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Wilson EA, Woodbury A, Williams KM, Coopersmith CM. OXIDATIVE study: A pilot prospective observational cohort study protocol examining the influence of peri-reperfusion hyperoxemia and immune dysregulation on early allograft dysfunction after orthotopic liver transplantation. PLoS One 2024; 19:e0301281. [PMID: 38547092 PMCID: PMC10977716 DOI: 10.1371/journal.pone.0301281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/10/2024] [Indexed: 04/02/2024] Open
Abstract
Early allograft dysfunction (EAD) is a functional hepatic insufficiency within a week of orthotopic liver transplantation (OLT) and is associated with morbidity and mortality. The etiology of EAD is multifactorial and largely driven by ischemia reperfusion injury (IRI), a phenomenon characterized by oxygen scarcity followed by paradoxical oxidative stress and inflammation. With the expanded use of marginal allografts more susceptible to IRI, the incidence of EAD may be increasing. This necessitates an in-depth understanding of the innate molecular mechanisms underlying EAD and interventions to mitigate its impact. Our central hypothesis is peri-reperfusion hyperoxemia and immune dysregulation exacerbate IRI and increase the risk of EAD. We will perform a pilot prospective single-center observational cohort study of 40 patients. The aims are to determine (1) the association between peri-reperfusion hyperoxemia and EAD and (2) whether peri-reperfusion perturbed cytokine, protein, and hypoxia inducible factor-1 alpha (HIF-1α) levels correlate with EAD after OLT. Inclusion criteria include age ≥ 18 years, liver failure, and donation after brain or circulatory death. Exclusion criteria include living donor donation, repeat OLT within a week of transplantation, multiple organ transplantation, and pregnancy. Partial pressure of arterial oxygen (PaO2) as the study measure allows for the examination of oxygen exposure within the confines of existing variability in anesthesiologist-administered fraction of inspired oxygen (FiO2) and the inclusion of patients with intrapulmonary shunting. The Olthoff et al. definition of EAD is the primary outcome. Secondary outcomes include postoperative acute kidney injury, pulmonary and biliary complications, surgical wound dehiscence and infection, and mortality. The goal of this study protocol is to identify EAD contributors that could be targeted to attenuate its impact and improve OLT outcomes. If validated, peri-reperfusion hyperoxemia and immune perturbations could be targeted via FiO2 titration to a goal PaO2 and/or administration of an immunomodulatory agent by the anesthesiologist intraoperatively.
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Affiliation(s)
- Elizabeth A Wilson
- Department of Anesthesiology, Emory University School of Medicine, Emory University Hospital, Atlanta, GA, United States of America
| | - Anna Woodbury
- Department of Anesthesiology, Emory University School of Medicine, Emory University Hospital, Atlanta, GA, United States of America
| | - Kirsten M Williams
- Department of Pediatrics, Division of Hematology and Oncology, Emory University School of Medicine, Children's Hospital of Atlanta, Atlanta, GA, United States of America
| | - Craig M Coopersmith
- Department of Surgery and Emory Critical Care Center, Emory University School of Medicine, Emory University Hospital, Atlanta, GA, United States of America
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Sundara Rajan S, Ludwig KR, Hall KL, Jones TL, Caplen NJ. Cancer biology functional genomics: From small RNAs to big dreams. Mol Carcinog 2020; 59:1343-1361. [PMID: 33043516 PMCID: PMC7702050 DOI: 10.1002/mc.23260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
The year 2021 marks the 20th anniversary of the first publications reporting the discovery of the gene silencing mechanism, RNA interference (RNAi) in mammalian cells. Along with the many studies that delineated the proteins and substrates that form the RNAi pathway, this finding changed our understanding of the posttranscriptional regulation of mammalian gene expression. Furthermore, the development of methods that exploited the RNAi pathway began the technological revolution that eventually enabled the interrogation of mammalian gene function-from a single gene to the whole genome-in only a few days. The needs of the cancer research community have driven much of this progress. In this perspective, we highlight milestones in the development and application of RNAi-based methods to study carcinogenesis. We discuss how RNAi-based functional genetic analysis of exemplar tumor suppressors and oncogenes furthered our understanding of cancer initiation and progression and explore how such studies formed the basis of genome-wide scale efforts to identify cancer or cancer-type specific vulnerabilities, including studies conducted in vivo. Furthermore, we examine how RNAi technologies have revealed new cancer-relevant molecular targets and the implications for cancer of the first RNAi-based drugs. Finally, we discuss the future of functional genetic analysis, highlighting the increasing availability of complementary approaches to analyze cancer gene function.
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Affiliation(s)
- Soumya Sundara Rajan
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Katelyn R. Ludwig
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Katherine L. Hall
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Tamara L. Jones
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
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3
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Laperrousaz B, Porte S, Gerbaud S, Härmä V, Kermarrec F, Hourtane V, Bottausci F, Gidrol X, Picollet-D'hahan N. Direct transfection of clonal organoids in Matrigel microbeads: a promising approach toward organoid-based genetic screens. Nucleic Acids Res 2019; 46:e70. [PMID: 29394376 PMCID: PMC6158603 DOI: 10.1093/nar/gky030] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/13/2018] [Indexed: 01/01/2023] Open
Abstract
Organoid cultures in 3D matrices are relevant models to mimic the complex in vivo environment that supports cell physiological and pathological behaviors. For instance, 3D epithelial organoids recapitulate numerous features of glandular tissues including the development of fully differentiated acini that maintain apico-basal polarity with hollow lumen. Effective genetic engineering in organoids would bring new insights in organogenesis and carcinogenesis. However, direct 3D transfection on already formed organoids remains challenging. One limitation is that organoids are embedded in extracellular matrix and grow into compact structures that hinder transfection using traditional techniques. To address this issue, we developed an innovative approach for transgene expression in 3D organoids by combining single-cell encapsulation in Matrigel microbeads using a microfluidic device and electroporation. We demonstrate that direct electroporation of encapsulated organoids reaches up to 80% of transfection efficiency. Using this technique and a morphological read-out that recapitulate the different stages of tumor development, we further validate the role of p63 and PTEN as key genes in acinar development in breast and prostate tissues. We believe that the combination of controlled organoid generation and efficient 3D transfection developed here opens new perspectives for flow-based high-throughput genetic screening and functional genomic applications.
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Affiliation(s)
| | - Stephanie Porte
- University of Grenoble Alpes, CEA, INSERM, BIG-BGE, 38000 Grenoble, France
| | - Sophie Gerbaud
- University of Grenoble Alpes, CEA, INSERM, BIG-BGE, 38000 Grenoble, France
| | - Ville Härmä
- University of Grenoble Alpes, CEA, INSERM, BIG-BGE, 38000 Grenoble, France
| | | | | | | | - Xavier Gidrol
- University of Grenoble Alpes, CEA, INSERM, BIG-BGE, 38000 Grenoble, France
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Wang T, Xie Z. Construction and Integration of a Synthetic MicroRNA Cluster for Multiplex RNA Interference in Mammalian Cells. Methods Mol Biol 2018; 1772:347-359. [PMID: 29754238 DOI: 10.1007/978-1-4939-7795-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Basic biological research and biomedical applications often require studying the multiple interactions between genes or proteins while multiplex RNA interference (RNAi) technology is still challenging in mammalian cells. In mammalian genomes, the natural microRNA (miRNA) clusters, of which the miRNAs often share similar expression patterns and target diverse genes, would provide a potential multiplex RNAi scaffold. Based on the natural pri-miR-155 precursor, we have developed and characterized a multiplex RNAi method by engineering synthetic miRNA clusters, among which the maturation and function of individual miRNA precursors are independent of their positions in the cluster. And the synthetic miRNA clusters are assembled by an efficient hierarchical Golden-Gate cloning method. Here, we describe the design rules and the hierarchical cloning methods to construct synthetic miRNA cluster, and the brief protocol for the integration of synthetic miRNA clusters into the mammalian genome.
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Affiliation(s)
- Tingting Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST, Department of Automation, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST, Department of Automation, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China.
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Transient Silencing of DNA Repair Genes Improves Targeted Gene Integration in the Filamentous Fungus Trichoderma reesei. Appl Environ Microbiol 2017; 83:AEM.00535-17. [PMID: 28550064 DOI: 10.1128/aem.00535-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 05/23/2017] [Indexed: 11/20/2022] Open
Abstract
Trichoderma reesei is a filamentous fungus that is used worldwide to produce industrial enzymes. Industrial strains have traditionally been created though systematic strain improvement using mutagenesis and screening approaches. It is also desirable to specifically manipulate the genes of the organism to further improve and to modify the strain. Targeted integration in filamentous fungi is typically hampered by very low frequencies of homologous recombination. To address this limitation, we have developed a simple transient method for silencing genes in T. reesei Using gene-specific small interfering RNAs (siRNAs) targeted to mus53, we could achieve up to 90% knockdown of mus53 mRNA. As a practical example, we demonstrated that transient silencing of DNA repair genes significantly improved homologous integration of DNA at a specific locus in a standard protoplast transformation. The best transient silencing of mus53 with siRNAs in protoplasts could achieve up to 59% marker gene integration.IMPORTANCE The previous solution for improving targeted integration efficiency has been deleting nonhomologous end joining (NHEJ) DNA repair genes. However, deleting these important repair genes may lead to unintended consequences for genomic stability and could lead to the accumulation of spontaneous mutations. Our method of transiently silencing NHEJ repair pathway genes allows recovery of their important repair functions. Here we report a silencing approach for improving targeted DNA integration in filamentous fungi. Furthermore, our transient silencing method is a truly flexible approach that is capable of knocking down the expression of a target gene in growing mycelial cultures, which could facilitate the broad study of gene functions in T. reesei.
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Whole-genome RNAi screen highlights components of the endoplasmic reticulum/Golgi as a source of resistance to immunotoxin-mediated cytotoxicity. Proc Natl Acad Sci U S A 2015; 112:E1135-42. [PMID: 25713356 DOI: 10.1073/pnas.1501958112] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Immunotoxins (antibody-toxin fusion proteins) target surface antigens on cancer cells and kill these cells via toxin-mediated inhibition of protein synthesis. To identify genes controlling this process, an RNAi whole-genome screen (∼ 22,000 genes at three siRNAs per gene) was conducted via monitoring the cytotoxicity of the mesothelin-directed immunotoxin SS1P. SS1P, a Pseudomonas exotoxin-based immunotoxin, was chosen because it is now in clinical trials and has produced objective tumor regressions in patients. High and low concentrations of SS1P were chosen to allow for the identification of both mitigators and sensitizers. As expected, silencing known essential genes in the immunotoxin pathway, such as mesothelin, furin, KDEL receptor 2, or members of the diphthamide pathway, protected cells. Of greater interest was the observation that many RNAi targets increased immunotoxin sensitivity, indicating that these gene products normally contribute to inefficiencies in the killing pathway. Of the top sensitizers, many genes encode proteins that locate to either the endoplasmic reticulum (ER) or Golgi and are annotated as part of the secretory system. Genes related to the ER-associated degradation system were not among high-ranking mitigator or sensitizer candidates. However, the p97 inhibitor eeyarestatin 1 enhanced immunotoxin killing. Our results highlight potential targets for chemical intervention that could increase immunotoxin killing of cancer cells and enhance our understanding of toxin trafficking.
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Ma J, Zhang Q, Chen S, Fang B, Yang Q, Chen C, Miele L, Sarkar FH, Xia J, Wang Z. Mitochondrial dysfunction promotes breast cancer cell migration and invasion through HIF1α accumulation via increased production of reactive oxygen species. PLoS One 2013; 8:e69485. [PMID: 23922721 PMCID: PMC3726697 DOI: 10.1371/journal.pone.0069485] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 06/10/2013] [Indexed: 01/12/2023] Open
Abstract
Although mitochondrial dysfunction has been observed in various types of human cancer cells, the molecular mechanism underlying mitochondrial dysfunction mediated tumorigenesis remains largely elusive. To further explore the function of mitochondria and their involvement in the pathogenic mechanisms of cancer development, mitochondrial dysfunction clones of breast cancer cells were generated by rotenone treatment, a specific inhibitor of mitochondrial electron transport complex I. These clones were verified by mitochondrial respiratory defect measurement. Moreover, those clones exhibited increased reactive oxygen species (ROS), and showed higher migration and invasive behaviors compared with their parental cells. Furthermore, antioxidant N-acetyl cysteine, PEG-catalase, and mito-TEMPO effectively inhibited cell migration and invasion in these clones. Notably, ROS regulated malignant cellular behavior was in part mediated through upregulation of hypoxia-inducible factor-1 α and vascular endothelial growth factor. Our results suggest that mitochondrial dysfunction promotes cancer cell motility partly through HIF1α accumulation mediated via increased production of reactive oxygen species.
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Affiliation(s)
- Jia Ma
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu, Anhui, China
| | - Qing Zhang
- Department of Orthopedics, The Center Hospital of Bengbu, Anhui, China
| | - Sulian Chen
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu, Anhui, China
| | - Binbin Fang
- Research Center of Clinical Laboratory Science, Bengbu Medical College, Bengbu, Anhui, China
| | - Qingling Yang
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu, Anhui, China
| | - Changjie Chen
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu, Anhui, China
| | - Lucio Miele
- University of Mississippi Cancer Institute, Jackson, Mississippi, United States of America
| | - Fazlul H. Sarkar
- Department of Pathology and Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, Michigan, United States of America
| | - Jun Xia
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu, Anhui, China
- * E-mail: (ZW); (JX)
| | - Zhiwei Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- * E-mail: (ZW); (JX)
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Kang K, Peng X, Zhang X, Wang Y, Zhang L, Gao L, Weng T, Zhang H, Ramchandran R, Raj JU, Gou D, Liu L. MicroRNA-124 suppresses the transactivation of nuclear factor of activated T cells by targeting multiple genes and inhibits the proliferation of pulmonary artery smooth muscle cells. J Biol Chem 2013; 288:25414-25427. [PMID: 23853098 DOI: 10.1074/jbc.m113.460287] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Abnormal proliferation and phenotypic modulation of pulmonary artery smooth muscle cells (PASMC) contributes to the pathogenesis of numerous cardiovascular disorders, including pulmonary arterial hypertension (PAH). The nuclear factor of activated T cells (NFAT) signaling pathway is linked to PASMC proliferation and PAH. MicroRNAs (miRNAs) are small non-coding RNAs that function in diverse biological processes. To systemically identify the specific miRNAs that regulate the NFAT pathway, a human primary miRNA library was applied for cell-based high throughput screening with the NFAT luciferase reporter system. Eight miRNAs were found to modulate NFAT activity efficiently. Of them, miR-124 robustly inhibited NFAT reporter activity and decreased both the dephosphorylation and the nuclear translocation of NFAT. miR-124 also inhibited NFAT-dependent transcription of IL-2 in Jurkat T cells. miR-124 exerted its effects by targeting multiple genes, including a known component of the NFAT pathway, NFATc1, and two new regulators of NFAT signaling, CAMTA1 (calmodulin-binding transcription activator 1) and PTBP1 (polypyrimidine tract-binding protein 1). Physiologically, miR-124 was down-regulated by hypoxia in human PASMC, consistent with the activation of NFAT during this process. Down-regulation of miR-124 was also observed in 3-week hypoxia-treated mouse lungs. Furthermore, the overexpression of miR-124 not only inhibited human PASMC proliferation but also maintained its differentiated phenotype by repressing the NFAT pathway. Taken together, our data provide the first evidence that miR-124 acts as an inhibitor of the NFAT pathway. Down-regulation of miR-124 in hypoxia-treated PASMC and its antiproliferative and prodifferentiation effects imply a potential value for miR-124 in the treatment of PAH.
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Affiliation(s)
- Kang Kang
- From the College of Life Sciences, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Xiao Peng
- From the College of Life Sciences, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Xiaoying Zhang
- From the College of Life Sciences, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yuna Wang
- From the College of Life Sciences, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Lishu Zhang
- the Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, and
| | - Li Gao
- the Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, and
| | - Tingting Weng
- the Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, and
| | - Honghao Zhang
- the Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, and
| | | | - J Usha Raj
- the Department of Pediatrics, University of Illinois, Chicago, Illinois 60612
| | - Deming Gou
- From the College of Life Sciences, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China,; the Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, and; the Department of Pediatrics, University of Illinois, Chicago, Illinois 60612.
| | - Lin Liu
- the Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, and.
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Sindhu A, Arora P, Chaudhury A. Illuminating the gateway of gene silencing: perspective of RNA interference technology in clinical therapeutics. Mol Biotechnol 2012; 51:289-302. [PMID: 21947958 PMCID: PMC7091241 DOI: 10.1007/s12033-011-9456-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A novel laboratory revolution for disease therapy, the RNA interference (RNAi) technology, has adopted a new era of molecular research as the next generation "Gene-targeted prophylaxis." In this review, we have focused on the chief technological challenges associated with the efforts to develop RNAi-based therapeutics that may guide the biomedical researchers. Many non-curable maladies, like neurodegenerative diseases and cancers have effectively been cured using this technology. Rapid advances are still in progress for the development of RNAi-based technologies that will be having a major impact on medical research. We have highlighted the recent discoveries associated with the phenomenon of RNAi, expression of silencing molecules in mammals along with the vector systems used for disease therapeutics.
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Affiliation(s)
- Annu Sindhu
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, 125001 Haryana India
| | - Pooja Arora
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, 125001 Haryana India
| | - Ashok Chaudhury
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, 125001 Haryana India
- Present Address: Crop Science Department, NC State University, Raleigh, NC 27606 USA
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10
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Hummon AB, Pitt JJ, Camps J, Emons G, Skube SB, Huppi K, Jones TL, Beissbarth T, Kramer F, Grade M, Difilippantonio MJ, Ried T, Caplen NJ. Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells. Mol Cancer 2012; 11:1. [PMID: 22216762 PMCID: PMC3281783 DOI: 10.1186/1476-4598-11-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 01/04/2012] [Indexed: 11/11/2022] Open
Abstract
Background Colorectal carcinomas (CRC) carry massive genetic and transcriptional alterations that influence multiple cellular pathways. The study of proteins whose loss-of-function (LOF) alters the growth of CRC cells can be used to further understand the cellular processes cancer cells depend upon for survival. Results A small-scale RNAi screen of ~400 genes conducted in SW480 CRC cells identified several candidate genes as required for the viability of CRC cells, most prominently CASP8AP2/FLASH. To understand the function of this gene in maintaining the viability of CRC cells in an unbiased manner, we generated gene specific expression profiles following RNAi. Silencing of CASP8AP2/FLASH resulted in altered expression of over 2500 genes enriched for genes associated with cellular growth and proliferation. Loss of CASP8AP2/FLASH function was significantly associated with altered transcription of the genes encoding the replication-dependent histone proteins as a result of the expression of the non-canonical polyA variants of these transcripts. Silencing of CASP8AP2/FLASH also mediated enrichment of changes in the expression of targets of the NFκB and MYC transcription factors. These findings were confirmed by whole transcriptome analysis of CASP8AP2/FLASH silenced cells at multiple time points. Finally, we identified and validated that CASP8AP2/FLASH LOF increases the expression of neurofilament heavy polypeptide (NEFH), a protein recently linked to regulation of the AKT1/ß-catenin pathway. Conclusions We have used unbiased RNAi based approaches to identify and characterize the function of CASP8AP2/FLASH, a protein not previously reported as required for cell survival. This study further defines the role CASP8AP2/FLASH plays in the regulating expression of the replication-dependent histones and shows that its LOF results in broad and reproducible effects on the transcriptome of colorectal cancer cells including the induction of expression of the recently described tumor suppressor gene NEFH.
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Affiliation(s)
- Amanda B Hummon
- Gene Silencing Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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Identification of the receptor tyrosine kinase AXL in breast cancer as a target for the human miR-34a microRNA. Breast Cancer Res Treat 2011; 130:663-79. [PMID: 21814748 DOI: 10.1007/s10549-011-1690-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 07/19/2011] [Indexed: 12/19/2022]
Abstract
The identification of molecular features that contribute to the progression of breast cancer can provide valuable insight into the pathogenesis of this disease. Deregulated microRNA expression represents one type of molecular event that has been associated with many different human cancers. In order to identify a miRNA/mRNA regulatory interaction that is biologically relevant to the triple-negative breast cancer genotype/phenotype, we initially conducted a miRNA profiling experiment to detect differentially expressed miRNAs in cell line models representing triple-negative (MDA-MB-231), ER(+) (MCF7), and HER-2 overexpressed (SK-BR-3) histotypes. We identified human miR-34a expression as being >3-fold down (from its median expression value across all cell lines) in MDA-MB-231 cells, and identified AXL as a putative mRNA target using multiple miRNA/target prediction algorithms. The miR-34a/AXL interaction was functionally characterized through ectopic overexpression experiments with a miR-34a mimic in two independent triple-negative breast cancer cell lines. In reporter assays, miR-34a binds to its putative target site within the AXL 3'UTR to inhibit luciferase expression. We also observed degradation of AXL mRNA and decreased AXL protein levels, as well as cell signaling effects on AKT phosphorylation and phenotypic effects on cell migration. Finally, we present an inverse correlative trend in miR-34a and AXL expression for both cell line and patient tumor samples.
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12
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Jiang M, Instrell R, Saunders B, Berven H, Howell M. Tales from an academic RNAi screening facility; FAQs. Brief Funct Genomics 2011; 10:227-37. [PMID: 21527443 DOI: 10.1093/bfgp/elr016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
RNAi technology is now a well-established and widely employed research technique that has been adopted by many researchers for use in large-scale screening campaigns. Here, we offer our experience of genome-wide siRNA screening from the perspective of a facility providing screening as a service to a wide range of researchers with diverse interests and approaches. We have experienced the emotional rollercoaster of screening from the exuberant early promise of a screen, the messy reality of the data through to the recognition of screen data as a potential information goldmine. Here, we use some of the questions we most frequently encounter to highlight the initial concerns of many researchers embarking on a siRNA screen and conclude that an informed view of what can be reasonably expected from a screen is essential to the most effective implementation of the technology. Along the way, we suggest that for this area of research at least, either centralization of the resources or close and open collaboration between interested parties offers distinct advantages.
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Affiliation(s)
- Ming Jiang
- High-Throughput Screening facility, Cancer Research UK, London Research Institute
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13
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Rantala JK, Mäkelä R, Aaltola AR, Laasola P, Mpindi JP, Nees M, Saviranta P, Kallioniemi O. A cell spot microarray method for production of high density siRNA transfection microarrays. BMC Genomics 2011; 12:162. [PMID: 21443765 PMCID: PMC3073923 DOI: 10.1186/1471-2164-12-162] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 03/28/2011] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND High-throughput RNAi screening is widely applied in biological research, but remains expensive, infrastructure-intensive and conversion of many assays to HTS applications in microplate format is not feasible. RESULTS Here, we describe the optimization of a miniaturized cell spot microarray (CSMA) method, which facilitates utilization of the transfection microarray technique for disparate RNAi analyses. To promote rapid adaptation of the method, the concept has been tested with a panel of 92 adherent cell types, including primary human cells. We demonstrate the method in the systematic screening of 492 GPCR coding genes for impact on growth and survival of cultured human prostate cancer cells. CONCLUSIONS The CSMA method facilitates reproducible preparation of highly parallel cell microarrays for large-scale gene knockdown analyses. This will be critical towards expanding the cell based functional genetic screens to include more RNAi constructs, allow combinatorial RNAi analyses, multi-parametric phenotypic readouts or comparative analysis of many different cell types.
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Affiliation(s)
- Juha K Rantala
- Medical Biotechnology, VTT Technical Research Centre of Finland, 20521 Turku, Finland.
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Wei J, Jones J, Kang J, Card A, Krimm M, Hancock P, Pei Y, Ason B, Payson E, Dubinina N, Cancilla M, Stroh M, Burchard J, Sachs AB, Hochman JH, Flanagan WM, Kuklin NA. RNA-induced silencing complex-bound small interfering RNA is a determinant of RNA interference-mediated gene silencing in mice. Mol Pharmacol 2011; 79:953-63. [PMID: 21427169 DOI: 10.1124/mol.110.070409] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Deeper knowledge of pharmacokinetic and pharmacodynamic (PK/PD) concepts for RNA therapeutics is important to streamline the drug development process and for rigorous selection of best performing drug candidates. Here we characterized the PK/PD relationship for small interfering RNAs (siRNAs) targeting luciferase by examining siRNA concentration in plasma and liver, the temporal RNA-induced silencing complex binding profiles, mRNA reduction, and protein inhibition measured by noninvasive bioluminescent imaging. A dose-dependent and time-related decrease in bioluminescence was detected over 25 days after a single treatment of a lipid nanoparticle-formulated siRNA targeting luciferase messenger RNA. A direct relationship was observed between the degree of in vivo mRNA and protein reduction and the Argonaute2 (Ago2)-bound siRNA fraction but not with the total amount of siRNA found in the liver, suggesting that the Ago2-siRNA complex is the key determinant of target inhibition. These observations were confirmed for an additional siRNA that targets endogenously expressed Sjögren syndrome antigen B (Ssb) mRNA, indicating that our observations are not limited to a transgenic mouse system. Our data provide detailed information of the temporal regulation of siRNA liver delivery, Ago2 loading, mRNA reduction, and protein inhibition that are essential for the rapid and cost-effective clinical development of siRNAs therapeutics.
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Affiliation(s)
- Jie Wei
- Sirna Therapeutics, San Francisco, CA 94158, USA
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15
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Grade M, Hummon AB, Camps J, Emons G, Spitzner M, Gaedcke J, Hoermann P, Ebner R, Becker H, Difilippantonio MJ, Ghadimi BM, Beissbarth T, Caplen NJ, Ried T. A genomic strategy for the functional validation of colorectal cancer genes identifies potential therapeutic targets. Int J Cancer 2011. [PMID: 20473941 DOI: 10.1002/ijc.25453.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genes that are highly overexpressed in tumor cells can be required for tumor cell survival and have the potential to be selective therapeutic targets. In an attempt to identify such targets, we combined a functional genomics and a systems biology approach to assess the consequences of RNAi-mediated silencing of overexpressed genes that were selected from 140 gene expression profiles from colorectal cancers (CRCs) and matched normal mucosa. In order to identify credible models for in-depth functional analysis, we first confirmed the overexpression of these genes in 25 different CRC cell lines. We then identified five candidate genes that profoundly reduced the viability of CRC cell lines when silenced with either siRNAs or short-hairpin RNAs (shRNAs), i.e., HMGA1, TACSTD2, RRM2, RPS2 and NOL5A. These genes were further studied by systematic analysis of comprehensive gene expression profiles generated following siRNA-mediated silencing. Exploration of these RNAi-specific gene expression signatures allowed the identification of the functional space in which the five genes operate and showed enrichment for cancer-specific signaling pathways, some known to be involved in CRC. By comparing the expression of the RNAi signature genes with their respective expression levels in an independent set of primary rectal carcinomas, we could recapitulate these defined RNAi signatures, therefore, establishing the biological relevance of our observations. This strategy identified the signaling pathways that are affected by the prominent oncogenes HMGA1 and TACSTD2, established a yet unknown link between RRM2 and PLK1 and identified RPS2 and NOL5A as promising potential therapeutic targets in CRC.
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Affiliation(s)
- Marian Grade
- Department of General and Visceral Surgery, University Medicine Göttingen, Georg-August-University, Göttingen, Germany
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16
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Grade M, Hummon AB, Camps J, Emons G, Spitzner M, Gaedcke J, Hoermann P, Ebner R, Becker H, Difilippantonio MJ, Ghadimi BM, Beissbarth T, Caplen NJ, Ried T. A genomic strategy for the functional validation of colorectal cancer genes identifies potential therapeutic targets. Int J Cancer 2011; 128:1069-79. [PMID: 20473941 DOI: 10.1002/ijc.25453] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Genes that are highly overexpressed in tumor cells can be required for tumor cell survival and have the potential to be selective therapeutic targets. In an attempt to identify such targets, we combined a functional genomics and a systems biology approach to assess the consequences of RNAi-mediated silencing of overexpressed genes that were selected from 140 gene expression profiles from colorectal cancers (CRCs) and matched normal mucosa. In order to identify credible models for in-depth functional analysis, we first confirmed the overexpression of these genes in 25 different CRC cell lines. We then identified five candidate genes that profoundly reduced the viability of CRC cell lines when silenced with either siRNAs or short-hairpin RNAs (shRNAs), i.e., HMGA1, TACSTD2, RRM2, RPS2 and NOL5A. These genes were further studied by systematic analysis of comprehensive gene expression profiles generated following siRNA-mediated silencing. Exploration of these RNAi-specific gene expression signatures allowed the identification of the functional space in which the five genes operate and showed enrichment for cancer-specific signaling pathways, some known to be involved in CRC. By comparing the expression of the RNAi signature genes with their respective expression levels in an independent set of primary rectal carcinomas, we could recapitulate these defined RNAi signatures, therefore, establishing the biological relevance of our observations. This strategy identified the signaling pathways that are affected by the prominent oncogenes HMGA1 and TACSTD2, established a yet unknown link between RRM2 and PLK1 and identified RPS2 and NOL5A as promising potential therapeutic targets in CRC.
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Affiliation(s)
- Marian Grade
- Department of General and Visceral Surgery, University Medicine Göttingen, Georg-August-University, Göttingen, Germany
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17
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Zhang YW, Jones TL, Martin SE, Caplen NJ, Pommier Y. Implication of checkpoint kinase-dependent up-regulation of ribonucleotide reductase R2 in DNA damage response. J Biol Chem 2009; 284:18085-95. [PMID: 19416980 DOI: 10.1074/jbc.m109.003020] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
To investigate drug mechanisms of action and identify molecular targets for the development of rational drug combinations, we conducted synthetic small interfering RNA (siRNA)-based RNAi screens to identify genes whose silencing affects anti-cancer drug responses. Silencing of RRM1 and RRM2, which encode the large and small subunits of the human ribonucleotide reductase complex, respectively, markedly enhanced the cytotoxicity of the topoisomerase I inhibitor camptothecin (CPT). Silencing of RRM2 was also found to enhance DNA damage as measured by histone gamma-H2AX. Further studies showed that CPT up-regulates both RRM1 and RRM2 mRNA and protein levels and induces the nuclear translocation of RRM2. The checkpoint kinase 1 (Chk1) was up-regulated and activated in response to CPT, and CHEK1 down-regulation by siRNA and small molecule inhibitors of Chk1 blocked RRM2 induction by CPT. CHEK1 siRNA also suppressed E2F1 up-regulation by CPT, and silencing of E2F1 suppressed the up-regulation of RRM2. Silencing of ATR or ATM and inhibition of ATM activity by KU-55933 blocked Chk1 activation and RRM2 up-regulation. This study links the known components of CPT-induced DNA damage response with proteins required for the synthesis of dNTPs and DNA repair. Specifically, we propose that upon DNA damage, Chk1 activation, mediated by ATM and ATR, up-regulates RRM2 expression through the E2F1 transcription factor. Up-regulation in RRM2 expression levels coupled with its nuclear recruitment suggests an active role for ribonucleotide reductase in the cellular response to CPT-mediated DNA damage that could potentially be exploited as a strategy for enhancing the efficacy of topoisomerase I inhibitors.
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Affiliation(s)
- Yong-Wei Zhang
- Laboratory of Molecular Pharmacology, Genetics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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18
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Ryan MC, Zeeberg BR, Caplen NJ, Cleland JA, Kahn AB, Liu H, Weinstein JN. SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. BMC Bioinformatics 2008; 9:313. [PMID: 18638396 PMCID: PMC2491637 DOI: 10.1186/1471-2105-9-313] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Accepted: 07/18/2008] [Indexed: 11/10/2022] Open
Abstract
Background Over 60% of protein-coding genes in vertebrates express mRNAs that undergo alternative splicing. The resulting collection of transcript isoforms poses significant challenges for contemporary biological assays. For example, RT-PCR validation of gene expression microarray results may be unsuccessful if the two technologies target different splice variants. Effective use of sequence-based technologies requires knowledge of the specific splice variant(s) that are targeted. In addition, the critical roles of alternative splice forms in biological function and in disease suggest that assay results may be more informative if analyzed in the context of the targeted splice variant. Results A number of contemporary technologies are used for analyzing transcripts or proteins. To enable investigation of the impact of splice variation on the interpretation of data derived from those technologies, we have developed SpliceCenter. SpliceCenter is a suite of user-friendly, web-based applications that includes programs for analysis of RT-PCR primer/probe sets, effectors of RNAi, microarrays, and protein-targeting technologies. Both interactive and high-throughput implementations of the tools are provided. The interactive versions of SpliceCenter tools provide visualizations of a gene's alternative transcripts and probe target positions, enabling the user to identify which splice variants are or are not targeted. The high-throughput batch versions accept user query files and provide results in tabular form. When, for example, we used SpliceCenter's batch siRNA-Check to process the Cancer Genome Anatomy Project's large-scale shRNA library, we found that only 59% of the 50,766 shRNAs in the library target all known splice variants of the target gene, 32% target some but not all, and 9% do not target any currently annotated transcript. Conclusion SpliceCenter provides unique, user-friendly applications for assessing the impact of transcript variation on the design and interpretation of RT-PCR, RNAi, gene expression microarrays, antibody-based detection, and mass spectrometry proteomics. The tools are intended for use by bench biologists as well as bioinformaticists.
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Affiliation(s)
- Michael C Ryan
- Genomics & Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.
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19
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Abstract
RNA interference (RNAi) can mediate the long- or short-term silencing of gene expression at the DNA, RNA, and/or protein level. Although several triggers of RNAi have been identified, the best characterized of these are small interfering RNAs (siRNAs), which can decrease gene expression through mRNA transcript cleavage, and endogenous microRNAs (miRNAs), which primarily inhibit protein translation. An improved understanding of RNAi has provided new, powerful tools for conducting functional studies in a gene-specific manner. In various applications, RNAi has been used to create model systems, to identify novel molecular targets, to study gene function in a genome-wide fashion, and to create new avenues for clinical therapeutics. Here, we review many of the ongoing applications of RNAi in mammalian and human systems, and discuss how advances in our knowledge of the RNAi machinery have enhanced the use of these technologies.
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Affiliation(s)
- Scott E Martin
- Gene Silencing Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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20
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RNAi screening of the tyrosine kinome identifies therapeutic targets in acute myeloid leukemia. Blood 2007; 111:2238-45. [PMID: 18025156 DOI: 10.1182/blood-2007-06-097253] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Despite vast improvements in our understanding of cancer genetics, a large percentage of cancer cases present without knowledge of the causative genetic events. Tyrosine kinases are frequently implicated in the pathogenesis of numerous types of cancer, but identification and validation of tyrosine kinase targets in cancer can be a time-consuming process. We report the establishment of an efficient, functional screening assay using RNAi technology to directly assess and compare the effect of individually targeting each member of the tyrosine kinase family. We demonstrate that siRNA screening can identify tyrosine kinase targets containing activating mutations in Janus kinase (JAK) 3 (A572V) in CMK cells and c-KIT (V560G) in HMC1.1 cells. In addition, this assay identifies targets that do not contain mutations, such as JAK1 and the focal adhesion kinases (FAK), that are crucial to the survival of the cancer cells. This technique, with additional development, might eventually offer the potential to match specific therapies with individual patients based on a functional assay.
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Li YL, Quarles LD, Zhou HH, Xiao ZS. RNA interference and its application in bone-related diseases. Biochem Biophys Res Commun 2007; 361:817-21. [PMID: 17686458 DOI: 10.1016/j.bbrc.2007.07.123] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 07/24/2007] [Indexed: 01/17/2023]
Abstract
RNA interference (RNAi) is the most exciting insight in biology in past decades, which provided new perspectives into the genome-wide surveys of gene function by targeted degradation of mRNA with the introduction of small interfering RNAs (siRNAs) or small hairpin RNAs (shRNAs) in a large variety of organisms, and turned out to be a more efficient and convenient method compared with the traditional knockout pathway. What's more, as the enhancement of its stability and improvement of its delivery vehicles, RNAi is bound to be a practical tool in determine gene function first in vitro and then in vivo. In this paper, we will focus on the recent achievements of RNAi and also depict the development of RNAi as a potentially powerful tool in studying bone-related diseases.
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Affiliation(s)
- Ya Lin Li
- Institute of Clinical Pharmacology, Central South University, Changsha 410078, China
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