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Higgins L, Gerdes H, Cutillas PR. Principles of phosphoproteomics and applications in cancer research. Biochem J 2023; 480:403-420. [PMID: 36961757 PMCID: PMC10212522 DOI: 10.1042/bcj20220220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/25/2023]
Abstract
Phosphorylation constitutes the most common and best-studied regulatory post-translational modification in biological systems and archetypal signalling pathways driven by protein and lipid kinases are disrupted in essentially all cancer types. Thus, the study of the phosphoproteome stands to provide unique biological information on signalling pathway activity and on kinase network circuitry that is not captured by genetic or transcriptomic technologies. Here, we discuss the methods and tools used in phosphoproteomics and highlight how this technique has been used, and can be used in the future, for cancer research. Challenges still exist in mass spectrometry phosphoproteomics and in the software required to provide biological information from these datasets. Nevertheless, improvements in mass spectrometers with enhanced scan rates, separation capabilities and sensitivity, in biochemical methods for sample preparation and in computational pipelines are enabling an increasingly deep analysis of the phosphoproteome, where previous bottlenecks in data acquisition, processing and interpretation are being relieved. These powerful hardware and algorithmic innovations are not only providing exciting new mechanistic insights into tumour biology, from where new drug targets may be derived, but are also leading to the discovery of phosphoproteins as mediators of drug sensitivity and resistance and as classifiers of disease subtypes. These studies are, therefore, uncovering phosphoproteins as a new generation of disruptive biomarkers to improve personalised anti-cancer therapies.
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Affiliation(s)
- Luke Higgins
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
| | - Henry Gerdes
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
| | - Pedro R. Cutillas
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
- Alan Turing Institute, The British Library, London, U.K
- Digital Environment Research Institute, Queen Mary University of London, London, U.K
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2
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Cell-Based Double-Screening Method to Identify a Reliable Candidate for Osteogenesis-Targeting Compounds. Biomedicines 2022; 10:biomedicines10020426. [PMID: 35203635 PMCID: PMC8962348 DOI: 10.3390/biomedicines10020426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 01/15/2023] Open
Abstract
Small-molecule compounds strongly affecting osteogenesis can form the basis of effective therapeutic strategies in bone regenerative medicine. A cell-based high-throughput screening system might be a powerful tool for identifying osteoblast-targeting candidates; however, this approach is generally limited with using only one molecule as a cell-based sensor that does not always reflect the activation of the osteogenic phenotype. In the present study, we used the MC3T3-E1 cell line stably transfected with the green fluorescent protein (GFP) reporter gene driven by a fragment of type I collagen promoter (Col-1a1GFP-MC3T3-E1) to evaluate a double-screening system to identify osteogenic inducible compounds using a combination of a cell-based reporter assay and detection of alkaline phosphatase (ALP) activity. Col-1a1GFP-MC3T3-E1 cells were cultured in an osteogenic induction medium after library screening of 1280 pharmacologically active compounds (Lopack1280). After 7 days, GFP fluorescence was measured using a microplate reader. After 14 days of osteogenic induction, the cells were stained with ALP. Library screening using the Col-1a1/GFP reporter and ALP staining assay detected three candidates with significant osteogenic induction ability. Furthermore, leflunomide, one of the three detected candidates, significantly promoted new bone formation in vivo. Therefore, this double-screening method could identify candidates for osteogenesis-targeting compounds more reliably than conventional methods.
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Pu X, Wang J, Li W, Fan W, Wang L, Mao Y, Yang S, Liu S, Xu J, Lv Z, Xu L, Shu Y. COPB2 promotes cell proliferation and tumorigenesis through up-regulating YAP1 expression in lung adenocarcinoma cells. Biomed Pharmacother 2018; 103:373-380. [PMID: 29674272 DOI: 10.1016/j.biopha.2018.04.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 04/01/2018] [Accepted: 04/02/2018] [Indexed: 12/15/2022] Open
Abstract
Lung adenocarcinoma is the most common subtype of non-small cell lung cancer and responsible for more than 500,000 deaths per year worldwide. In this study, we aimed to explore the effects of COPB2 in the progression of lung adenocarcinoma and its underlying mechanism. The mRNA and protein levels of COPB2 in tumor tissues and cell lines were determined by qRT-PCR and western blotting analysis. siRNAs and over-expressed vector targeting COPB2 were used to down-regulate and up-regulate COPB2 expression in lung adenocarcinoma cell lines H1975. Cell apoptosis rate, proliferation and tumorigenesis of H1975 cells were determined by flow cytometry analysis, MTT assay and in vivo xenotransplantation assay, respectively. Western blotting and immunofluorescence assays were performed to evaluate the effects of COPB on the expression and subcellular location of YAP. Results showed COPB2 was significantly up-regulated in lung adenocarcinoma tissues and cell lines, which showed a close correlation with advanced clinical symptoms, such as tumor differentiation, TNM stage and the occurrence of lymph node metastasis and distance metastasis. Besides, the overall survival time of patients with high expression of COPB2 was shorter than that of patients with low COPB2 expression. After knockdown of COPB2, cell apoptosis rate was increased, whereas cell proliferation was decreased. Compared with that in the normal lung cell line H1688 cells, YAP1 expression was obviously increased in H1975, and over-expression of COPB2 translocated YAP1 from cytoplasm to nuclear, whereas knockdown of COPB2 showed the opposite effect. Overexpression of COPB2 enhanced cell proliferation, tumorigenesis and inhibited cell apoptosis. However, these effects were abolished when down-regulated YAP1 expression on the base of COPB2 over-expression. In conclusion, the increased expression of COPB2 was significantly correlated with the progression of lung adenocarcinoma. Up-regulation of COPB2 inhibited cell apoptosis and promoted cell growth and tumorigenesis through up-regulating YAP1 expression in lung adenocarcinoma.
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Affiliation(s)
- Xiaolin Pu
- Oncology, Jiangsu Province Geriatric Institute, Nanjing, People's Republic of China; Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Jun Wang
- Oncology, Jiangsu Province Geriatric Institute, Nanjing, People's Republic of China
| | - Wei Li
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Weifei Fan
- Oncology, Jiangsu Province Geriatric Institute, Nanjing, People's Republic of China
| | - Lin Wang
- Oncology, Jiangsu Province Geriatric Institute, Nanjing, People's Republic of China
| | - Yuan Mao
- Oncology, Jiangsu Province Geriatric Institute, Nanjing, People's Republic of China
| | - Shu Yang
- Oncology, Jiangsu Province Geriatric Institute, Nanjing, People's Republic of China
| | - Suyao Liu
- Oncology, Jiangsu Province Geriatric Institute, Nanjing, People's Republic of China
| | - Juqing Xu
- Oncology, Jiangsu Province Geriatric Institute, Nanjing, People's Republic of China
| | - Zhigang Lv
- Central laboratory, Jiangsu Province Geriatric Institute, Nanjing, People's Republic of China
| | - Lin Xu
- Department of thoracic surgery, Jiangsu Cancer Hospital, Nanjing, People's Republic of China
| | - Yongqian Shu
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China.
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Birkenkamp-Demtröder K, Hahn SA, Mansilla F, Thorsen K, Maghnouj A, Christensen R, Øster B, Ørntoft TF. Keratin23 (KRT23) knockdown decreases proliferation and affects the DNA damage response of colon cancer cells. PLoS One 2013; 8:e73593. [PMID: 24039993 PMCID: PMC3767798 DOI: 10.1371/journal.pone.0073593] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 07/25/2013] [Indexed: 11/18/2022] Open
Abstract
Keratin 23 (KRT23) is strongly expressed in colon adenocarcinomas but absent in normal colon mucosa. Array based methylation profiling of 40 colon samples showed that the promoter of KRT23 was methylated in normal colon mucosa, while hypomethylated in most adenocarcinomas. Promoter methylation correlated with absent expression, while increased KRT23 expression in tumor samples correlated with promoter hypomethylation, as confirmed by bisulfite sequencing. Demethylation induced KRT23 expression in vitro. Expression profiling of shRNA mediated stable KRT23 knockdown in colon cancer cell lines showed that KRT23 depletion affected molecules of the cell cycle and DNA replication, recombination and repair. In vitro analyses confirmed that KRT23 depletion significantly decreased the cellular proliferation of SW948 and LS1034 cells and markedly decreased the expression of genes involved in DNA damage response, mainly molecules of the double strand break repair homologous recombination pathway. KRT23 knockdown decreased the transcript and protein expression of key molecules as e.g. MRE11A, E2F1, RAD51 and BRCA1. Knockdown of KRT23 rendered colon cancer cells more sensitive to irradiation and reduced proliferation of the KRT23 depleted cells compared to irradiated control cells.
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Affiliation(s)
| | - Stephan A. Hahn
- Department of Molecular GI-Oncology, Center of Clinical Research, Ruhr-University Bochum, Bochum, Germany
| | - Francisco Mansilla
- Department of Molecular Medicine MOMA, Aarhus University Hospital, Skejby, Aarhus N, Denmark
| | - Kasper Thorsen
- Department of Molecular Medicine MOMA, Aarhus University Hospital, Skejby, Aarhus N, Denmark
| | - Abdelouahid Maghnouj
- Department of Molecular GI-Oncology, Center of Clinical Research, Ruhr-University Bochum, Bochum, Germany
| | - Rikke Christensen
- Department of Clinical Genetics, Aarhus University Hospital, Skejby, Aarhus N, Denmark
| | - Bodil Øster
- Department of Molecular Medicine MOMA, Aarhus University Hospital, Skejby, Aarhus N, Denmark
| | - Torben Falck Ørntoft
- Department of Molecular Medicine MOMA, Aarhus University Hospital, Skejby, Aarhus N, Denmark
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Pileczki V, Braicu C, Gherman CD, Berindan-Neagoe I. TNF-α gene knockout in triple negative breast cancer cell line induces apoptosis. Int J Mol Sci 2012; 14:411-20. [PMID: 23263670 PMCID: PMC3565271 DOI: 10.3390/ijms14010411] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 11/30/2012] [Accepted: 12/06/2012] [Indexed: 12/16/2022] Open
Abstract
Tumor necrosis factor alpha (TNF-α) is a pro-inflammatory cytokine involved in the promotion and progression of cancer, including triple negative breast cancer cells. Thus, there is significant interest in understanding the molecular signaling pathways that connect TNF-α with the survival of tumor cells. In our experiments, we used as an in vitro model for triple negative breast cancer the cell line Hs578T. The purpose of this study is to determine the gene expression profiling of apoptotic signaling networks after blocking TNF-α formation by using specially designed siRNA molecules to target TNF-α messenger RNA. Knockdown of TNF-α gene was associated with cell proliferation inhibition and apoptosis, as observed by monitoring the cell index using the xCELLigence RTCA System and flow cytometry. PCR array technology was used to examine the transcript levels of 84 genes involved in apoptosis. 15 genes were found to be relevant after comparing the treated group with the untreated one of which 3 were down-regulated and 12 up-regulated. The down-regulated genes are all involved in cell survival, whereas the up-regulated ones are involved in and interact with pro-apoptotic pathways. The results described here indicate that the direct target of TNF-α in the Hs578T breast cancer cell line increases the level of certain pro-apoptotic factors that modulate different cellular networks that direct the cells towards death.
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Affiliation(s)
- Valentina Pileczki
- Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, 4 Pasteur Street, Cluj-Napoca 400349, Romania; E-Mail:
| | - Cornelia Braicu
- Department of Functional Genomics and Experimental Pathology, Cancer Institute “Ioan Chiricută”, 34–36 Republici Street, Cluj-Napoca 400015, Romania; E-Mails: (C.B.); (I.B.-N.)
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8 Victor Babes Street, Cluj-Napoca 400012, Romania
| | - Claudia D. Gherman
- Surgical Clinic II, 4–6 Clinicilor Street, Cluj-Napoca 400006, Romania
- Department of Surgery, “Iuliu Haţieganu” University of Medicine and Pharmacy, 8 Victor Babes Street, Cluj-Napoca 400012, Romania
| | - Ioana Berindan-Neagoe
- Department of Functional Genomics and Experimental Pathology, Cancer Institute “Ioan Chiricută”, 34–36 Republici Street, Cluj-Napoca 400015, Romania; E-Mails: (C.B.); (I.B.-N.)
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8 Victor Babes Street, Cluj-Napoca 400012, Romania
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Batra R, Harder N, Gogolin S, Diessl N, Soons Z, Jäger-Schmidt C, Lawerenz C, Eils R, Rohr K, Westermann F, König R. Time-lapse imaging of neuroblastoma cells to determine cell fate upon gene knockdown. PLoS One 2012; 7:e50988. [PMID: 23251412 PMCID: PMC3521006 DOI: 10.1371/journal.pone.0050988] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 10/29/2012] [Indexed: 11/22/2022] Open
Abstract
Neuroblastoma is the most common extra-cranial solid tumor of early childhood. Standard therapies are not effective in case of poor prognosis and chemotherapy resistance. To improve drug therapy, it is imperative to discover new targets that play a substantial role in tumorigenesis of neuroblastoma. The mitotic machinery is an attractive target for therapeutic interventions and inhibitors can be developed to target mitotic entry, spindle apparatus, spindle activation checkpoint, and mitotic exit. We present an elaborate analysis pipeline to determine cancer specific therapeutic targets by first performing a focused gene expression analysis to select genes followed by a gene knockdown screening assay of live cells. We interrogated gene expression studies of neuroblastoma tumors and selected 240 genes relevant for tumorigenesis and cell cycle. With these genes we performed time-lapse screening of gene knockdowns in neuroblastoma cells. We classified cellular phenotypes and used the temporal context of the perturbation effect to determine the sequence of events, particularly the mitotic entry preceding cell death. Based upon this phenotype kinetics from the gene knockdown screening, we inferred dynamic gene functions in mitosis and cell proliferation. We identified six genes (DLGAP5, DSCC1, SMO, SNRPD1, SSBP1, and UBE2C) with a vital role in mitosis and these are promising therapeutic targets for neuroblastoma. Images and movies of every time point of all screened genes are available at https://ichip.bioquant.uni-heidelberg.de.
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Affiliation(s)
- Richa Batra
- Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Heidelberg, Germany
- Division of Theoretical Bioinformatics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Nathalie Harder
- Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Heidelberg, Germany
- Division of Theoretical Bioinformatics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Sina Gogolin
- Division of Tumor Genetics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Nicolle Diessl
- Department of Genomics and Proteomics Core Facility, High-Throughput Screening, German Cancer Research Center, Heidelberg, Germany
| | - Zita Soons
- Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Heidelberg, Germany
- Division of Theoretical Bioinformatics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Christina Jäger-Schmidt
- Division of Theoretical Bioinformatics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Christian Lawerenz
- Division of Theoretical Bioinformatics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Roland Eils
- Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Heidelberg, Germany
- Division of Theoretical Bioinformatics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Karl Rohr
- Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Heidelberg, Germany
- Division of Theoretical Bioinformatics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Frank Westermann
- Division of Tumor Genetics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Rainer König
- Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Heidelberg, Germany
- Division of Theoretical Bioinformatics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- * E-mail:
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Abstract
The ability of cells to invade into the dermis is a critical event in the development of cutaneous melanoma and ultimately an indicator of poor prognosis. However, the molecular events surrounding the acquisition of this invasive phenotype remain incompletely understood. Mutations in B-RAF are frequent in melanoma and are known to regulate the invasive phenotype. In this study, we sought to determine the molecular mechanisms controlling melanoma invasion. We found that mutant B-RAF signaling regulates a cadherin switch. In melanoma cells expressing mutant B-RAF we observed high levels of N-cadherin and low levels of E-cadherin. Depletion of mutant B-RAF, by siRNA, caused a decrease in the levels of N-cadherin and an increase in the levels of E-cadherin. Mechanistically, we found that this cadherin switch required the activity of Rac1 and its GEF, Tiam1, both of which show suppressed activity in the presence of mutant B-RAF. Consistent with the work of others, we found that depletion of mutant B-RAF decreased the invasive capacity of the melanoma cells. However, simultaneous depletion of B-RAF and Rac or Tiam1 resulted in invasive capacity similar to that of control cells. Taken together, our results suggest that mutant B-RAF signaling downregulates Tiam1/Rac activity resulting in an increase in N-cadherin levels and a decrease in E-cadherin levels and ultimately enhanced invasion.
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Lee CY, Johnson RL, Wichterman-Kouznetsova J, Guha R, Ferrer M, Tuzmen P, Martin SE, Zhu W, DePamphilis ML. High-throughput screening for genes that prevent excess DNA replication in human cells and for molecules that inhibit them. Methods 2012; 57:234-48. [PMID: 22503772 PMCID: PMC4149752 DOI: 10.1016/j.ymeth.2012.03.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 03/27/2012] [Accepted: 03/29/2012] [Indexed: 12/13/2022] Open
Abstract
High-throughput screening (HTS) provides a rapid and comprehensive approach to identifying compounds that target specific biological processes as well as genes that are essential to those processes. Here we describe a HTS assay for small molecules that induce either DNA re-replication or endoreduplication (i.e. excess DNA replication) selectively in cells derived from human cancers. Such molecules will be useful not only to investigate cell division and differentiation, but they may provide a novel approach to cancer chemotherapy. Since induction of DNA re-replication results in apoptosis, compounds that selectively induce DNA re-replication in cancer cells without doing so in normal cells could kill cancers in vivo without preventing normal cell proliferation. Furthermore, the same HTS assay can be adapted to screen siRNA molecules to identify genes whose products restrict genome duplication to once per cell division. Some of these genes might regulate the formation of terminally differentiated polyploid cells during normal human development, whereas others will prevent DNA re-replication during each cell division. Based on previous studies, we anticipate that one or more of the latter genes will prove to be essential for proliferation of cancer cells but not for normal cells, since many cancer cells are deficient in mechanisms that maintain genome stability.
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Affiliation(s)
- Chrissie Y. Lee
- National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892-2753, United States
| | - Ronald L. Johnson
- NIH Center for Translational Therapeutics, Probe Development Branch, 9800 Medical Center Drive, Rockville, MD 20892-3370, United States
| | - Jennifer Wichterman-Kouznetsova
- NIH Center for Translational Therapeutics, Probe Development Branch, 9800 Medical Center Drive, Rockville, MD 20892-3370, United States
| | - Rajarshi Guha
- NIH Center for Translational Therapeutics, Probe Development Branch, 9800 Medical Center Drive, Rockville, MD 20892-3370, United States
| | - Marc Ferrer
- NIH Center for Translational Therapeutics, Probe Development Branch, 9800 Medical Center Drive, Rockville, MD 20892-3370, United States
| | - Pinar Tuzmen
- NIH Center for Translational Therapeutics, Chemical Genomics Branch, 5 Research Court, Room 1A13, Rockville, MD 20850, United States
| | - Scott E. Martin
- NIH Center for Translational Therapeutics, Chemical Genomics Branch, 5 Research Court, Room 1A13, Rockville, MD 20850, United States
| | - Wenge Zhu
- National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892-2753, United States
| | - Melvin L. DePamphilis
- National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892-2753, United States
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Mohr SE, Perrimon N. RNAi screening: new approaches, understandings, and organisms. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:145-58. [PMID: 21953743 DOI: 10.1002/wrna.110] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA interference (RNAi) leads to sequence-specific knockdown of gene function. The approach can be used in large-scale screens to interrogate function in various model organisms and an increasing number of other species. Genome-scale RNAi screens are routinely performed in cultured or primary cells or in vivo in organisms such as C. elegans. High-throughput RNAi screening is benefitting from the development of sophisticated new instrumentation and software tools for collecting and analyzing data, including high-content image data. The results of large-scale RNAi screens have already proved useful, leading to new understandings of gene function relevant to topics such as infection, cancer, obesity, and aging. Nevertheless, important caveats apply and should be taken into consideration when developing or interpreting RNAi screens. Some level of false discovery is inherent to high-throughput approaches and specific to RNAi screens, false discovery due to off-target effects (OTEs) of RNAi reagents remains a problem. The need to improve our ability to use RNAi to elucidate gene function at large scale and in additional systems continues to be addressed through improved RNAi library design, development of innovative computational and analysis tools and other approaches.
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Affiliation(s)
- Stephanie E Mohr
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, Boston, MA, USA
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