi Chou
- National RNAi Core Facility Platform, Academia Sinica, Taipei, 11529 Taiwan ; Institute of Molecular Biology, Academia Sinica, Taipei, 11529 Taiwan
| | - Michael Mc Lai
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529 Taiwan ; Research Center for Emerging Viruses, China Medical University Hospital, Room 602, 6 F, Cancer Center Building, No. 6, Hsueh-Shih Road, Taichung, 40402 Taiwan ; China Medical University, Room 602, 6 F, Cancer Center Building, No. 6, Hsueh-Shih Road, Taichung, 40402 Taiwan ; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, 70101 Taiwan
| | - Yi-Chen Wu
- National RNAi Core Facility Platform, Academia Sinica, Taipei, 11529 Taiwan
| | - Nai-Chi Hsu
- National RNAi Core Facility Platform, Academia Sinica, Taipei, 11529 Taiwan
| | - King-Song Jeng
- National RNAi Core Facility Platform, Academia Sinica, Taipei, 11529 Taiwan ; Institute of Molecular Biology, Academia Sinica, Taipei, 11529 Taiwan
| | - Wen-Chi Su
- Research Center for Emerging Viruses, China Medical University Hospital, Room 602, 6 F, Cancer Center Building, No. 6, Hsueh-Shih Road, Taichung, 40402 Taiwan ; China Medical University, Room 602, 6 F, Cancer Center Building, No. 6, Hsueh-Shih Road, Taichung, 40402 Taiwan
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25
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Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature 2014; 518:355-359. [PMID: 25533951 PMCID: PMC4336237 DOI: 10.1038/nature13990] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 10/21/2014] [Indexed: 12/16/2022]
Abstract
Models derived from human pluripotent stem cells that accurately recapitulate neural development in vitro and allow for the generation of specific neuronal subtypes are of major interest to the stem cell and biomedical community. Notch signalling, particularly through the Notch effector HES5, is a major pathway critical for the onset and maintenance of neural progenitor cells in the embryonic and adult nervous system. Here we report the transcriptional and epigenomic analysis of six consecutive neural progenitor cell stages derived from a HES5::eGFP reporter human embryonic stem cell line. Using this system, we aimed to model cell-fate decisions including specification, expansion and patterning during the ontogeny of cortical neural stem and progenitor cells. In order to dissect regulatory mechanisms that orchestrate the stage-specific differentiation process, we developed a computational framework to infer key regulators of each cell-state transition based on the progressive remodelling of the epigenetic landscape and then validated these through a pooled short hairpin RNA screen. We were also able to refine our previous observations on epigenetic priming at transcription factor binding sites and suggest here that they are mediated by combinations of core and stage-specific factors. Taken together, we demonstrate the utility of our system and outline a general framework, not limited to the context of the neural lineage, to dissect regulatory circuits of differentiation.
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Li T, Zhu YY, Chen L, Sun Y, Yuan J, Graham M, French P. Size unbiased representative enzymatically generated RNAi (SURER) library and application for RNAi therapeutic screens. Nucleic Acid Ther 2014; 25:35-46. [PMID: 25493330 DOI: 10.1089/nat.2014.0514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
RNA interference (RNAi) libraries screens have become widely used for small RNA (sRNA) therapeutic targets development. However, conventional enzymatically libraries, typically prepared using the type 2 restriction enzyme MmeI, produce sRNAs between 18 and 20 bp, much shorter than the usual lengths of 19-23 bp. Here we develop a size unbiased representative enzymatically generated RNAi (SURER) library, which employs type 3 restriction modification enzyme EcoP15I to produce sRNAs ranging from 19 to 23 bp using a group of rationally designed linkers, which can completely mimic the length of sRNAs naturally generated by Dicer enzyme in living cells, and the screening results of SURER libraries showed high recombination rate and knockdown efficiency. SURER library provides a useful tool for RNAi therapeutics screening in a fast and simple way.
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Affiliation(s)
- Tiejun Li
- 1 Small RNA Technology and Application Institute, Nantong University , Nantong, China
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Maruyama Y, Miyazaki T, Ikeda K, Okumura T, Sato W, Horie-Inoue K, Okamoto K, Takeda S, Inoue S. Short hairpin RNA library-based functional screening identified ribosomal protein L31 that modulates prostate cancer cell growth via p53 pathway. PLoS One 2014; 9:e108743. [PMID: 25285958 PMCID: PMC4186824 DOI: 10.1371/journal.pone.0108743] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/25/2014] [Indexed: 11/22/2022] Open
Abstract
Androgen receptor is a primary transcription factor involved in the proliferation of prostate cancer cells. Thus, hormone therapy using antiandrogens, such as bicalutamide, is a first-line treatment for the disease. Although hormone therapy initially reduces the tumor burden, many patients eventually relapse, developing tumors with acquired endocrine resistance. Elucidation of the molecular mechanisms underlying endocrine resistance is therefore a fundamental issue for the understanding and development of alternative therapeutics for advanced prostate cancer. In the present study, we performed short hairpin RNA (shRNA)-mediated functional screening to identify genes involved in bicalutamide-mediated effects on LNCaP prostate cancer cells. Among such candidate genes selected by screening using volcano plot analysis, ribosomal protein L31 (RPL31) was found to be essential for cell proliferation and cell-cycle progression in bicalutamide-resistant LNCaP (BicR) cells, based on small interfering RNA (siRNA)-mediated knockdown experiments. Of note, RPL31 mRNA is more abundantly expressed in BicR cells than in parental LNCaP cells, and clinical data from ONCOMINE and The Cancer Genome Altas showed that RPL31 is overexpressed in prostate carcinomas compared with benign prostate tissues. Intriguingly, protein levels of the tumor suppressor p53 and its targets, p21 and MDM2, were increased in LNCaP and BicR cells treated with RPL31 siRNA. We observed decreased degradation of p53 protein after RPL31 knockdown. Moreover, the suppression of growth and cell cycle upon RPL31 knockdown was partially recovered with p53 siRNA treatment. These results suggest that RPL31 is involved in bicalutamide-resistant growth of prostate cancer cells. The shRNA-mediated functional screen in this study provides new insight into the molecular mechanisms and therapeutic targets of advanced prostate cancer.
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Affiliation(s)
- Yojiro Maruyama
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Tokyo, Japan
| | - Toshiaki Miyazaki
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Kazuhiro Ikeda
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Toshiyuki Okumura
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Wataru Sato
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Kuniko Horie-Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Koji Okamoto
- Division of Cancer Differentiation, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Tokyo, Japan
| | - Satoshi Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
- Departments of Geriatric Medicine and Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- * E-mail:
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Shain AH, Salari K, Giacomini CP, Pollack JR. Integrative genomic and functional profiling of the pancreatic cancer genome. BMC Genomics 2013; 14:624. [PMID: 24041470 PMCID: PMC3848637 DOI: 10.1186/1471-2164-14-624] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 09/12/2013] [Indexed: 11/20/2022] Open
Abstract
Background Pancreatic cancer is a deadly disease with a five-year survival of less than 5%. A better understanding of the underlying biology may suggest novel therapeutic targets. Recent surveys of the pancreatic cancer genome have uncovered numerous new alterations; yet systematic functional characterization of candidate cancer genes has lagged behind. To address this challenge, here we have devised a highly-parallel RNA interference-based functional screen to evaluate many genomically-nominated candidate pancreatic cancer genes simultaneously. Results For 185 candidate pancreatic cancer genes, selected from recurrently altered genomic loci, we performed a pooled shRNA library screen of cell growth/viability across 10 different cell lines. Knockdown-associated effects on cell growth were assessed by enrichment or depletion of shRNA hairpins, by hybridization to barcode microarrays. A novel analytical approach (COrrelated Phenotypes for On-Target Effects; COPOTE) was used to discern probable on-target knockdown, based on identifying different shRNAs targeting the same gene and displaying concordant phenotypes across cell lines. Knockdown data were integrated with genomic architecture and gene-expression profiles, and selected findings validated using individual shRNAs and/or independent siRNAs. The pooled shRNA library design delivered reproducible data. In all, COPOTE analysis identified 52 probable on-target gene-knockdowns. Knockdown of known oncogenes (KRAS, MYC, SMURF1 and CCNE1) and a tumor suppressor (CDKN2A) showed the expected contrasting effects on cell growth. In addition, the screen corroborated purported roles of PLEKHG2 and MED29 as 19q13 amplicon drivers. Most notably, the analysis also revealed novel possible oncogenic functions of nucleoporin NUP153 (ostensibly by modulating TGFβ signaling) and Kruppel-like transcription factor KLF5 in pancreatic cancer. Conclusions By integrating physical and functional genomic data, we were able to simultaneously evaluate many candidate pancreatic cancer genes. Our findings uncover new facets of pancreatic cancer biology, with possible therapeutic implications. More broadly, our study provides a general strategy for the efficient characterization of candidate genes emerging from cancer genome studies.
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Affiliation(s)
- A Hunter Shain
- Departments of Pathology, Stanford University School of Medicine, 269 Campus Drive, CCSR-3245A, Stanford, CA 94305-5176, USA.
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Mulcahy LA, Carter DRF. RNAi2013: RNAi at Oxford. JOURNAL OF RNAI AND GENE SILENCING : AN INTERNATIONAL JOURNAL OF RNA AND GENE TARGETING RESEARCH 2013; 9:486-9. [PMID: 23946766 PMCID: PMC3717312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 05/02/2013] [Indexed: 12/02/2022]
Affiliation(s)
- Laura A Mulcahy
- Oxford Brookes University, Faculty of Health and Life Sciences, Department of Biological and Medical Sciences. Gypsy Lane, Oxford, OX3 0BP, UK
| | - David RF Carter
- Oxford Brookes University, Faculty of Health and Life Sciences, Department of Biological and Medical Sciences. Gypsy Lane, Oxford, OX3 0BP, UK,*Correspondence to: David Carter, , Tel: +44 1865 484216, Fax: +44 1865 483242
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