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Loss-of-function screening to identify miRNAs involved in senescence: tumor suppressor activity of miRNA-335 and its new target CARF. Sci Rep 2016; 6:30185. [PMID: 27457128 PMCID: PMC4960484 DOI: 10.1038/srep30185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 06/30/2016] [Indexed: 12/13/2022] Open
Abstract
Significance of microRNAs (miRs), small non-coding molecules, has been implicated in a variety of biological processes. Here, we recruited retroviral insertional mutagenesis to obtain induction of an arbitrary noncoding RNAs, and coupled it with a cell based loss-of-function (5-Aza-2′-deoxycytidine (5Aza-dC)-induced senescence bypass) screening system. Cells that escaped 5-Aza-dC-induced senescence were subjected to miR-microarray analysis with respect to the untreated control. We identified miR-335 as one of the upregulated miRs. In order to characterize the functional significance, we overexpressed miR-335 in human cancer cells and found that it caused growth suppression. We demonstrate that the latter accounted for inhibition of 5-Aza-dC incorporation into the cell genome, enabling them to escape from induction of senescence. We also report that CARF (Collaborator of ARF) is a new target of miR-335 that regulates its growth suppressor function by complex crosstalk with other proteins including p16INK4A, pRB, HDM2 and p21WAF1.
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Widodo N, Priyandoko D, Shah N, Wadhwa R, Kaul SC. Selective killing of cancer cells by Ashwagandha leaf extract and its component Withanone involves ROS signaling. PLoS One 2010; 5:e13536. [PMID: 20975835 PMCID: PMC2958829 DOI: 10.1371/journal.pone.0013536] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 09/23/2010] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND AND PURPOSE Ashwagandha is a popular Ayurvedic herb used in Indian traditional home medicine. It has been assigned a variety of health-promoting effects of which the mechanisms remain unknown. We previously reported the selective killing of cancer cells by leaf extract of Ashwagandha (i-Extract) and its purified component Withanone. In the present study, we investigated its mechanism by loss-of-function screening (abrogation of i-Extract induced cancer cell killing) of the cellular targets and gene pathways. METHODOLOGY/PRINCIPAL FINDINGS Randomized ribozyme library was introduced into cancer cells prior to the treatment with i-Extract. Ribozymes were recovered from cells that survived the i-Extract treatment. Gene targets of the selected ribozymes (as predicted by database search) were analyzed by bioinformatics and pathway analyses. The targets were validated for their role in i-Extract induced selective killing of cancer cells by biochemical and molecular assays. Fifteen gene-targets were identified and were investigated for their role in specific cancer cell killing activity of i-Extract and its two major components (Withaferin A and Withanone) by undertaking the shRNA-mediated gene silencing approach. Bioinformatics on the selected gene-targets revealed the involvement of p53, apoptosis and insulin/IGF signaling pathways linked to the ROS signaling. We examined the involvement of ROS-signaling components (ROS levels, DNA damage, mitochondrial structure and membrane potential) and demonstrate that the selective killing of cancer cells is mediated by induction of oxidative stress. CONCLUSION Ashwagandha leaf extract and Withanone cause selective killing of cancer cells by induction of ROS-signaling and hence are potential reagents that could be recruited for ROS-mediated cancer chemotherapy.
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Affiliation(s)
- Nashi Widodo
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Malang, Indonesia
| | - Didik Priyandoko
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Navjot Shah
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Renu Wadhwa
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- * E-mail: (SCK); (RW)
| | - Sunil C. Kaul
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- * E-mail: (SCK); (RW)
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Lu T, Stark GR. Use of forward genetics to discover novel regulators of NF-kappaB. Cold Spring Harb Perspect Biol 2009; 2:a001966. [PMID: 20516132 DOI: 10.1101/cshperspect.a001966] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Forward and reverse genetic experiments have both played important roles in revealing critical aspects of mammalian signal transduction pathways in cell culture experiments. Only recently have we begun to comprehend the depth, breadth, and complexity of these pathways and of their interrelationships. Here, we summarize successful examples in which different forward genetic approaches have led to novel discoveries in NF-kappaB signaling. We believe that forward genetics will continue to play an irreplaceable role in advancing our understanding of the complexities of the pathways that regulate the functions of this key transcription factor.
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Affiliation(s)
- Tao Lu
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
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Tedeschi L, Lande C, Cecchettini A, Citti L. Hammerhead ribozymes in therapeutic target discovery and validation. Drug Discov Today 2009; 14:776-83. [PMID: 19477286 DOI: 10.1016/j.drudis.2009.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 05/11/2009] [Accepted: 05/12/2009] [Indexed: 10/20/2022]
Abstract
Gene function assessment is a main task in biological networking investigations and system biology. High throughput technologies provide an impressive body of data that enables the design of hypotheses linking genes to phenotypes. When a putative scenario is depicted, gene knockdown technologies and RNA-dependent gene silencing are the most frequent approaches to assess the role of key effectors. In this paper, we discuss the relevance of hammerhead ribozymes in target discovery and validation, describing their properties and applications and highlighting their selectivity. In particular, similarities with siRNAs are presented and advantages and drawbacks are discussed. A description of the perspectives of ribozyme application in wide range studies is also provided, strengthening the value of these inhibitors for target validation purposes.
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Affiliation(s)
- Lorena Tedeschi
- Institute of Clinical Physiology, National Research Council, CNR, via Moruzzi, 1, 56124 Pisa, Italy.
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5
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Use of a U16 snoRNA-containing ribozyme library to identify ribozyme targets in HIV-1. Mol Ther 2008; 16:1113-9. [PMID: 18388915 DOI: 10.1038/mt.2008.54] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Hammerhead ribozymes have been shown to silence human immunodeficiency virus-1 (HIV-1) gene expression by site-specific cleavage of viral mRNA. The two major factors that determine whether ribozymes will be effective for post-transcriptional gene silencing are colocalization of the ribozyme and the target RNAs, and the choice of an appropriate target site on the mRNA. An effective screening strategy for potential targets on the viral genome is the use of ribozyme libraries in cell culture. Capitalizing on previous findings that HIV-1 and ribozymes can be colocalized in the nucleolus, we created a novel hammerhead ribozyme library by inserting hammerhead ribozymes with fully randomized stems 1 and 2 into the body of the U16 small nucleolar RNA (snoRNA). Following three rounds of cotransfection with an HIV-1 proviral DNA harboring the herpes simplex virus thymidine kinase (HSV-TK) gene, we selected for gancyclovir-resistant cells and identified a ribozyme sequence that could potentially target both the U5 and gag genes of HIV-1 regions on the HIV-1 genome through partial homologies with these targets. When the ribozymes were converted to full complementarity with the targets, they provided potent inhibition of HIV-1 replication in cell culture. These results provide a novel approach for identifying ribozyme targets in HIV-1.
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Deocaris CC, Kaul SC, Wadhwa R. Use of ribozymes in cellular aging research. Methods Mol Biol 2007; 371:209-26. [PMID: 17634584 DOI: 10.1007/978-1-59745-361-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Ribozymes are naturally-occurring catalytic RNAs from the viroid world and are being engineered in the laboratory to perform sequence-specific cleavage of a desired mRNA target. Since their Nobel Prize-winning discovery, there has been considerable interest in the utility of ribozymes as gene therapeutic agents to silence disease-causing genes. This technology is not perfect, but extensive efforts to improve upon natural design of ribozymes have enabled these RNA molecules to perform various tasks. In this chapter, we highlight the construction of two types of ribozymes: conventional and hybrid hammerhead ribozymes. The hybrid ribozyme described here is an improved version of the basic hammerhead motif with the following features: (a) the use of the RNA polymerase III (polIII) tRNAVal promoter to achieve a high level of transcription, (b) 5' linkage to the cloverleaf-shaped tRNAVal to enhance intracellular stability and cytoplasmic transport, and (c) a 3' end poly-(A) tail to act as a "molecular anchor" for endogenous RNA helicases endowing the ribozyme ability to disentangle higher-order structures of the target mRNA. Randomized hybrid ribozyme libraries have been used successfully for revelation of gene functions involved in metastasis, invasion, differentiation, apoptosis, endoplasmic reticulum stress and may be extended to gene functions involved in innate or induced cellular senescence of human cells.
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Affiliation(s)
- Custer C Deocaris
- National Institute of Advanced Indutrial Science & Technology (AIST), Tsukuba Scince City, Japan
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Zaher HS, Unrau PJ. Selection of an improved RNA polymerase ribozyme with superior extension and fidelity. RNA (NEW YORK, N.Y.) 2007; 13:1017-26. [PMID: 17586759 PMCID: PMC1894930 DOI: 10.1261/rna.548807] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Accepted: 04/14/2007] [Indexed: 05/13/2023]
Abstract
Our current understanding of biology suggests that early life relied predominantly on RNA for catalysis and replication. Here, we report the isolation of an RNA polymerase ribozyme called B6.61 that exhibits superior extension and fidelity relative to its progenitor, the Round-18 polymerase. The B6.61 polymerase was selected from a mutagenized pool containing approximately 9 x 10(14) sequence variants through the use of a novel large-scale in vitro compartmentalization system. B6.61 polymerized all tested primer-template (PT) complexes faster than the Round-18 variant. For one PT, B6.61 exhibited dramatically faster elongation past one full helical turn and incorporated at least 20 nucleotides of sequence, setting a new extension record for an RNA polymerase ribozyme. The increased efficiency of the B6.61 construct was related to improvements in fidelity, with the new variant incorporating less incorrect wobble base pairs than its parent. This new polymerase demonstrates the feasibility of evolving an artificial RNA replicase ribozyme in the foreseeable future.
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Affiliation(s)
- Hani S Zaher
- Department of Molecular Biology and Biochemistry, Simon Fraser University, BC, Canada
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Widodo N, Kaur K, Shrestha BG, Takagi Y, Ishii T, Wadhwa R, Kaul SC. Selective killing of cancer cells by leaf extract of Ashwagandha: identification of a tumor-inhibitory factor and the first molecular insights to its effect. Clin Cancer Res 2007; 13:2298-306. [PMID: 17404115 DOI: 10.1158/1078-0432.ccr-06-0948] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Ashwagandha is regarded as a wonder shrub of India and is commonly used in Ayurvedic medicine and health tonics that claim its variety of health-promoting effects. Surprisingly, these claims are not well supported by adequate studies, and the molecular mechanisms of its action remain largely unexplored to date. We undertook a study to identify and characterize the antitumor activity of the leaf extract of ashwagandha. EXPERIMENTAL DESIGN Selective tumor-inhibitory activity of the leaf extract (i-Extract) was identified by in vivo tumor formation assays in nude mice and by in vitro growth assays of normal and human transformed cells. To investigate the cellular targets of i-Extract, we adopted a gene silencing approach using a selected small hairpin RNA library and found that p53 is required for the killing activity of i-Extract. RESULTS By molecular analysis of p53 function in normal and a variety of tumor cells, we found that it is selectively activated in tumor cells, causing either their growth arrest or apoptosis. By fractionation, purification, and structural analysis of the i-Extract constituents, we have identified its p53-activating tumor-inhibiting factor as with a none. CONCLUSION We provide the first molecular evidence that the leaf extract of ashwagandha selectively kills tumor cells and, thus, is a natural source for safe anticancer medicine.
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Affiliation(s)
- Nashi Widodo
- Research Institute for Cell Engineering, GENE Therapeutics, Inc., National Institute of Advanced Industrial Science and Technology, Higashi, Tsukuba, Japan
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Narayanaswamy R, Ellington AD. Engineering RNA-based circuits. Handb Exp Pharmacol 2006:423-45. [PMID: 16594629 DOI: 10.1007/3-540-27262-3_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nucleic acids can modulate gene function by base-pairing, via the molecular recognition of proteins and metabolites, and by catalysis. This diversity of functions can be combined with the ability to engineer nucleic acids based on Watson-Crick base-pairing rules to create a modular set of molecular "tools" for biotechnological and medical interventions in cellular metabolism. However, these individual RNA-based tools are most powerful when combined into rational logical or regulatory circuits, and the circuits can in turn be evolved for optimal function. Examples of genetic circuits that control translation and transcription are herein detailed, and more complex circuits with medical applications are anticipated.
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Affiliation(s)
- R Narayanaswamy
- Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station A4800, Austin TX, 78712-0159, USA
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Matsumoto S, Akashi H, Taira K. Screening and determination of gene function using randomized ribozyme and siRNA libraries. Handb Exp Pharmacol 2006:197-221. [PMID: 16594617 DOI: 10.1007/3-540-27262-3_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Rapid progress in the sequencing of the genomes of model organisms, such as the mouse, rat, nematode, fly, and Arabidopsis, as well as the human genome, has provided abundant sequence information, but functions of long stretches of these genomes remain to be determined. RNA-based technologies hold promise as tools that allow us to identify the specific functions of portions of these genomes. In particular, catalytic RNAs, known also as ribozymes, can be engineered for optimization of their activities in the intracellular environment. The introduction of a library of active ribozymes into cells, with subsequent screening for phenotypic changes, can be used for the rapid identification ofa gene function. Ribozyme technology complements another RNA-based tool for the determination of gene function, which is based on libraries of small interfering RNAs (siRNAs).
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Affiliation(s)
- S Matsumoto
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, 113-8656 Tokyo, Japan
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Levy M, Griswold KE, Ellington AD. Direct selection of trans-acting ligase ribozymes by in vitro compartmentalization. RNA (NEW YORK, N.Y.) 2005; 11:1555-62. [PMID: 16131588 PMCID: PMC1370839 DOI: 10.1261/rna.2121705] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We have used a compartmentalized in vitro selection method to directly select for ligase ribozymes that are capable of acting on and turning over separable oligonucleotide substrates. Starting from a degenerate pool, we selected a trans-acting variant of the Bartel class I ligase which statistically may have been the only active variant in the starting pool. The isolation of this sequence from the population suggests that this selection method is extremely robust at selecting optimal ribozymes and should, therefore, prove useful for the selection and optimization of other trans-acting nucleic acid catalysts capable of multiple turnover catalysis.
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Affiliation(s)
- Matthew Levy
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78751, USA
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Ito M, Kawano K, Miyagishi M, Taira K. Genome-wide application of RNAi to the discovery of potential drug targets. FEBS Lett 2005; 579:5988-95. [PMID: 16153642 DOI: 10.1016/j.febslet.2005.08.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Revised: 08/05/2005] [Accepted: 08/11/2005] [Indexed: 12/23/2022]
Abstract
Progress is being made in the development of RNA interference-based (RNAi-based) strategies for the control of gene expression. It has been demonstrated that small interfering RNAs (siRNAs) can silence the expression of target genes in a sequence-specific manner in mammalian cells. Various groups, including our own, have developed systems for vector-mediated specific RNAi. Vector-based siRNA- (or shRNA) expression libraries directed against the entire human genome and siRNA libraries based on chemically synthesized oligonucleotides now allow the rapid identification of functional genes and potential drug targets. Use of such libraries will enhance our understanding of numerous biological phenomena and contribute to the rational design of drugs against heritable, infectious and malignant diseases.
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Affiliation(s)
- Masanori Ito
- Gene Function Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 4, 1-1-1 Higashi, Tsukuba Science City 305-8562, Japan
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Abstract
Catalytic RNAs, also known as ribozymes, can be engineered to optimize their activities in the intracellular environment. The introduction of a library of active ribozymes into cells, and the subsequent screening for phenotypic changes, allows the rapid identification of gene function. For the determination of gene function, ribozyme technology complements another RNA-based tool that is based on libraries of small interfering RNAs.
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Affiliation(s)
- Hideo Akashi
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-8656, Japan
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Sano M, Kato Y, Taira K. Functional gene-discovery systems based on libraries of hammerhead and hairpin ribozymes and short hairpin RNAs. MOLECULAR BIOSYSTEMS 2005; 1:27-35. [PMID: 16880960 DOI: 10.1039/b503235k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abundant information about the nucleotide sequence of the human genome has become readily available and it is now necessary to develop methods for the identification of genes that are involved in important cellular, developmental and disease-related processes. Identification methods based on the activities of hammerhead and hairpin ribozymes and of short hairpin RNAs (shRNAs), whose target specificities are coupled with loss-of-function phenotypes, have received increasing attention as possible tools for the rapid identification of key genes involved in such processes. We describe here recent advances that have been made with libraries of ribozymes and shRNAs and compare the advantages of the different types of library. The use of such libraries has already revealed new details of several important physiological phenomena.
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Affiliation(s)
- Masayuki Sano
- Gene Function Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Science City, Japan
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